[{"scopus_import":"1","publication_identifier":{"isbn":["9781557528209"]},"article_processing_charge":"No","month":"07","day":"15","citation":{"apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group. https://doi.org/10.1364/NLO.2019.NM2A.5","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019.","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.","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","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.","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.","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."},"publication":"Nonlinear Optics, OSA Technical Digest","quality_controlled":"1","date_published":"2019-07-15T00:00:00Z","doi":"10.1364/NLO.2019.NM2A.5","conference":{"name":"NLO: Nonlinear Optics","end_date":"2019-07-19","location":"Waikoloa Beach, Hawaii (HI), United States","start_date":"2019-07-15"},"language":[{"iso":"eng"}],"type":"conference","article_number":"NM2A.5","abstract":[{"lang":"eng","text":"We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm."}],"year":"2019","_id":"7233","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","publication_status":"published","status":"public","author":[{"full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","last_name":"Rueda Sanchez"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Madhuri","last_name":"Kumari","full_name":"Kumari, Madhuri"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"oa_version":"None","date_created":"2020-01-05T23:00:48Z","date_updated":"2023-10-17T12:14:46Z"},{"citation":{"chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare. Institut Henri Poincaré, 2019. https://doi.org/10.1214/18-AIHP894.","mla":"Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare, vol. 55, no. 2, Institut Henri Poincaré, 2019, pp. 661–96, doi:10.1214/18-AIHP894.","short":"J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 661–696.","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.","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","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.","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"},"publication":"Annales de l'institut Henri Poincare","page":"661-696","date_published":"2019-05-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","_id":"6240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 55","status":"public","title":"Location of the spectrum of Kronecker random matrices","oa_version":"Preprint","type":"journal_article","issue":"2","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"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.08343"}],"oa":1,"external_id":{"isi":["000467793600003"],"arxiv":["1706.08343"]},"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"quality_controlled":"1","isi":1,"doi":"10.1214/18-AIHP894","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0246-0203"]},"month":"05","year":"2019","publisher":"Institut Henri Poincaré","department":[{"_id":"LaEr"}],"publication_status":"published","related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","first_name":"Torben H","last_name":"Krüger"},{"full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","last_name":"Nemish","first_name":"Yuriy"}],"volume":55,"date_updated":"2023-10-17T12:20:20Z","date_created":"2019-04-08T14:05:04Z","ec_funded":1},{"status":"public","ddc":["570"],"title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","intvolume":" 15","_id":"7399","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2302307,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_PlosGenetics_Andergassen.pdf","checksum":"2f51fc91e4a4199827adc51d432ad864","date_created":"2020-02-04T10:11:55Z","date_updated":"2020-07-14T12:47:57Z","file_id":"7446","relation":"main_file"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"7","article_type":"original","publication":"PLoS Genetics","citation":{"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.","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","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.","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).","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.","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."},"date_published":"2019-07-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Public Library of Science","year":"2019","pmid":1,"date_created":"2020-01-29T16:14:07Z","date_updated":"2023-10-17T12:30:27Z","volume":15,"author":[{"last_name":"Andergassen","first_name":"Daniel","full_name":"Andergassen, Daniel"},{"full_name":"Muckenhuber, Markus","first_name":"Markus","last_name":"Muckenhuber"},{"full_name":"Bammer, Philipp C.","first_name":"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","first_name":"Takahiko","full_name":"Shimizu, Takahiko"},{"full_name":"Penninger, Josef M.","last_name":"Penninger","first_name":"Josef M."},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"last_name":"Hudson","first_name":"Quanah J.","full_name":"Hudson, Quanah J."}],"article_number":"e1008268","file_date_updated":"2020-07-14T12:47:57Z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31329595"],"isi":["000478689100025"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1008268","month":"07","publication_identifier":{"issn":["1553-7404"]}},{"article_number":"e1007268","ec_funded":1,"file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","pmid":1,"year":"2019","volume":15,"date_created":"2019-11-25T08:20:47Z","date_updated":"2023-10-17T12:30:07Z","author":[{"first_name":"Jilin W. J. L.","last_name":"Wang","full_name":"Wang, Jilin W. J. L."},{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi","full_name":"Lombardi, Fabrizio"},{"last_name":"Zhang","first_name":"Xiyun","full_name":"Zhang, Xiyun"},{"last_name":"Anaclet","first_name":"Christelle","full_name":"Anaclet, Christelle"},{"full_name":"Ivanov, Plamen Ch.","last_name":"Ivanov","first_name":"Plamen Ch."}],"publication_identifier":{"issn":["1553-7358"]},"month":"11","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000500976100014"],"pmid":["31725712"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1007268","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics."}],"intvolume":" 15","title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","ddc":["570","000"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7103","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_PLOSComBio_Wang.pdf","file_size":3982516,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7104","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T08:24:01Z"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","article_type":"original","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.","short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (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.","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","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.","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15, no. 11. Public Library of Science, 2019.","apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268"},"publication":"PLoS Computational Biology","date_published":"2019-11-01T00:00:00Z"},{"type":"conference","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"}],"status":"public","ddc":["000"],"title":"Towards understanding knowledge distillation","intvolume":" 97","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6569","file":[{"file_id":"6570","relation":"main_file","checksum":"a66d00e2694d749250f8507f301320ca","date_created":"2019-06-20T18:22:56Z","date_updated":"2020-07-14T12:47:33Z","access_level":"open_access","file_name":"paper.pdf","creator":"bphuong","file_size":686432,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"13","article_processing_charge":"No","has_accepted_license":"1","page":"5142-5151","publication":"Proceedings of the 36th International Conference on Machine Learning","citation":{"ama":"Phuong M, Lampert C. Towards understanding knowledge distillation. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:5142-5151.","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.","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.","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.","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.","short":"M. Phuong, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 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."},"date_published":"2019-06-13T00:00:00Z","file_date_updated":"2020-07-14T12:47:33Z","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"ChLa"}],"year":"2019","date_updated":"2023-10-17T12:31:38Z","date_created":"2019-06-20T18:23:03Z","volume":97,"author":[{"full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","last_name":"Bui Thi Mai","first_name":"Phuong"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"month":"06","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2019-06-15","start_date":"2019-06-10","location":"Long Beach, CA, United States","name":"ICML: International Conference on Machine Learning"}},{"date_published":"2019-06-01T00:00:00Z","page":"3488-3498","citation":{"short":"N.H. Konstantinov, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 3488–3498.","mla":"Konstantinov, Nikola H., and Christoph Lampert. “Robust Learning from Untrusted Sources.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 3488–98.","chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Robust Learning from Untrusted Sources.” In Proceedings of the 36th International Conference on Machine Learning, 97:3488–98. ML Research Press, 2019.","ama":"Konstantinov NH, Lampert C. Robust learning from untrusted sources. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:3488-3498.","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.","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.","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."},"publication":"Proceedings of the 36th International Conference on Machine Learning","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 97","title":"Robust learning from untrusted sources","status":"public","_id":"6590","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Modern machine learning methods often require more data for training than a single expert can provide. Therefore, it has become a standard procedure to collect data from external sources, e.g. via crowdsourcing. Unfortunately, the quality of these sources is not always guaranteed. As additional complications, the data might be stored in a distributed way, or might even have to remain private. In this work, we address the question of how to learn robustly in such scenarios. Studying the problem through the lens of statistical learning theory, we derive a procedure that allows for learning from all available sources, yet automatically suppresses irrelevant or corrupted data. We show by extensive experiments that our method provides significant improvements over alternative approaches from robust statistics and distributed optimization. ","lang":"eng"}],"type":"conference","language":[{"iso":"eng"}],"conference":{"start_date":"2019-06-10","location":"Long Beach, CA, USA","end_date":"2919-06-15","name":"ICML: International Conference on Machine Learning"},"project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1901.10310"]},"main_file_link":[{"url":"https://arxiv.org/abs/1901.10310","open_access":"1"}],"month":"06","volume":97,"date_created":"2019-06-27T14:18:23Z","date_updated":"2023-10-17T12:31:55Z","related_material":{"record":[{"id":"10799","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H","full_name":"Konstantinov, Nikola H"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"department":[{"_id":"ChLa"}],"publisher":"ML Research Press","publication_status":"published","year":"2019","ec_funded":1},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"15","page":"21274-21284","article_type":"original","citation":{"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","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.","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","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.","mla":"Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42, Proceedings of the National Academy of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116.","short":"D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran, L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 21274–21284.","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."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2019-10-15T00:00:00Z","type":"journal_article","issue":"42","abstract":[{"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.","lang":"eng"}],"intvolume":" 116","status":"public","ddc":["580"],"title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","_id":"6999","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:47:46Z","date_created":"2019-11-13T08:22:28Z","checksum":"258c666bc6253eab81961f61169eefae","relation":"main_file","file_id":"7012","content_type":"application/pdf","file_size":3287466,"creator":"dernst","file_name":"2019_PNAS_Huang.pdf","access_level":"open_access"}],"oa_version":"Published Version","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"10","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000490183000068"],"pmid":["31575745"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1911892116","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"JiFr"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","pmid":1,"year":"2019","volume":116,"date_created":"2019-11-12T11:42:05Z","date_updated":"2023-10-17T12:32:37Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2004738117"}]},"author":[{"full_name":"Huang, D","last_name":"Huang","first_name":"D"},{"full_name":"Sun, Y","first_name":"Y","last_name":"Sun"},{"first_name":"Z","last_name":"Ma","full_name":"Ma, Z"},{"first_name":"M","last_name":"Ke","full_name":"Ke, M"},{"last_name":"Cui","first_name":"Y","full_name":"Cui, Y"},{"first_name":"Z","last_name":"Chen","full_name":"Chen, Z"},{"last_name":"Chen","first_name":"C","full_name":"Chen, C"},{"first_name":"C","last_name":"Ji","full_name":"Ji, C"},{"last_name":"Tran","first_name":"TM","full_name":"Tran, TM"},{"last_name":"Yang","first_name":"L","full_name":"Yang, L"},{"last_name":"Lam","first_name":"SM","full_name":"Lam, SM"},{"first_name":"Y","last_name":"Han","full_name":"Han, Y"},{"first_name":"G","last_name":"Shu","full_name":"Shu, G"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Miao, Y","last_name":"Miao","first_name":"Y"},{"full_name":"Jiang, L","first_name":"L","last_name":"Jiang"},{"full_name":"Chen, X","first_name":"X","last_name":"Chen"}]},{"volume":116,"date_created":"2019-07-07T21:59:25Z","date_updated":"2023-10-17T12:44:15Z","author":[{"full_name":"Wright, Alison E.","first_name":"Alison E.","last_name":"Wright"},{"first_name":"Iulia","last_name":"Darolti","full_name":"Darolti, Iulia"},{"last_name":"Bloch","first_name":"Natasha I.","full_name":"Bloch, Natasha I."},{"full_name":"Oostra, Vicencio","last_name":"Oostra","first_name":"Vicencio"},{"first_name":"Benjamin A.","last_name":"Sandkam","full_name":"Sandkam, Benjamin A."},{"last_name":"Buechel","first_name":"Séverine D.","full_name":"Buechel, Séverine D."},{"last_name":"Kolm","first_name":"Niclas","full_name":"Kolm, Niclas"},{"last_name":"Breden","first_name":"Felix","full_name":"Breden, Felix"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"},{"full_name":"Mank, Judith E.","last_name":"Mank","first_name":"Judith E."}],"department":[{"_id":"BeVi"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","pmid":1,"year":"2019","month":"06","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1905555116","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000472719100010"],"pmid":["31213531"]},"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1905555116","open_access":"1"}],"issue":"26","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 116","title":"On the power to detect rare recombination events","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6621","article_processing_charge":"No","day":"25","scopus_import":"1","date_published":"2019-06-25T00:00:00Z","page":"12607-12608","article_type":"letter_note","citation":{"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.","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.","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","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.","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.","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"},"publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:42Z","author":[{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Brandvain, Yaniv","first_name":"Yaniv","last_name":"Brandvain"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"full_name":"Yakimowski, Sarah","first_name":"Sarah","last_name":"Yakimowski"},{"first_name":"Tanmay","last_name":"Dixit","full_name":"Dixit, Tanmay"},{"full_name":"Lexer, Christian","last_name":"Lexer","first_name":"Christian"},{"full_name":"Cereghetti, Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","first_name":"Eva","last_name":"Cereghetti"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"volume":224,"date_created":"2019-09-07T14:35:40Z","date_updated":"2023-10-18T08:47:08Z","pmid":1,"year":"2019","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"month":"11","doi":"10.1111/nph.16180","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31505037"]},"project":[{"name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960"},{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463","name":"Sex chromosomes and species barriers","call_identifier":"FWF"}],"quality_controlled":"1","issue":"3","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"7011","relation":"main_file","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","checksum":"21e4c95599bbcaf7c483b89954658672","file_name":"2019_NewPhytologist_Pickup.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1511958}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6856","intvolume":" 224","ddc":["570"],"status":"public","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","citation":{"ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","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.","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.","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.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180."},"publication":"New Phytologist","page":"1035-1047","article_type":"original"},{"date_created":"2023-09-06T12:48:47Z","date_updated":"2023-11-07T12:17:31Z","volume":13,"author":[{"full_name":"FAS, Engelhardt","last_name":"FAS","first_name":"Engelhardt"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M","full_name":"Praetorius, Florian M"},{"first_name":"CH","last_name":"Wachauf","full_name":"Wachauf, CH"},{"first_name":"G","last_name":"Brüggenthies","full_name":"Brüggenthies, G"},{"full_name":"Kohler, F","last_name":"Kohler","first_name":"F"},{"full_name":"Kick, B","last_name":"Kick","first_name":"B"},{"full_name":"Kadletz, KL","last_name":"Kadletz","first_name":"KL"},{"last_name":"Pham","first_name":"PN","full_name":"Pham, PN"},{"full_name":"Behler, KL","last_name":"Behler","first_name":"KL"},{"full_name":"Gerling, T","last_name":"Gerling","first_name":"T"},{"first_name":"H","last_name":"Dietz","full_name":"Dietz, H"}],"publication_status":"published","publisher":"ACS Publications","year":"2019","pmid":1,"extern":"1","language":[{"iso":"eng"}],"doi":"10.1021/acsnano.9b01025","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsnano.9b01025"}],"external_id":{"pmid":["30990672"]},"oa":1,"month":"04","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086x"]},"oa_version":"Published Version","status":"public","title":"Custom-size, functional, and durable DNA origami with design-specific scaffolds","intvolume":" 13","_id":"14299","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"DNA origami nano-objects are usually designed around generic single-stranded “scaffolds”. Many properties of the target object are determined by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable production methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence composition on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent cross-linking of DNA origami via UV irradiation, and we built DNAzyme-containing scaffolds that allow postfolding DNA origami domain separation."}],"issue":"5","type":"journal_article","date_published":"2019-04-16T00:00:00Z","article_type":"original","page":"5015-5027","publication":"ACS Nano","citation":{"ieee":"E. FAS et al., “Custom-size, functional, and durable DNA origami with design-specific scaffolds,” ACS Nano, vol. 13, no. 5. ACS Publications, pp. 5015–5027, 2019.","apa":"FAS, E., Praetorius, F. M., Wachauf, C., Brüggenthies, G., Kohler, F., Kick, B., … Dietz, H. (2019). Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. ACS Publications. https://doi.org/10.1021/acsnano.9b01025","ista":"FAS E, Praetorius FM, Wachauf C, Brüggenthies G, Kohler F, Kick B, Kadletz K, Pham P, Behler K, Gerling T, Dietz H. 2019. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 13(5), 5015–5027.","ama":"FAS E, Praetorius FM, Wachauf C, et al. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 2019;13(5):5015-5027. doi:10.1021/acsnano.9b01025","chicago":"FAS, Engelhardt, Florian M Praetorius, CH Wachauf, G Brüggenthies, F Kohler, B Kick, KL Kadletz, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano. ACS Publications, 2019. https://doi.org/10.1021/acsnano.9b01025.","short":"E. FAS, F.M. Praetorius, C. Wachauf, G. Brüggenthies, F. Kohler, B. Kick, K. Kadletz, P. Pham, K. Behler, T. Gerling, H. Dietz, ACS Nano 13 (2019) 5015–5027.","mla":"FAS, Engelhardt, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano, vol. 13, no. 5, ACS Publications, 2019, pp. 5015–27, doi:10.1021/acsnano.9b01025."},"day":"16","article_processing_charge":"No","scopus_import":"1"},{"project":[{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"quality_controlled":"1","external_id":{"arxiv":["1812.04911"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPICS.SOCG.2019.38","conference":{"location":"Portland, OR, United States","start_date":"2019-06-18","end_date":"2019-06-21","name":"SoCG 2019: Symposium on Computational Geometry"},"publication_identifier":{"isbn":["9783959771047"],"issn":["1868-8969"]},"month":"06","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2019","volume":129,"date_created":"2019-07-17T10:35:04Z","date_updated":"2023-12-13T12:03:35Z","related_material":{"record":[{"id":"13974","status":"public","relation":"later_version"}]},"author":[{"last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav"},{"first_name":"Bernd","last_name":"Gärtner","full_name":"Gärtner, Bernd"},{"full_name":"Kupavskii, Andrey","last_name":"Kupavskii","first_name":"Andrey"},{"full_name":"Valtr, Pavel","last_name":"Valtr","first_name":"Pavel"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"file_date_updated":"2020-07-14T12:47:35Z","page":"38:1-38:13","citation":{"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.","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","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.","ama":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:38:1-38:13. doi:10.4230/LIPICS.SOCG.2019.38","chicago":"Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” In 35th International Symposium on Computational Geometry, 129:38:1-38:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38.","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.","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."},"publication":"35th International Symposium on Computational Geometry","date_published":"2019-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 129","status":"public","ddc":["000","510"],"title":"The crossing Tverberg theorem","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6647","oa_version":"Published Version","file":[{"date_created":"2019-07-24T06:54:52Z","date_updated":"2020-07-14T12:47:35Z","checksum":"d6d017f8b41291b94d102294fa96ae9c","file_id":"6667","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":559837,"file_name":"2019_LIPICS_Fulek.pdf","access_level":"open_access"}],"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2."}]},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"986-996","citation":{"ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. ACM Press; 2019:986-996. doi:10.1145/3313276.3316407","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 986–996.","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.","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","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–96, doi:10.1145/3313276.3316407.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–996.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, 986–96. ACM Press, 2019. https://doi.org/10.1145/3313276.3316407."},"publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","date_published":"2019-06-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power."}],"title":"Why extension-based proofs fail","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6676","oa_version":"Preprint","publication_identifier":{"isbn":["9781450367059"]},"month":"06","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1811.01421","open_access":"1"}],"external_id":{"isi":["000523199100089"],"arxiv":["1811.01421"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3313276.3316407","conference":{"start_date":"2019-06-23","location":"Phoenix, AZ, United States","end_date":"2019-06-26","name":"STOC: Symposium on Theory of Computing"},"publisher":"ACM Press","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2019","date_updated":"2023-12-13T12:28:28Z","date_created":"2019-07-24T09:13:05Z","related_material":{"record":[{"id":"14364","relation":"later_version","status":"public"}]},"author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"last_name":"Ellen","first_name":"Faith","full_name":"Ellen, Faith"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"full_name":"Zhu, Leqi","first_name":"Leqi","last_name":"Zhu"}]},{"article_processing_charge":"No","month":"03","day":"16","date_published":"2019-03-16T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. arXiv.","ieee":"A. Biniaz 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.","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. Token swapping on trees. arXiv, 1903.06981.","short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, ArXiv (n.d.).","mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981.","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” ArXiv, n.d."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.06981"}],"external_id":{"arxiv":["1903.06981"]},"oa":1,"publication":"arXiv","abstract":[{"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.","lang":"eng"}],"type":"preprint","article_number":"1903.06981","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7944"},{"id":"12833","relation":"later_version","status":"public"}]},"author":[{"last_name":"Biniaz","first_name":"Ahmad","full_name":"Biniaz, 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","orcid":"0000-0002-6660-1322","first_name":"Zuzana","last_name":"Masárová","full_name":"Masárová, Zuzana"},{"last_name":"Miltzow","first_name":"Tillmann","full_name":"Miltzow, Tillmann"},{"first_name":"Debajyoti","last_name":"Mondal","full_name":"Mondal, Debajyoti"},{"full_name":"Naredla, Anurag Murty","last_name":"Naredla","first_name":"Anurag Murty"},{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"full_name":"Turcotte, Alexi","last_name":"Turcotte","first_name":"Alexi"}],"oa_version":"Preprint","date_created":"2020-06-08T12:25:25Z","date_updated":"2024-01-04T12:42:08Z","year":"2019","_id":"7950","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}],"status":"public","title":"Token swapping on trees","publication_status":"submitted"},{"type":"journal_article","issue":"4","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"}],"intvolume":" 11","status":"public","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","ddc":["570"],"_id":"6418","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"6446","relation":"main_file","checksum":"7d0ede297b6741f3dc89cd59017c7642","date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-14T08:29:38Z","access_level":"open_access","file_name":"2019_GBE_Huylmans.pdf","creator":"dernst","file_size":1256303,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"1033-1044","citation":{"apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","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.","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","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz053.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053."},"publication":"Genome biology and evolution","date_published":"2019-04-01T00:00:00Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","publication_status":"published","year":"2019","volume":11,"date_updated":"2024-02-21T12:45:41Z","date_created":"2019-05-13T07:58:38Z","related_material":{"record":[{"id":"6060","relation":"popular_science","status":"public"}]},"author":[{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K"},{"full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"first_name":"William J","last_name":"Gammerdinger","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","full_name":"Gammerdinger, William J"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"publication_identifier":{"eissn":["1759-6653"]},"month":"04","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000476569800003"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/gbe/evz053"},{"year":"2019","_id":"7016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"status":"public","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7652"}]},"contributor":[{"last_name":"Guet","contributor_type":"project_leader","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Tomanek, Isabella","first_name":"Isabella","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X"}],"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:47Z","date_created":"2019-11-13T08:52:21Z","checksum":"72441055043eda4cbf1398a422e2c118","relation":"main_file","file_id":"7017","title":"Locus1_amplified","file_size":2456192500,"content_type":"application/octet-stream","creator":"itomanek","description":"Illumina whole genome sequence data for Locus 1 - 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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":1,"citation":{"chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","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.","short":"I. Tomanek, (2019).","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.","ieee":"I. 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Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.","short":"B. Vicoso, (2019).","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.","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.","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. 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","file_date_updated":"2020-07-14T12:47:17Z","type":"research_data"},{"oa_version":"Published Version","file":[{"creator":"dernst","file_size":33202743,"content_type":"application/zip","access_level":"open_access","file_name":"Setd5_paper.zip","checksum":"bc1b285edca9e98a2c63d153c79bb75b","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-07T13:37:19Z","file_id":"6084","relation":"supplementary_material"}],"date_created":"2019-03-07T13:32:35Z","date_updated":"2024-02-21T13:41:01Z","related_material":{"record":[{"status":"public","relation":"research_paper","id":"3"}]},"author":[{"orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","first_name":"Christoph","full_name":"Dotter, Christoph"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaNo"}],"ddc":["570"],"status":"public","title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","_id":"6074","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","file_date_updated":"2020-07-14T12:47:18Z","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"}],"type":"research_data","doi":"10.15479/AT:ISTA:6074","date_published":"2019-01-09T00:00:00Z","oa":1,"citation":{"short":"C. Dotter, G. Novarino, (2019).","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.","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.","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","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","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."},"article_processing_charge":"No","has_accepted_license":"1","month":"01","day":"09"},{"type":"research_data","license":"https://creativecommons.org/licenses/by-sa/4.0/","file_date_updated":"2020-07-14T12:47:18Z","abstract":[{"text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7).","lang":"eng"}],"status":"public","title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"_id":"6062","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-03-04T14:20:58Z","date_updated":"2024-02-21T12:46:04Z","file":[{"title":"Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","file_id":"6068","relation":"main_file","date_created":"2019-03-05T09:29:37Z","date_updated":"2020-07-14T12:47:18Z","checksum":"48e7b9a02939b763417733239522a236","file_name":"Online_data.zip","access_level":"open_access","creator":"mnardin","file_size":37002186,"content_type":"application/zip"}],"oa_version":"Published Version","author":[{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","first_name":"Michele"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"6194"}]},"day":"29","month":"03","article_processing_charge":"No","has_accepted_license":"1","oa":1,"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"citation":{"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.","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.","short":"M. Nardin, (2019).","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.","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","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.","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"},"date_published":"2019-03-29T00:00:00Z","doi":"10.15479/AT:ISTA:6062"},{"date_published":"2019-03-01T00:00:00Z","page":"500-515","citation":{"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.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","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.","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","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.","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.","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"},"publication":"Molecular biology and evolution","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 36","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","status":"public","_id":"6089","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","abstract":[{"lang":"eng","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."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy246","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"external_id":{"pmid":["30590559"],"isi":["000462585100006"]},"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"month":"03","volume":36,"date_created":"2019-03-10T22:59:19Z","date_updated":"2024-02-21T13:59:17Z","related_material":{"record":[{"id":"5757","relation":"popular_science","status":"public"}]},"author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2019"},{"date_published":"2019-03-18T00:00:00Z","citation":{"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.","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.","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.","ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria."},"page":"375","has_accepted_license":"1","article_processing_charge":"No","day":"18","file":[{"file_id":"6180","relation":"source_file","checksum":"6926f66f28079a81c4937e3764be00fc","date_created":"2019-03-28T08:53:52Z","date_updated":"2020-07-14T12:47:21Z","access_level":"closed","file_name":"2019_Schroeder_Thesis.tar.gz","creator":"dernst","content_type":"application/x-gzip","file_size":7104482},{"checksum":"7d0ebb8d1207e89768cdd497a5bf80fb","date_updated":"2020-07-14T12:47:21Z","date_created":"2019-03-28T08:53:52Z","relation":"main_file","file_id":"6181","file_size":4228794,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_Schroeder_Thesis.pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6179","ddc":["515","519"],"title":"From Dyson to Pearcey: Universal statistics in random matrix theory","status":"public","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."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:th6179","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"}],"degree_awarded":"PhD","oa":1,"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"publication_identifier":{"issn":["2663-337X"]},"month":"03","related_material":{"record":[{"id":"1144","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6186"},{"status":"public","relation":"part_of_dissertation","id":"6185"},{"id":"6182","status":"public","relation":"part_of_dissertation"},{"id":"1012","status":"public","relation":"part_of_dissertation"},{"id":"6184","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"}],"date_created":"2019-03-28T08:58:59Z","date_updated":"2024-02-22T14:34:33Z","year":"2019","department":[{"_id":"LaEr"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:21Z"},{"date_created":"2019-05-24T09:48:36Z","date_updated":"2024-02-22T14:57:29Z","volume":11269,"author":[{"last_name":"Sun","first_name":"Rémy","full_name":"Sun, Rémy"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"6944"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ChLa"}],"year":"2019","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2018-10-09","location":"Stuttgart, Germany","end_date":"2018-10-12","name":"GCPR: Conference on Pattern Recognition"},"doi":"10.1007/978-3-030-12939-2_18","quality_controlled":"1","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"oa":1,"external_id":{"arxiv":["1804.04171"]},"main_file_link":[{"url":"https://arxiv.org/abs/1804.04171","open_access":"1"}],"month":"02","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030129385","9783030129392"],"issn":["0302-9743"]},"oa_version":"Preprint","status":"public","title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications","intvolume":" 11269","_id":"6482","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2019-02-14T00:00:00Z","page":"244-259","citation":{"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.","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.","short":"R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.","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.","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","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.","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"},"day":"14","article_processing_charge":"No","scopus_import":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6642","intvolume":" 2107","status":"public","title":"On diffusive variants of some classical viscoelastic rate-type models","oa_version":"Preprint","type":"conference","abstract":[{"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.","lang":"eng"}],"citation":{"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","ista":"Dostalík M, Pruša V, Skrivan T. 2019. On diffusive variants of some classical viscoelastic rate-type models. AIP Conference Proceedings. 8th International Conference on Novel Trends in Rheology vol. 2107, 020002.","apa":"Dostalík, M., Pruša, V., & Skrivan, T. (2019). On diffusive variants of some classical viscoelastic rate-type models. In AIP Conference Proceedings (Vol. 2107). Zlin, Czech Republic: AIP Publishing. https://doi.org/10.1063/1.5109493","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.","mla":"Dostalík, Mark, et al. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” AIP Conference Proceedings, vol. 2107, 020002, AIP Publishing, 2019, doi:10.1063/1.5109493.","short":"M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing, 2019.","chicago":"Dostalík, Mark, Vít Pruša, and Tomas Skrivan. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” In AIP Conference Proceedings, Vol. 2107. AIP Publishing, 2019. https://doi.org/10.1063/1.5109493."},"publication":"AIP Conference Proceedings","date_published":"2019-05-21T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"21","year":"2019","publisher":"AIP Publishing","department":[{"_id":"ChWo"}],"publication_status":"published","author":[{"first_name":"Mark","last_name":"Dostalík","full_name":"Dostalík, Mark"},{"last_name":"Pruša","first_name":"Vít","full_name":"Pruša, Vít"},{"full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","first_name":"Tomas"}],"volume":2107,"date_updated":"2024-02-28T13:01:28Z","date_created":"2019-07-15T10:07:09Z","article_number":"020002","external_id":{"isi":["000479303100002"],"arxiv":["1902.07983"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1902.07983","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1063/1.5109493","conference":{"name":"8th International Conference on Novel Trends in Rheology","location":"Zlin, Czech Republic","start_date":"2019-07-30","end_date":"2019-07-31"},"language":[{"iso":"eng"}],"month":"05"},{"publication_identifier":{"issn":["00222488"]},"month":"12","external_id":{"isi":["000505529800002"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1063/1.5138135","language":[{"iso":"eng"}],"article_number":"123504","file_date_updated":"2020-07-14T12:47:54Z","year":"2019","department":[{"_id":"RoSe"}],"publisher":"AIP Publishing","publication_status":"published","author":[{"last_name":"Jaksic","first_name":"Vojkan","full_name":"Jaksic, Vojkan"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"volume":60,"date_updated":"2024-02-28T13:01:45Z","date_created":"2020-01-05T23:00:46Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"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.","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","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.","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","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.","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","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."},"publication":"Journal of Mathematical Physics","article_type":"letter_note","date_published":"2019-12-01T00:00:00Z","type":"journal_article","issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7226","intvolume":" 60","title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","ddc":["500"],"status":"public","file":[{"file_name":"2019_JournalMathPhysics_Jaksic.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1025015,"file_id":"7244","relation":"main_file","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:59:13Z","checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22"}],"oa_version":"Published Version"},{"author":[{"first_name":"D.","last_name":"Huber","full_name":"Huber, D."},{"first_name":"H.-W.","last_name":"Hammer","full_name":"Hammer, H.-W."},{"full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"volume":1,"date_created":"2019-12-17T13:03:41Z","date_updated":"2024-02-28T13:11:40Z","year":"2019","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:52Z","article_number":"033177","doi":"10.1103/physrevresearch.1.033177","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1908.02483"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","publication_identifier":{"issn":["2643-1564"]},"month":"12","oa_version":"Published Version","file":[{"file_name":"2019_PhysRevResearch_Huber.pdf","access_level":"open_access","creator":"dernst","file_size":1370022,"content_type":"application/pdf","file_id":"7193","relation":"main_file","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-18T07:13:14Z","checksum":"382eb67e62a77052a23887332d363f96"}],"_id":"7190","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 1","title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","status":"public","ddc":["530"],"issue":"3","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."}],"type":"journal_article","date_published":"2019-12-16T00:00:00Z","citation":{"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.","short":"D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).","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.","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","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.","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","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."},"publication":"Physical Review Research","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"16"},{"scopus_import":"1","day":"07","article_processing_charge":"No","publication":"Physical Review Letters","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.","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","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.","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","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.","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).","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."},"article_type":"original","date_published":"2019-06-07T00:00:00Z","type":"journal_article","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."}],"issue":"22","_id":"6575","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Emergent SU(2) dynamics and perfect quantum many-body scars","status":"public","intvolume":" 122","oa_version":"Preprint","month":"06","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"external_id":{"isi":["000470885800005"],"arxiv":["1812.05561"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1812.05561","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1103/PhysRevLett.122.220603","language":[{"iso":"eng"}],"article_number":"220603","year":"2019","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"author":[{"last_name":"Choi","first_name":"Soonwon","full_name":"Choi, Soonwon"},{"last_name":"Turner","first_name":"Christopher J.","full_name":"Turner, Christopher J."},{"first_name":"Hannes","last_name":"Pichler","full_name":"Pichler, Hannes"},{"full_name":"Ho, Wen Wei","last_name":"Ho","first_name":"Wen Wei"},{"last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"full_name":"Lukin, Mikhail D.","last_name":"Lukin","first_name":"Mikhail D."},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."}],"date_updated":"2024-02-28T13:12:22Z","date_created":"2019-06-23T21:59:13Z","volume":122},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6092","status":"public","title":"Quantum many-body dynamics of the Einstein-de Haas effect","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."}],"issue":"6","type":"journal_article","date_published":"2019-02-01T00:00:00Z","publication":"Physical Review B","citation":{"ista":"Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 99(6), 064428.","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","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.","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","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.","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.","short":"J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019)."},"day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Mentink, Johann H","last_name":"Mentink","first_name":"Johann H"},{"full_name":"Katsnelson, Mikhail","last_name":"Katsnelson","first_name":"Mikhail"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"date_created":"2019-03-10T22:59:20Z","date_updated":"2024-02-28T13:11:54Z","volume":99,"year":"2019","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"article_number":"064428","doi":"10.1103/PhysRevB.99.064428","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01638"}],"external_id":{"arxiv":["1802.01638"],"isi":["000459223400004"]},"quality_controlled":"1","isi":1,"project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"month":"02"},{"_id":"6090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Receptor crosstalk improves concentration sensing of multiple ligands","status":"public","intvolume":" 99","oa_version":"Preprint","type":"journal_article","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"}],"issue":"2","publication":"Physical Review E","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.","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.","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","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.","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","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."},"date_published":"2019-02-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"No","year":"2019","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"American Physical Society","author":[{"last_name":"Carballo-Pacheco","first_name":"Martín","full_name":"Carballo-Pacheco, Martín"},{"full_name":"Desponds, Jonathan","last_name":"Desponds","first_name":"Jonathan"},{"first_name":"Tatyana","last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana"},{"full_name":"Mayer, Andreas","first_name":"Andreas","last_name":"Mayer"},{"last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"},{"full_name":"Reddy, Gautam","first_name":"Gautam","last_name":"Reddy"},{"last_name":"Nemenman","first_name":"Ilya","full_name":"Nemenman, Ilya"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"}],"date_created":"2019-03-10T22:59:20Z","date_updated":"2024-02-28T13:12:06Z","volume":99,"article_number":"022423","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"oa":1,"external_id":{"isi":["000459916500007"]},"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevE.99.022423","language":[{"iso":"eng"}],"month":"02"},{"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2019","date_updated":"2024-02-28T13:12:48Z","date_created":"2019-08-11T21:59:20Z","volume":9,"author":[{"first_name":"Colin","last_name":"Hubert","full_name":"Hubert, Colin"},{"full_name":"Baruchi, Yifat","first_name":"Yifat","last_name":"Baruchi"},{"first_name":"Yotam","last_name":"Mazuz-Harpaz","full_name":"Mazuz-Harpaz, Yotam"},{"first_name":"Kobi","last_name":"Cohen","full_name":"Cohen, Kobi"},{"full_name":"Biermann, Klaus","first_name":"Klaus","last_name":"Biermann"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"first_name":"Ken","last_name":"West","full_name":"West, Ken"},{"last_name":"Pfeiffer","first_name":"Loren","full_name":"Pfeiffer, Loren"},{"last_name":"Rapaport","first_name":"Ronen","full_name":"Rapaport, Ronen"},{"full_name":"Santos, Paulo","last_name":"Santos","first_name":"Paulo"}],"article_number":"021026","file_date_updated":"2020-07-14T12:47:40Z","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1807.11238"],"isi":["000467402900001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevX.9.021026","month":"05","publication_identifier":{"eissn":["2160-3308"]},"status":"public","ddc":["530"],"title":"Attractive dipolar coupling between stacked exciton fluids","intvolume":" 9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6786","file":[{"file_id":"6802","relation":"main_file","checksum":"065ff82ee4a1d2c3773ce4b76ff4213c","date_created":"2019-08-12T12:14:18Z","date_updated":"2020-07-14T12:47:40Z","access_level":"open_access","file_name":"2019_PhysReviewX_Hubert.pdf","creator":"dernst","file_size":1193550,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","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"}],"issue":"2","article_type":"original","publication":"Physical Review X","citation":{"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.","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).","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.","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","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.","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"},"date_published":"2019-05-08T00:00:00Z","scopus_import":"1","day":"08","article_processing_charge":"No","has_accepted_license":"1"},{"year":"2019","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","author":[{"first_name":"Tuure","last_name":"Orell","full_name":"Orell, Tuure"},{"full_name":"Michailidis, Alexios","first_name":"Alexios","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"full_name":"Silveri, Matti","last_name":"Silveri","first_name":"Matti"}],"volume":100,"date_updated":"2024-02-28T13:13:13Z","date_created":"2019-11-13T08:25:48Z","article_number":"134504","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.04043"}],"external_id":{"arxiv":["1907.04043"],"isi":["000489036500004"]},"isi":1,"quality_controlled":"1","doi":"10.1103/physrevb.100.134504","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7013","intvolume":" 100","title":"Probing the many-body localization phase transition with superconducting circuits","status":"public","oa_version":"Preprint","type":"journal_article","issue":"13","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"}],"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","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.","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.","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","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.","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."},"publication":"Physical Review B","article_type":"original","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"scopus_import":"1","article_processing_charge":"No","day":"25","article_type":"original","citation":{"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.","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.","short":"P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).","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.","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.","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"},"publication":"Physical Review B","date_published":"2019-11-25T00:00:00Z","type":"journal_article","issue":"17","abstract":[{"lang":"eng","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)."}],"intvolume":" 100","status":"public","title":"Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7200","oa_version":"Preprint","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"11","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.13579"}],"external_id":{"arxiv":["1907.13579"],"isi":["000498845700006"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.100.174518","article_number":"174518","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","year":"2019","volume":100,"date_created":"2019-12-22T23:00:41Z","date_updated":"2024-02-28T13:14:08Z","author":[{"first_name":"Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro"},{"last_name":"Grilli","first_name":"Marco","full_name":"Grilli, Marco"},{"first_name":"Brigitte","last_name":"Leridon","full_name":"Leridon, Brigitte"},{"full_name":"Caprara, Sergio","last_name":"Caprara","first_name":"Sergio"}]},{"intvolume":" 100","title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","status":"public","ddc":["532"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6779","oa_version":"Preprint","type":"journal_article","issue":"1","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"}],"article_type":"original","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.","short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","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.","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","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.","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.","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"},"publication":"Physical Review E","date_published":"2019-07-25T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"25","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2019","volume":100,"date_created":"2019-08-09T09:40:41Z","date_updated":"2024-02-28T13:13:00Z","author":[{"id":"47A5E706-F248-11E8-B48F-1D18A9856A87","last_name":"Suri","first_name":"Balachandra","full_name":"Suri, Balachandra"},{"last_name":"Pallantla","first_name":"Ravi Kumar","full_name":"Pallantla, Ravi Kumar"},{"full_name":"Schatz, Michael F.","last_name":"Schatz","first_name":"Michael F."},{"full_name":"Grigoriev, Roman O.","first_name":"Roman O.","last_name":"Grigoriev"}],"article_number":"013112","ec_funded":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.05860","open_access":"1"}],"external_id":{"isi":["000477911800012"],"arxiv":["1907.05860"]},"language":[{"iso":"eng"}],"doi":"10.1103/physreve.100.013112","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"month":"07"},{"oa_version":"Preprint","intvolume":" 100","status":"public","title":"Floating Wigner crystal with no boundary charge fluctuations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7015","issue":"3","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"}],"type":"journal_article","date_published":"2019-07-25T00:00:00Z","article_type":"original","citation":{"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.","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","ista":"Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 100(3), 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","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.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (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."},"publication":"Physical Review B","article_processing_charge":"No","day":"25","scopus_import":"1","volume":100,"date_updated":"2024-02-28T13:13:23Z","date_created":"2019-11-13T08:41:48Z","author":[{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"last_name":"Lieb","first_name":"Elliott H.","full_name":"Lieb, Elliott H."},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"department":[{"_id":"RoSe"}],"publisher":"American Physical Society","publication_status":"published","year":"2019","ec_funded":1,"article_number":"035127","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.100.035127","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1905.09138"],"isi":["000477888200001"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1905.09138","open_access":"1"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"07"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7145","title":"End-to-end correlated subgap states in hybrid nanowires","status":"public","intvolume":" 100","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"}],"issue":"20","type":"journal_article","date_published":"2019-11-15T00:00:00Z","publication":"Physical Review B","citation":{"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","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.","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.","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).","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."},"article_type":"original","day":"15","article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"G. L. R.","last_name":"Anselmetti","full_name":"Anselmetti, G. L. R."},{"full_name":"Martinez, E. A.","first_name":"E. A.","last_name":"Martinez"},{"full_name":"Ménard, G. C.","last_name":"Ménard","first_name":"G. C."},{"last_name":"Puglia","first_name":"D.","full_name":"Puglia, D."},{"full_name":"Malinowski, F. K.","first_name":"F. K.","last_name":"Malinowski"},{"first_name":"J. S.","last_name":"Lee","full_name":"Lee, J. S."},{"first_name":"S.","last_name":"Choi","full_name":"Choi, S."},{"full_name":"Pendharkar, M.","first_name":"M.","last_name":"Pendharkar"},{"last_name":"Palmstrøm","first_name":"C. J.","full_name":"Palmstrøm, C. J."},{"full_name":"Marcus, C. M.","first_name":"C. M.","last_name":"Marcus"},{"full_name":"Casparis, L.","first_name":"L.","last_name":"Casparis"},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham"}],"date_updated":"2024-02-28T13:13:51Z","date_created":"2019-12-04T16:02:25Z","volume":100,"year":"2019","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"AnHi"}],"article_number":"205412","doi":"10.1103/physrevb.100.205412","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.05549"}],"oa":1,"external_id":{"isi":["000495967500006"],"arxiv":["1908.05549"]},"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]}},{"date_published":"2019-02-01T00:00:00Z","publication":"Physical Review Letters","citation":{"ista":"Goremykina A, Vasseur R, Serbyn M. 2019. Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. 122(4), 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","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.","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","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.","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.","short":"A. Goremykina, R. Vasseur, M. Serbyn, Physical Review Letters 122 (2019)."},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"5906","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Analytically solvable renormalization group for the many-body localization transition","status":"public","intvolume":" 122","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","type":"journal_article","doi":"10.1103/physrevlett.122.040601","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1807.04285","open_access":"1"}],"external_id":{"isi":["000456783700001"],"arxiv":["1807.04285"]},"oa":1,"isi":1,"quality_controlled":"1","month":"02","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"author":[{"full_name":"Goremykina, Anna","first_name":"Anna","last_name":"Goremykina"},{"full_name":"Vasseur, Romain","first_name":"Romain","last_name":"Vasseur"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-28T13:13:38Z","date_created":"2019-02-01T08:22:28Z","volume":122,"year":"2019","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"article_number":"040601"},{"type":"journal_article","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"}],"issue":"6","title":"Coupled superfluidity of binary Bose mixtures in two dimensions","status":"public","intvolume":" 99","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6632","oa_version":"Preprint","scopus_import":"1","day":"28","article_processing_charge":"No","publication":"Physical Review A","citation":{"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","ista":"Karle V, Defenu N, Enss T. 2019. Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. 99(6), 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.","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.","short":"V. Karle, N. Defenu, T. Enss, Physical Review A 99 (2019).","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."},"date_published":"2019-06-28T00:00:00Z","article_number":"063627","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2019","date_updated":"2024-02-28T13:12:34Z","date_created":"2019-07-14T21:59:17Z","volume":99,"author":[{"full_name":"Karle, Volker","last_name":"Karle","first_name":"Volker"},{"full_name":"Defenu, Nicolò","last_name":"Defenu","first_name":"Nicolò"},{"last_name":"Enss","first_name":"Tilman","full_name":"Enss, Tilman"}],"month":"06","publication_identifier":{"issn":["24699926"],"eissn":["24699934"]},"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1903.06759","open_access":"1"}],"oa":1,"external_id":{"isi":["000473133600007"],"arxiv":["1903.06759"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.99.063627"},{"intvolume":" 91","status":"public","title":"Quantum control of molecular rotation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7396","oa_version":"Preprint","type":"journal_article","issue":"3","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."}],"article_type":"original","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.","short":"C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (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.","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","ista":"Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation. Reviews of Modern Physics. 91(3), 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","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."},"publication":"Reviews of Modern Physics","date_published":"2019-09-18T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"18","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2019","volume":91,"date_updated":"2024-02-28T13:15:33Z","date_created":"2020-01-29T16:04:19Z","author":[{"full_name":"Koch, Christiane P.","first_name":"Christiane P.","last_name":"Koch"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"full_name":"Sugny, Dominique","first_name":"Dominique","last_name":"Sugny"}],"article_number":"035005 ","project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.11338"}],"external_id":{"isi":["000486661700001"],"arxiv":["1810.11338"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/revmodphys.91.035005","publication_identifier":{"issn":["0034-6861"],"eissn":["1539-0756"]},"month":"09"},{"isi":1,"quality_controlled":"1","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1812.01475","open_access":"1"}],"external_id":{"isi":["000540384500015"],"arxiv":["1812.01475"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-08-28","start_date":"2019-08-25","location":"Visby, Sweden","name":"Information Theory Workshop"},"doi":"10.1109/ITW44776.2019.8989292","month":"08","publication_identifier":{"isbn":["9781538669006"]},"publication_status":"published","publisher":"IEEE","department":[{"_id":"GaTk"}],"year":"2019","date_created":"2020-03-22T23:00:47Z","date_updated":"2024-03-06T14:22:51Z","author":[{"full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Hledik"},{"full_name":"Sokolowski, Thomas R","last_name":"Sokolowski","first_name":"Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"15020","relation":"dissertation_contains","status":"public"}]},"article_number":"8989292","ec_funded":1,"publication":"IEEE Information Theory Workshop, ITW 2019","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.","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.","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","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.","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.","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"},"date_published":"2019-08-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"A tight upper bound on mutual information","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7606","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","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."}]},{"month":"08","publication_identifier":{"isbn":["9781450362177"]},"language":[{"iso":"eng"}],"conference":{"name":"PODC: Symposium on Principles of Distributed Computing","start_date":"2019-07-29","location":"Toronto, ON, Canada","end_date":"2019-08-02"},"doi":"10.1145/3293611.3331633","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.05956"}],"oa":1,"external_id":{"arxiv":["1903.05956"],"isi":["000570442000011"]},"date_updated":"2024-03-07T14:43:38Z","date_created":"2019-10-08T12:48:42Z","author":[{"first_name":"Keren","last_name":"Censor-Hillel","full_name":"Censor-Hillel, Keren"},{"full_name":"Dory, Michal","last_name":"Dory","first_name":"Michal"},{"full_name":"Korhonen, Janne","first_name":"Janne","last_name":"Korhonen","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"full_name":"Leitersdorf, Dean","first_name":"Dean","last_name":"Leitersdorf"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"7939"}]},"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ACM","year":"2019","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-08-01T00:00:00Z","page":"74-83","publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin","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.","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","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.","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.","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."},"abstract":[{"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.","lang":"eng"}],"type":"conference","oa_version":"Preprint","title":"Fast approximate shortest paths in the congested clique","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6933"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/740464"}],"oa":1,"citation":{"ieee":"J. L. Fribourgh et al., “Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms,” bioRxiv. 2019.","apa":"Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L., Rakers, C., … Partch, C. L. (2019). Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv. https://doi.org/10.1101/740464","ista":"Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. 2019. Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv, 10.1101/740464.","ama":"Fribourgh JL, Srivastava A, Sandate CR, et al. Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv. 2019. doi:10.1101/740464","chicago":"Fribourgh, Jennifer L., Ashutosh Srivastava, Colby R. Sandate, Alicia K. Michael, Peter L. Hsu, Christin Rakers, Leslee T. Nguyen, et al. “Protein Dynamics Regulate Distinct Biochemical Properties of Cryptochromes in Mammalian Circadian Rhythms.” BioRxiv, 2019. https://doi.org/10.1101/740464.","short":"J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers, L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander, T. Hirota, F. Tama, C.L. Partch, BioRxiv (2019).","mla":"Fribourgh, Jennifer L., et al. “Protein Dynamics Regulate Distinct Biochemical Properties of Cryptochromes in Mammalian Circadian Rhythms.” BioRxiv, 2019, doi:10.1101/740464."},"publication":"bioRxiv","date_published":"2019-08-20T00:00:00Z","doi":"10.1101/740464","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"08","day":"20","_id":"15147","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms","author":[{"first_name":"Jennifer L.","last_name":"Fribourgh","full_name":"Fribourgh, Jennifer L."},{"full_name":"Srivastava, Ashutosh","first_name":"Ashutosh","last_name":"Srivastava"},{"full_name":"Sandate, Colby R.","first_name":"Colby R.","last_name":"Sandate"},{"full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","first_name":"Alicia"},{"first_name":"Peter L.","last_name":"Hsu","full_name":"Hsu, Peter L."},{"full_name":"Rakers, Christin","first_name":"Christin","last_name":"Rakers"},{"first_name":"Leslee T.","last_name":"Nguyen","full_name":"Nguyen, Leslee T."},{"first_name":"Megan R.","last_name":"Torgrimson","full_name":"Torgrimson, Megan R."},{"last_name":"Parico","first_name":"Gian Carlo G.","full_name":"Parico, Gian Carlo G."},{"full_name":"Tripathi, Sarvind","last_name":"Tripathi","first_name":"Sarvind"},{"last_name":"Zheng","first_name":"Ning","full_name":"Zheng, Ning"},{"first_name":"Gabriel C.","last_name":"Lander","full_name":"Lander, Gabriel C."},{"first_name":"Tsuyoshi","last_name":"Hirota","full_name":"Hirota, Tsuyoshi"},{"full_name":"Tama, Florence","last_name":"Tama","first_name":"Florence"},{"full_name":"Partch, Carrie L.","last_name":"Partch","first_name":"Carrie L."}],"oa_version":"None","date_created":"2024-03-21T07:51:10Z","date_updated":"2024-03-25T12:44:44Z","type":"preprint","abstract":[{"text":"Circadian rhythms are generated by a transcription-based feedback loop where CLOCK:BMAL1 drive transcription of their repressors (PER1/2, CRY1/2), which bind to CLOCK:BMAL1 to close the feedback loop with ~24-hour periodicity. Here we identify a key biochemical and structural difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. While both cryptochromes bind the BMAL1 transactivation domain with similar affinity to sequester it from coactivators, CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We identify a dynamic loop in the secondary pocket that regulates differential binding of cryptochromes to the PAS domain core. Notably, PER2 binding remodels this loop in CRY2 to enhance its affinity for CLOCK:BMAL1, explaining why CRY2 forms an obligate heterodimer with PER2, while CRY1 is capable of repressing CLOCK:BMAL1 both with and without PER2.","lang":"eng"}],"extern":"1"},{"month":"05","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-001-5"]},"doi":"10.15479/AT:ISTA:6392","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"supervisor":[{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach"}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2021-02-11T11:17:16Z","extern":"1","author":[{"full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177","first_name":"Martin","last_name":"Lukacisin"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1029"}]},"date_created":"2019-05-09T19:53:00Z","date_updated":"2023-09-22T09:19:41Z","year":"2019","publication_status":"published","department":[{"_id":"ToBo"}],"publisher":"IST Austria","day":"09","has_accepted_license":"1","date_published":"2019-05-09T00:00:00Z","citation":{"mla":"Lukacisin, Martin. Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory. IST Austria, 2019, doi:10.15479/AT:ISTA:6392.","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","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.","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:10.15479/AT:ISTA:6392","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","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","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019."},"page":"103","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"}],"type":"dissertation","alternative_title":["IST Austria Thesis"],"file":[{"relation":"hidden","file_id":"6409","checksum":"829bda074444857c7935171237bb7c0c","date_created":"2019-05-10T13:51:49Z","date_updated":"2020-07-14T12:47:29Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Draft_v3.4Final.docx","file_size":43740796,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mlukacisin"},{"date_updated":"2021-02-11T11:17:16Z","date_created":"2019-05-10T14:13:42Z","checksum":"56cb5e97f5f8fc41692401b53832d8e0","relation":"main_file","embargo":"2020-04-17","file_id":"6410","content_type":"application/pdf","file_size":35228388,"creator":"mlukacisin","file_name":"Thesis_Draft_v3.4FinalA.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"6392","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","ddc":["570"]},{"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."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_size":3895187,"content_type":"application/pdf","creator":"casillas","access_level":"open_access","file_name":"tesisDoctoradoBC.pdf","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","date_updated":"2021-02-11T11:17:15Z","date_created":"2019-05-13T09:16:20Z","relation":"main_file","file_id":"6438","embargo":"2020-05-08"},{"access_level":"closed","embargo_to":"open_access","file_name":"tesisDoctoradoBC.zip","content_type":"application/zip","file_size":7365118,"creator":"casillas","relation":"source_file","file_id":"6439","checksum":"3d221aaff7559a7060230a1ff610594f","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-13T09:16:20Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6435","ddc":["570","006","578","592"],"title":"Collective defenses of garden ants against a fungal pathogen","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"07","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"date_published":"2019-05-07T00:00:00Z","citation":{"ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","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","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:10.15479/AT:ISTA:6435","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.","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."},"page":"183","ec_funded":1,"file_date_updated":"2021-02-11T11:17:15Z","related_material":{"record":[{"id":"1999","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E"}],"date_updated":"2023-09-07T12:57:04Z","date_created":"2019-05-13T08:58:35Z","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"SyCr"}],"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"05","doi":"10.15479/AT:ISTA:6435","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"supervisor":[{"full_name":"Cremer, Sylvia M","first_name":"Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"oa":1,"project":[{"call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}]},{"day":"04","has_accepted_license":"1","article_processing_charge":"No","date_published":"2019-02-04T00:00:00Z","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.","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.","ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","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","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075"},"page":"138","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"}],"type":"dissertation","alternative_title":["ISTA 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Austrian Pharmacological Society, 2019. 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.","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.","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","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.","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.","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"},"publication":"Intrinsic Activity","issue":"Suppl. 1","type":"conference_abstract","oa_version":"Published Version","intvolume":" 7","status":"public","title":"Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11222","publication_identifier":{"issn":["2309-8503"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.25006/ia.7.s1-a3.27","conference":{"end_date":"2019-09-27","start_date":"2019-09-25","location":"Innsbruck, Austria","name":"ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society"},"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020","grant_number":"708497","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425"},{"name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","grant_number":"W01205"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.intrinsicactivity.org/2019/7/S1/A3.27/"}],"ec_funded":1,"article_number":"A3.27","volume":7,"date_created":"2022-04-20T15:06:05Z","date_updated":"2024-03-28T23:30:07Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11196"}]},"author":[{"full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","first_name":"Olena"},{"full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"department":[{"_id":"PeJo"}],"publisher":"Austrian Pharmacological Society","publication_status":"published","year":"2019","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)."},{"citation":{"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.","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","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.","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 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.","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","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019."},"page":"142","date_published":"2019-10-09T00:00:00Z","day":"9","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6947","status":"public","ddc":["570"],"title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","oa_version":"Published Version","file":[{"embargo_to":"open_access","file_name":"PhDthesis_FrankAssen_revised2.docx","access_level":"closed","file_size":214172667,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"fassen","relation":"source_file","file_id":"6990","date_created":"2019-11-06T12:30:02Z","date_updated":"2020-11-07T23:30:03Z","checksum":"53a739752a500f84d0f8ec953cbbd0b6"},{"relation":"main_file","file_id":"6991","embargo":"2020-11-06","date_created":"2019-11-06T12:30:57Z","date_updated":"2020-11-07T23:30:03Z","checksum":"8c156b65d9347bb599623a4b09f15d15","file_name":"PhDthesis_FrankAssen_revised2.pdf","access_level":"open_access","file_size":83637532,"content_type":"application/pdf","creator":"fassen"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"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."}],"oa":1,"doi":"10.15479/AT:ISTA:6947","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["2663-337X"]},"year":"2019","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Assen","first_name":"Frank P","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","full_name":"Assen, Frank P"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"664"},{"id":"402","status":"public","relation":"part_of_dissertation"}]},"date_created":"2019-10-14T16:54:52Z","date_updated":"2023-09-13T08:50:57Z","file_date_updated":"2020-11-07T23:30:03Z"},{"month":"09","publication_identifier":{"issn":["2663-337X"],"isbn":["9783990780039"]},"doi":"10.15479/AT:ISTA:6849","supervisor":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2021-02-10T23:30:09Z","author":[{"full_name":"Rangel Guerrero, Dámaris K","first_name":"Dámaris K","last_name":"Rangel Guerrero","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5914"}]},"date_created":"2019-09-06T06:54:16Z","date_updated":"2023-09-19T10:01:12Z","year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"day":"09","has_accepted_license":"1","article_processing_charge":"No","date_published":"2019-09-09T00:00:00Z","citation":{"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.","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.","short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria.","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","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"},"page":"97","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"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"access_level":"closed","file_name":"Thesis_Damaris_Rangel_source.docx","embargo_to":"open_access","creator":"drangel","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":18253100,"file_id":"6865","relation":"source_file","checksum":"244dc4f74dbfc94f414156092298831f","date_updated":"2021-02-10T23:30:09Z","date_created":"2019-09-09T13:09:45Z"},{"request_a_copy":0,"content_type":"application/pdf","file_size":2160109,"creator":"drangel","access_level":"open_access","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","checksum":"59c73be40eeaa1c4db24067270151555","date_created":"2019-09-09T13:09:52Z","date_updated":"2020-09-11T22:30:04Z","relation":"main_file","file_id":"6866","embargo":"2020-09-10"}],"oa_version":"Published Version","_id":"6849","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"The role of CCK-interneurons in regulating hippocampal network dynamics"},{"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31051107"],"isi":["000466843000015"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/j.cell.2019.04.015","publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"month":"05","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","volume":177,"date_updated":"2024-03-28T23:30:10Z","date_created":"2019-04-28T21:59:14Z","related_material":{"record":[{"id":"9992","status":"public","relation":"dissertation_contains"}],"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/"}]},"author":[{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","last_name":"Marhavá","full_name":"Marhavá, Petra"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","first_name":"Peter","last_name":"Marhavy","full_name":"Marhavy, Peter"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:47:28Z","page":"957-969.e13","citation":{"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","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.","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.","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.","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","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."},"publication":"Cell","date_published":"2019-05-02T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"02","intvolume":" 177","ddc":["570"],"status":"public","title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6351","file":[{"date_created":"2019-05-13T06:12:45Z","date_updated":"2020-07-14T12:47:28Z","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","file_id":"6411","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":10272032,"file_name":"2019_Cell_Marhava.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","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."}]},{"oa_version":"Published Version","file":[{"creator":"dernst","file_size":1659288,"content_type":"application/pdf","file_name":"2019_CurrentOpinionPlant_Hoermayer.pdf","access_level":"open_access","date_created":"2019-10-14T14:48:21Z","date_updated":"2020-07-14T12:47:45Z","checksum":"d6fd68a6e965f1efe3f0bf2d2070a616","file_id":"6946","relation":"main_file"}],"intvolume":" 52","title":"Targeted cell ablation-based insights into wound healing and restorative patterning","status":"public","ddc":["580"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6943","abstract":[{"lang":"eng","text":"Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration."}],"type":"journal_article","date_published":"2019-12-01T00:00:00Z","page":"124-130","article_type":"original","citation":{"ista":"Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.","apa":"Hörmayer, L., & Friml, J. (2019). Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.08.006","ieee":"L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound healing and restorative patterning,” Current Opinion in Plant Biology, vol. 52. Elsevier, pp. 124–130, 2019.","ama":"Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 2019;52:124-130. doi:10.1016/j.pbi.2019.08.006","chicago":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.08.006.","mla":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology, vol. 52, Elsevier, 2019, pp. 124–30, doi:10.1016/j.pbi.2019.08.006.","short":"L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130."},"publication":"Current Opinion in Plant Biology","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","volume":52,"date_created":"2019-10-14T07:00:24Z","date_updated":"2024-03-28T23:30:10Z","related_material":{"record":[{"id":"9992","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","first_name":"Lukas"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"publisher":"Elsevier","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:45Z","language":[{"iso":"eng"}],"doi":"10.1016/j.pbi.2019.08.006","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31585333"],"isi":["000502890600017"]},"publication_identifier":{"issn":["1369-5266"]},"month":"12"},{"month":"12","publication_identifier":{"issn":["2589-0042"]},"doi":"10.1016/j.isci.2019.11.025","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":[":000504652000020"],"pmid":["31786521"]},"quality_controlled":"1","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"},{"call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:47:57Z","ec_funded":1,"author":[{"full_name":"Tabata, Shigekazu","id":"4427179E-F248-11E8-B48F-1D18A9856A87","first_name":"Shigekazu","last_name":"Tabata"},{"full_name":"Jevtic, Marijo","last_name":"Jevtic","first_name":"Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nobutaka","last_name":"Kurashige","full_name":"Kurashige, Nobutaka"},{"first_name":"Hirokazu","last_name":"Fuchida","full_name":"Fuchida, Hirokazu"},{"last_name":"Kido","first_name":"Munetsugu","full_name":"Kido, Munetsugu"},{"full_name":"Tani, Kazushi","last_name":"Tani","first_name":"Kazushi"},{"full_name":"Zenmyo, Naoki","last_name":"Zenmyo","first_name":"Naoki"},{"last_name":"Uchinomiya","first_name":"Shohei","full_name":"Uchinomiya, Shohei"},{"full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","first_name":"Harumi"},{"full_name":"Itakura, Makoto","first_name":"Makoto","last_name":"Itakura"},{"full_name":"Hamachi, Itaru","first_name":"Itaru","last_name":"Hamachi"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"last_name":"Ojida","first_name":"Akio","full_name":"Ojida, Akio"}],"related_material":{"record":[{"id":"11393","relation":"dissertation_contains","status":"public"}]},"date_updated":"2024-03-28T23:30:12Z","date_created":"2020-01-29T15:56:56Z","volume":22,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Elsevier","day":"20","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-12-20T00:00:00Z","publication":"iScience","citation":{"ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 2019;22(12):256-268. doi:10.1016/j.isci.2019.11.025","ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268.","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.11.025","ieee":"S. Tabata et al., “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” iScience, vol. 22, no. 12. Elsevier, pp. 256–268, 2019.","mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:10.1016/j.isci.2019.11.025.","short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268.","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.11.025."},"article_type":"original","page":"256-268","abstract":[{"lang":"eng","text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM."}],"issue":"12","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7448","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T10:48:36Z","checksum":"f3e90056a49f09b205b1c4f8c739ffd1","file_name":"2019_iScience_Tabata.pdf","access_level":"open_access","file_size":7197776,"content_type":"application/pdf","creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7391","title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","ddc":["570"],"status":"public","intvolume":" 22"},{"month":"09","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"external_id":{"pmid":["31462775"],"isi":["000485415400061"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"doi":"10.1038/s41586-019-1519-2","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-11-26T16:33:44Z","ec_funded":1,"acknowledgement":" We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing was performed at the IST high-performance computing cluster.\r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385.","year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Springer Nature","author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","first_name":"Domen"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/","description":"News on IST Website","relation":"press_release"}],"record":[{"id":"8340","status":"public","relation":"dissertation_contains"}]},"date_created":"2019-09-04T06:21:41Z","date_updated":"2024-03-28T23:30:15Z","volume":573,"scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1","publication":"Nature","citation":{"ama":"Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 2019;573(7773):291–295. doi:10.1038/s41586-019-1519-2","ista":"Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 573(7773), 291–295.","apa":"Kampjut, D., & Sazanov, L. A. (2019). Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1519-2","ieee":"D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating transhydrogenase,” Nature, vol. 573, no. 7773. Springer Nature, pp. 291–295, 2019.","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” Nature, vol. 573, no. 7773, Springer Nature, 2019, pp. 291–295, doi:10.1038/s41586-019-1519-2.","short":"D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1519-2."},"article_type":"letter_note","page":"291–295","date_published":"2019-09-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Proton-translocating transhydrogenase (also known as nicotinamide nucleotide transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride between NADH and NADP+, coupled to the translocation of one proton across the membrane. Its main physiological function is the generation of NADPH, which is a substrate in anabolic reactions and a regulator of oxidative status; however, NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid deficiency in humans and metabolic abnormalities in mice, similar to those observed in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve a rotation of around 180° of the entire NADP(H)-binding domain that alternately participates in hydride transfer and proton-channel gating. However, owing to the lack of high-resolution structures of intact NNT, the details of this process remain unclear5,6. Here we present the cryo-electron microscopy structure of intact mammalian NNT in different conformational states. We show how the NADP(H)-binding domain opens the proton channel to the opposite sides of the membrane, and we provide structures of these two states. We also describe the catalytically important interfaces and linkers between the membrane and the soluble domains and their roles in nucleotide exchange. These structures enable us to propose a revised mechanism for a coupling process in NNT that is consistent with a large body of previous biochemical work. Our results are relevant to the development of currently unavailable NNT inhibitors, which may have therapeutic potential in ischaemia reperfusion injury, metabolic syndrome and some cancers7,8,9."}],"issue":"7773","_id":"6848","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Structure and mechanism of mitochondrial proton-translocating transhydrogenase","ddc":["572"],"status":"public","intvolume":" 573","oa_version":"Submitted Version","file":[{"file_name":"Manuscript_final_acc_withFigs_SI_opt_red.pdf","access_level":"open_access","creator":"lsazanov","content_type":"application/pdf","file_size":3066206,"file_id":"8821","relation":"main_file","date_created":"2020-11-26T16:33:44Z","date_updated":"2020-11-26T16:33:44Z","success":1,"checksum":"52728cda5210a3e9b74cc204e8aed3d5"}]},{"page":"1443-1447","article_type":"original","citation":{"chicago":"Boccara, Charlotte N., Michele Nardin, Federico Stella, Joseph O’Neill, and Jozsef L Csicsvari. “The Entorhinal Cognitive Map Is Attracted to Goals.” Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aav4837.","short":"C.N. Boccara, M. Nardin, F. Stella, J. O’Neill, J.L. Csicsvari, Science 363 (2019) 1443–1447.","mla":"Boccara, Charlotte N., et al. “The Entorhinal Cognitive Map Is Attracted to Goals.” Science, vol. 363, no. 6434, American Association for the Advancement of Science, 2019, pp. 1443–47, doi:10.1126/science.aav4837.","apa":"Boccara, C. N., Nardin, M., Stella, F., O’Neill, J., & Csicsvari, J. L. (2019). The entorhinal cognitive map is attracted to goals. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aav4837","ieee":"C. N. Boccara, M. Nardin, F. Stella, J. O’Neill, and J. L. Csicsvari, “The entorhinal cognitive map is attracted to goals,” Science, vol. 363, no. 6434. American Association for the Advancement of Science, pp. 1443–1447, 2019.","ista":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. 2019. The entorhinal cognitive map is attracted to goals. Science. 363(6434), 1443–1447.","ama":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. The entorhinal cognitive map is attracted to goals. Science. 2019;363(6434):1443-1447. doi:10.1126/science.aav4837"},"publication":"Science","date_published":"2019-03-29T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"29","intvolume":" 363","status":"public","ddc":["570"],"title":"The entorhinal cognitive map is attracted to goals","_id":"6194","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"5e6b16742cde10a560cfaf2130764da1","date_created":"2020-05-14T09:11:10Z","date_updated":"2020-07-14T12:47:23Z","file_id":"7826","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":9045923,"access_level":"open_access","file_name":"2019_Science_Boccara.pdf"}],"oa_version":"Submitted Version","type":"journal_article","issue":"6434","abstract":[{"lang":"eng","text":"Grid cells with their rigid hexagonal firing fields are thought to provide an invariant metric to the hippocampal cognitive map, yet environmental geometrical features have recently been shown to distort the grid structure. Given that the hippocampal role goes beyond space, we tested the influence of nonspatial information on the grid organization. We trained rats to daily learn three new reward locations on a cheeseboard maze while recording from the medial entorhinal cortex and the hippocampal CA1 region. Many grid fields moved toward goal location, leading to long-lasting deformations of the entorhinal map. Therefore, distortions in the grid structure contribute to goal representation during both learning and recall, which demonstrates that grid cells participate in mnemonic coding and do not merely provide a simple metric of space."}],"project":[{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000462738000034"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1126/science.aav4837","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"03","department":[{"_id":"JoCs"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","year":"2019","volume":363,"date_created":"2019-04-04T08:39:30Z","date_updated":"2024-03-28T23:30:16Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/grid-cells-create-treasure-map-in-rat-brain/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"6062","status":"public","relation":"popular_science"},{"id":"11932","relation":"dissertation_contains","status":"public"}]},"author":[{"orcid":"0000-0001-7237-5109","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","last_name":"Boccara","first_name":"Charlotte N.","full_name":"Boccara, Charlotte N."},{"full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","first_name":"Michele","last_name":"Nardin"},{"full_name":"Stella, Federico","last_name":"Stella","first_name":"Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","full_name":"O'Neill, Joseph"},{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:47:23Z"},{"degree_awarded":"PhD","supervisor":[{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:7132","oa":1,"month":"06","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2024-03-28T23:30:21Z","date_created":"2019-11-27T09:07:14Z","author":[{"first_name":"Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine"}],"related_material":{"record":[{"id":"6266","status":"public","relation":"old_edition"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HaJa"}],"year":"2019","file_date_updated":"2020-07-14T12:47:50Z","date_published":"2019-06-27T00:00:00Z","page":"95","citation":{"ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019.","apa":"Mckenzie, C. (2019). Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:7132","ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:10.15479/at:ista:7132","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:7132.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019.","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:7132."},"day":"27","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Published Version","file":[{"date_created":"2019-11-27T09:06:10Z","date_updated":"2020-07-14T12:47:50Z","checksum":"34d0fe0f6e0af97b5937205a3e350423","relation":"source_file","file_id":"7133","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":5054633,"creator":"dernst","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx","access_level":"closed"},{"relation":"main_file","file_id":"7134","checksum":"140dfb5e3df7edca34f4b6fcc55d876f","date_created":"2019-11-27T09:06:10Z","date_updated":"2020-07-14T12:47:50Z","access_level":"open_access","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","content_type":"application/pdf","file_size":3231837,"creator":"dernst"}],"status":"public","ddc":["571","573"],"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7132","abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5949","ddc":["570"],"title":"Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization","status":"public","intvolume":" 29","file":[{"checksum":"5e8de271ca04aef92a5de42d6aac4404","date_created":"2019-02-11T10:42:51Z","date_updated":"2020-07-14T12:47:13Z","relation":"main_file","file_id":"5950","file_size":2132893,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_Hippocampus_Kaefer.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms.","lang":"eng"}],"issue":"9","publication":"Hippocampus","citation":{"chicago":"Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” Hippocampus. Wiley, 2019. https://doi.org/10.1002/hipo.23076.","short":"K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth, J.L. Csicsvari, Hippocampus 29 (2019) 802–816.","mla":"Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” Hippocampus, vol. 29, no. 9, Wiley, 2019, pp. 802–16, doi:10.1002/hipo.23076.","apa":"Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V., Korth, C., & Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. Wiley. https://doi.org/10.1002/hipo.23076","ieee":"K. Käfer et al., “Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization,” Hippocampus, vol. 29, no. 9. Wiley, pp. 802–816, 2019.","ista":"Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 29(9), 802–816.","ama":"Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 2019;29(9):802-816. doi:10.1002/hipo.23076"},"article_type":"original","page":"802-816","date_published":"2019-09-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","year":"2019","publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Wiley","author":[{"full_name":"Käfer, Karola","first_name":"Karola","last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Malagon-Vina, Hugo","first_name":"Hugo","last_name":"Malagon-Vina"},{"id":"444EB89E-F248-11E8-B48F-1D18A9856A87","first_name":"Desiree","last_name":"Dickerson","full_name":"Dickerson, Desiree"},{"full_name":"O'Neill, Joseph","first_name":"Joseph","last_name":"O'Neill"},{"full_name":"Trossbach, Svenja V.","first_name":"Svenja V.","last_name":"Trossbach"},{"first_name":"Carsten","last_name":"Korth","full_name":"Korth, Carsten"},{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6825"}]},"date_created":"2019-02-10T22:59:18Z","date_updated":"2024-03-28T23:30:22Z","volume":29,"file_date_updated":"2020-07-14T12:47:13Z","ec_funded":1,"external_id":{"isi":["000480635400003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"257BBB4C-B435-11E9-9278-68D0E5697425","grant_number":"607616","call_identifier":"FP7","name":"Inter-and intracellular signalling in schizophrenia"}],"doi":"10.1002/hipo.23076","language":[{"iso":"eng"}],"month":"09"},{"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5949"}]},"author":[{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","first_name":"Karola","full_name":"Käfer, Karola"}],"date_created":"2019-08-21T15:00:57Z","date_updated":"2023-09-07T13:01:42Z","year":"2019","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2020-09-15T22:30:05Z","doi":"10.15479/AT:ISTA:6825","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"08","file":[{"creator":"kkaefer","content_type":"application/pdf","file_size":3205202,"request_a_copy":0,"file_name":"Thesis_Kaefer_PDFA.pdf","access_level":"open_access","date_updated":"2020-09-06T22:30:03Z","date_created":"2019-09-03T08:07:13Z","checksum":"2664420e332a33338568f4f3bfc59287","embargo":"2020-09-05","file_id":"6846","relation":"main_file"},{"access_level":"closed","file_name":"Thesis_Kaefer.zip","embargo_to":"open_access","creator":"kkaefer","content_type":"application/zip","file_size":2506835,"file_id":"6847","relation":"main_file","checksum":"9a154eab6f07aa590a3d2651dc0d926a","date_created":"2019-09-03T08:07:17Z","date_updated":"2020-09-15T22:30:05Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6825","ddc":["570"],"status":"public","title":"The hippocampus and medial prefrontal cortex during flexible behavior","abstract":[{"text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2019-08-24T00:00:00Z","citation":{"mla":"Käfer, Karola. The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6825.","short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6825.","ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:10.15479/AT:ISTA:6825","ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria.","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019.","apa":"Käfer, K. (2019). The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6825"},"page":"89","article_processing_charge":"No","has_accepted_license":"1","day":"24"},{"oa_version":"Published Version","file":[{"date_created":"2019-07-29T07:41:18Z","date_updated":"2020-07-14T12:47:38Z","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","relation":"main_file","file_id":"6721","content_type":"application/pdf","file_size":6748249,"creator":"apreinsp","file_name":"2019_eLife_Castro.pdf","access_level":"open_access"}],"_id":"6713","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["576"],"title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","intvolume":" 8","abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"type":"journal_article","date_published":"2019-06-06T00:00:00Z","publication":"eLife","citation":{"ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","ieee":"J. P. Castro et al., “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42014","ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 2019;8. doi:10.7554/eLife.42014","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014, eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019)."},"day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"last_name":"Yancoskie","first_name":"Michelle N.","full_name":"Yancoskie, Michelle N."},{"first_name":"Marta","last_name":"Marchini","full_name":"Marchini, Marta"},{"orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","first_name":"Stefanie","full_name":"Belohlavy, Stefanie"},{"last_name":"Hiramatsu","first_name":"Layla","full_name":"Hiramatsu, Layla"},{"full_name":"Kučka, Marek","first_name":"Marek","last_name":"Kučka"},{"first_name":"William H.","last_name":"Beluch","full_name":"Beluch, William H."},{"last_name":"Naumann","first_name":"Ronald","full_name":"Naumann, Ronald"},{"last_name":"Skuplik","first_name":"Isabella","full_name":"Skuplik, Isabella"},{"last_name":"Cobb","first_name":"John","full_name":"Cobb, John"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"first_name":"Campbell","last_name":"Rolian","full_name":"Rolian, Campbell"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9804"},{"id":"11388","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:23Z","date_created":"2019-07-28T21:59:17Z","volume":8,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:47:38Z","article_number":"e42014","doi":"10.7554/eLife.42014","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000473588700001"],"pmid":["31169497"]},"isi":1,"quality_controlled":"1","month":"06"},{"article_number":"1910.05841","type":"preprint","abstract":[{"lang":"eng","text":"We study double quantum dots in a Ge/SiGe heterostructure and test their maturity towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability, from two single quantum dots to a double quantum dot. We measure Pauli spin blockade and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for sensing charge transitions in the double quantum dot at interest. In conclusion, Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit."}],"ec_funded":1,"title":"Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits","publication_status":"submitted","status":"public","department":[{"_id":"GeKa"}],"acknowledgement":"We thank Matthias Brauns for helpful discussions and careful proofreading of the manuscript. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 844511 and from the FWF project P30207. The research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA machine shop and the nanofabrication\r\nfacility.","_id":"10065","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","date_created":"2021-10-01T12:14:51Z","date_updated":"2024-03-28T23:30:27Z","oa_version":"Preprint","author":[{"id":"340F461A-F248-11E8-B48F-1D18A9856A87","last_name":"Hofmann","first_name":"Andrea C","full_name":"Hofmann, Andrea C"},{"full_name":"Jirovec, Daniel","first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"},{"first_name":"Maxim","last_name":"Borovkov","full_name":"Borovkov, Maxim"},{"full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","first_name":"Ivan"},{"last_name":"Ballabio","first_name":"Andrea","full_name":"Ballabio, Andrea"},{"first_name":"Jacopo","last_name":"Frigerio","full_name":"Frigerio, Jacopo"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10058"}]},"day":"13","month":"10","article_processing_charge":"No","project":[{"grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures"},{"call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207"}],"publication":"arXiv","citation":{"ama":"Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv. doi:10.48550/arXiv.1910.05841","apa":"Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A., Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv. https://doi.org/10.48550/arXiv.1910.05841","ieee":"A. C. Hofmann et al., “Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits,” arXiv. .","ista":"Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv, 1910.05841.","short":"A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J. Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","mla":"Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” ArXiv, 1910.05841, doi:10.48550/arXiv.1910.05841.","chicago":"Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez, Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1910.05841."},"main_file_link":[{"url":"https://arxiv.org/abs/1910.05841","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1910.05841"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.1910.05841","date_published":"2019-10-13T00:00:00Z"},{"publication":"eLife","citation":{"apa":"Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M., … Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.41801","ieee":"K. Valosková et al., “A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” eLife, vol. 8. eLife Sciences Publications, 2019.","ista":"Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh A, Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. 2019. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.","ama":"Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 2019;8. doi:10.7554/elife.41801","chicago":"Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.41801.","short":"K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A. Ratheesh, P. Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev, H. Clausen, D.E. Siekhaus, ELife 8 (2019).","mla":"Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” ELife, vol. 8, e41801, eLife Sciences Publications, 2019, doi:10.7554/elife.41801."},"date_published":"2019-03-26T00:00:00Z","scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6187","status":"public","title":"A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion","ddc":["570"],"intvolume":" 8","file":[{"relation":"main_file","file_id":"6188","checksum":"cc0d1a512559d52e7e7cb0e9b9854b40","date_created":"2019-03-28T14:00:41Z","date_updated":"2020-07-14T12:47:23Z","access_level":"open_access","file_name":"2019_eLife_Valoskova.pdf","content_type":"application/pdf","file_size":4496017,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000462530200001"]},"quality_controlled":"1","isi":1,"project":[{"_id":"253CDE40-B435-11E9-9278-68D0E5697425","grant_number":"24283","name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells"},{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7"},{"grant_number":"329540","_id":"25388084-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Breaking barriers: Investigating the junctional and mechanobiological changes underlying the ability of Drosophila immune cells to invade an epithelium"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"doi":"10.7554/elife.41801","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["2050-084X"]},"year":"2019","publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"eLife Sciences Publications","author":[{"id":"46F146FC-F248-11E8-B48F-1D18A9856A87","last_name":"Valosková","first_name":"Katarina","full_name":"Valosková, Katarina"},{"last_name":"Biebl","first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","full_name":"Biebl, Julia"},{"full_name":"Roblek, Marko","last_name":"Roblek","first_name":"Marko","orcid":"0000-0001-9588-1389","id":"3047D808-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Emtenani, Shamsi","first_name":"Shamsi","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938"},{"first_name":"Attila","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","full_name":"György, Attila"},{"full_name":"Misova, Michaela","last_name":"Misova","first_name":"Michaela","orcid":"0000-0003-2427-6856","id":"495A3C32-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ratheesh","first_name":"Aparna","orcid":"0000-0001-7190-0776","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","full_name":"Ratheesh, Aparna"},{"full_name":"Rodrigues, Patricia","id":"2CE4065A-F248-11E8-B48F-1D18A9856A87","first_name":"Patricia","last_name":"Rodrigues"},{"last_name":"Shkarina","first_name":"Katerina","full_name":"Shkarina, Katerina"},{"last_name":"Larsen","first_name":"Ida Signe Bohse","full_name":"Larsen, Ida Signe Bohse"},{"first_name":"Sergey Y","last_name":"Vakhrushev","full_name":"Vakhrushev, Sergey Y"},{"full_name":"Clausen, Henrik","first_name":"Henrik","last_name":"Clausen"},{"last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/"}],"record":[{"relation":"dissertation_contains","id":"6530"},{"id":"8983","relation":"dissertation_contains","status":"public"},{"id":"6546","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:30Z","date_created":"2019-03-28T13:37:45Z","volume":8,"article_number":"e41801","file_date_updated":"2020-07-14T12:47:23Z","ec_funded":1},{"author":[{"id":"46F146FC-F248-11E8-B48F-1D18A9856A87","last_name":"Valosková","first_name":"Katarina","full_name":"Valosková, Katarina"}],"related_material":{"record":[{"id":"6187","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"544"}]},"date_created":"2019-06-07T12:49:19Z","date_updated":"2023-09-19T10:15:54Z","year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"DaSi"}],"file_date_updated":"2021-02-11T11:17:14Z","doi":"10.15479/AT:ISTA:6546","acknowledged_ssus":[{"_id":"Bio"}],"supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","grant_number":"24283","_id":"253CDE40-B435-11E9-9278-68D0E5697425"}],"month":"06","publication_identifier":{"issn":["2663-337X"]},"file":[{"access_level":"closed","embargo_to":"open_access","file_name":"Katarina Valoskova_PhD thesis_final version.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":14110626,"creator":"khribikova","relation":"source_file","file_id":"6549","checksum":"68949c2d96210b45b981a23e9c9cd93c","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-07T13:00:04Z"},{"file_name":"Katarina Valoskova_PhD thesis_final version.pdf","access_level":"open_access","content_type":"application/pdf","file_size":10054156,"creator":"khribikova","relation":"main_file","embargo":"2020-06-07","file_id":"6550","date_created":"2019-06-07T13:00:08Z","date_updated":"2021-02-11T11:17:14Z","checksum":"555329cd76e196c96f5278c480ee2e6e"}],"oa_version":"Published Version","_id":"6546","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","status":"public","abstract":[{"text":"Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator that orchestrates O-glycosylation on a protein subset to activate \r\na program governing migration steps important for both development and cancer metastasis. \r\n","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2019-06-07T00:00:00Z","citation":{"ama":"Valosková K. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. 2019. doi:10.15479/AT:ISTA:6546","ieee":"K. Valosková, “The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration,” Institute of Science and Technology Austria, 2019.","apa":"Valosková, K. (2019). The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6546","ista":"Valosková K. 2019. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria.","short":"K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration, Institute of Science and Technology Austria, 2019.","mla":"Valosková, Katarina. The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6546.","chicago":"Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6546."},"page":"141","day":"07","has_accepted_license":"1","article_processing_charge":"No"},{"file":[{"checksum":"77c6c05cfe8b58c8abcf1b854375d084","date_updated":"2021-02-11T11:17:15Z","date_created":"2019-05-07T16:00:39Z","file_id":"6389","embargo":"2020-05-09","relation":"main_file","creator":"cespinoza","content_type":"application/pdf","file_size":13966891,"access_level":"open_access","file_name":"Espinozathesis_all2.pdf"},{"creator":"cespinoza","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":11159900,"access_level":"closed","file_name":"Espinoza_Thesis.docx","embargo_to":"open_access","checksum":"f6aa819f127691a2b0fc21c76eb09746","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-05-07T16:00:48Z","file_id":"6390","relation":"source_file"}],"oa_version":"Published Version","_id":"6363","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","ddc":["570"],"abstract":[{"lang":"eng","text":"Distinguishing between similar experiences is achieved by the brain in a process called pattern separation. In the hippocampus, pattern separation reduces the interference of memories and increases the storage capacity by decorrelating similar inputs patterns of neuronal activity into non-overlapping output firing patterns. Winners-take-all (WTA) mechanism is a theoretical model for pattern separation in which a \"winner\" cell suppresses the activity of the neighboring neurons through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of feedback inhibition in which a GC inhibits other GCs but not itself through the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron connectivity was more spatially confined but less abundant than PV+interneurons–GC connectivity, leading to an asymmetrical distribution of excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the primary mechanism. This process relied on lateral inhibition, fast-signaling properties of PV+interneurons and the asymmetrical distribution of excitatory and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in vivoleads to acute deficits in discrimination between similar environments, suggesting that PV+interneuron networks are necessary for behavioral relevant computations. Our results demonstrate that PV+interneurons possess unique connectivity and fast signaling properties that confer to the dentate gyrus network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2019-04-30T00:00:00Z","citation":{"ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019.","apa":"Espinoza Martinez, C. (2019). Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6363","ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:10.15479/AT:ISTA:6363","chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6363.","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","mla":"Espinoza Martinez, Claudia. Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6363."},"page":"140","day":"30","article_processing_charge":"No","has_accepted_license":"1","author":[{"full_name":"Espinoza Martinez, Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","first_name":"Claudia ","last_name":"Espinoza Martinez"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"21"}]},"date_created":"2019-04-30T11:56:10Z","date_updated":"2023-09-15T12:03:48Z","year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"PeJo"}],"file_date_updated":"2021-02-11T11:17:15Z","doi":"10.15479/AT:ISTA:6363","supervisor":[{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"month":"04","publication_identifier":{"isbn":["978-3-99078-000-8"],"issn":["2663-337X"]}},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","date_published":"2019-10-01T00:00:00Z","publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications ","citation":{"mla":"Huang, Mingzhang, et al. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , vol. 3, 129, ACM, 2019, doi:10.1145/3360555.","short":"M. Huang, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , ACM, 2019.","chicago":"Huang, Mingzhang, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , Vol. 3. ACM, 2019. https://doi.org/10.1145/3360555.","ama":"Huang M, Fu H, Chatterjee K, Goharshady AK. Modular verification for almost-sure termination of probabilistic programs. In: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications . Vol 3. ACM; 2019. doi:10.1145/3360555","ista":"Huang M, Fu H, Chatterjee K, Goharshady AK. 2019. Modular verification for almost-sure termination of probabilistic programs. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications . OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 129.","apa":"Huang, M., Fu, H., Chatterjee, K., & Goharshady, A. K. (2019). Modular verification for almost-sure termination of probabilistic programs. In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360555","ieee":"M. Huang, H. Fu, K. Chatterjee, and A. K. Goharshady, “Modular verification for almost-sure termination of probabilistic programs,” in Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , Athens, Greece, 2019, vol. 3."},"abstract":[{"lang":"eng","text":"In this work, we consider the almost-sure termination problem for probabilistic programs that asks whether a\r\ngiven probabilistic program terminates with probability 1. Scalable approaches for program analysis often\r\nrely on modularity as their theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)\r\nof Floyd-Hoare logic provides the foundation for modular analysis. Extension of this rule to almost-sure\r\ntermination of probabilistic programs is quite tricky, and a probabilistic variant was proposed in [16]. While the\r\nproposed probabilistic variant cautiously addresses the key issue of integrability, we show that the proposed\r\nmodular rule is still not sound for almost-sure termination of probabilistic programs.\r\nBesides establishing unsoundness of the previous rule, our contributions are as follows: First, we present a\r\nsound modular rule for almost-sure termination of probabilistic programs. Our approach is based on a novel\r\nnotion of descent supermartingales. Second, for algorithmic approaches, we consider descent supermartingales\r\nthat are linear and show that they can be synthesized in polynomial time. Finally, we present experimental\r\nresults on a variety of benchmarks and several natural examples that model various types of nested while\r\nloops in probabilistic programs and demonstrate that our approach is able to efficiently prove their almost-sure\r\ntermination property"}],"type":"conference","oa_version":"Published Version","file":[{"file_id":"6807","relation":"main_file","date_created":"2019-08-12T15:40:57Z","date_updated":"2020-07-14T12:47:40Z","checksum":"3482d8ace6fb4991eb7810e3b70f1b9f","file_name":"oopsla-2019.pdf","access_level":"open_access","creator":"akafshda","file_size":1024643,"content_type":"application/pdf"},{"creator":"dernst","content_type":"application/pdf","file_size":538579,"access_level":"open_access","file_name":"2019_ACM_Huang.pdf","checksum":"4e5a6fb2b59a75222a4e8335a5a60eac","date_updated":"2020-07-14T12:47:40Z","date_created":"2020-05-12T15:15:14Z","file_id":"7821","relation":"main_file"}],"title":"Modular verification for almost-sure termination of probabilistic programs","status":"public","ddc":["000"],"intvolume":" 3","_id":"6780","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"10","language":[{"iso":"eng"}],"conference":{"end_date":"2019-10-25","location":"Athens, Greece","start_date":"2019-10-23","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications"},"doi":"10.1145/3360555","quality_controlled":"1","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"arxiv":["1901.06087"]},"oa":1,"file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"article_number":"129","date_created":"2019-08-09T09:54:20Z","date_updated":"2024-03-28T23:30:34Z","volume":3,"author":[{"full_name":"Huang, Mingzhang","first_name":"Mingzhang","last_name":"Huang"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"year":"2019"},{"related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady"},{"first_name":"Nastaran","last_name":"Okati","full_name":"Okati, Nastaran"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"volume":3,"date_updated":"2024-03-28T23:30:33Z","date_created":"2019-05-06T12:18:17Z","year":"2019","publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:29Z","article_number":"53","doi":"10.1145/3290366","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","publication_identifier":{"issn":["2475-1421"]},"month":"01","pubrep_id":"1056","file":[{"checksum":"c157752f96877b36685ad7063ada4524","date_created":"2019-05-06T12:23:11Z","date_updated":"2020-07-14T12:47:29Z","relation":"main_file","file_id":"6381","content_type":"application/pdf","file_size":1294962,"creator":"dernst","access_level":"open_access","file_name":"2019_ACM_POPL_Chatterjee.pdf"}],"oa_version":"Published Version","_id":"6380","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 3","title":"Efficient parameterized algorithms for data packing","ddc":["004"],"status":"public","issue":"POPL","abstract":[{"text":"There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses. ","lang":"eng"}],"type":"journal_article","date_published":"2019-01-01T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” Proceedings of the ACM on Programming Languages. ACM, 2019. https://doi.org/10.1145/3290366.","mla":"Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data Packing.” Proceedings of the ACM on Programming Languages, vol. 3, no. POPL, 53, ACM, 2019, doi:10.1145/3290366.","short":"K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 3 (2019).","ista":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 3(POPL), 53.","ieee":"K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient parameterized algorithms for data packing,” Proceedings of the ACM on Programming Languages, vol. 3, no. POPL. ACM, 2019.","apa":"Chatterjee, K., Goharshady, A. K., Okati, N., & Pavlogiannis, A. (2019). Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. ACM. https://doi.org/10.1145/3290366","ama":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 2019;3(POPL). doi:10.1145/3290366"},"publication":"Proceedings of the ACM on Programming Languages","has_accepted_license":"1","day":"01"},{"publication_status":"published","publisher":"IEEE","department":[{"_id":"KrCh"}],"year":"2019","date_updated":"2024-03-28T23:30:33Z","date_created":"2019-02-26T09:03:15Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"},{"first_name":"Arash","last_name":"Pourdamghani","full_name":"Pourdamghani, Arash"}],"related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"article_number":"8751326","ec_funded":1,"quality_controlled":"1","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07986"}],"external_id":{"arxiv":["1902.07986"]},"language":[{"iso":"eng"}],"conference":{"name":"IEEE International Conference on Blockchain and Cryptocurrency","location":"Seoul, Korea","start_date":"2019-05-14","end_date":"2019-05-17"},"doi":"10.1109/BLOC.2019.8751326","month":"05","title":"Probabilistic smart contracts: Secure randomness on the blockchain","status":"public","_id":"6056","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"conference","abstract":[{"text":"In today's programmable blockchains, smart contracts are limited to being deterministic and non-probabilistic. This lack of randomness is a consequential limitation, given that a wide variety of real-world financial contracts, such as casino games and lotteries, depend entirely on randomness. As a result, several ad-hoc random number generation approaches have been developed to be used in smart contracts. These include ideas such as using an oracle or relying on the block hash. However, these approaches are manipulatable, i.e. their output can be tampered with by parties who might not be neutral, such as the owner of the oracle or the miners.We propose a novel game-theoretic approach for generating provably unmanipulatable pseudorandom numbers on the blockchain. Our approach allows smart contracts to access a trustworthy source of randomness that does not rely on potentially compromised miners or oracles, hence enabling the creation of a new generation of smart contracts that are not limited to being non-probabilistic and can be drawn from the much more general class of probabilistic programs.","lang":"eng"}],"publication":"IEEE International Conference on Blockchain and Cryptocurrency","citation":{"short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, IEEE International Conference on Blockchain and Cryptocurrency, IEEE, 2019.","mla":"Chatterjee, Krishnendu, et al. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” IEEE International Conference on Blockchain and Cryptocurrency, 8751326, IEEE, 2019, doi:10.1109/BLOC.2019.8751326.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” In IEEE International Conference on Blockchain and Cryptocurrency. IEEE, 2019. https://doi.org/10.1109/BLOC.2019.8751326.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Probabilistic smart contracts: Secure randomness on the blockchain. In: IEEE International Conference on Blockchain and Cryptocurrency. IEEE; 2019. doi:10.1109/BLOC.2019.8751326","apa":"Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Probabilistic smart contracts: Secure randomness on the blockchain. In IEEE International Conference on Blockchain and Cryptocurrency. Seoul, Korea: IEEE. https://doi.org/10.1109/BLOC.2019.8751326","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Probabilistic smart contracts: Secure randomness on the blockchain,” in IEEE International Conference on Blockchain and Cryptocurrency, Seoul, Korea, 2019.","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Probabilistic smart contracts: Secure randomness on the blockchain. IEEE International Conference on Blockchain and Cryptocurrency. IEEE International Conference on Blockchain and Cryptocurrency, 8751326."},"date_published":"2019-05-01T00:00:00Z","scopus_import":1,"day":"01"},{"month":"04","publication_identifier":{"isbn":["9781450359337"]},"conference":{"name":"ACM Symposium on Applied Computing","end_date":"2019-04-12","location":"Limassol, Cyprus","start_date":"2019-04-08"},"doi":"10.1145/3297280.3297319","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000474685800049"]},"quality_controlled":"1","isi":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:47:29Z","ec_funded":1,"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Pourdamghani, Arash","last_name":"Pourdamghani","first_name":"Arash"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"date_created":"2019-05-06T12:11:36Z","date_updated":"2024-03-28T23:30:34Z","volume":"Part F147772","year":"2019","publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-04-01T00:00:00Z","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","citation":{"ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. Proceedings of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing vol. Part F147772, 374–381.","apa":"Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772, pp. 374–381). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297319","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving,” in Proceedings of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, 2019, vol. Part F147772, pp. 374–381.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; 2019:374-381. doi:10.1145/3297280.3297319","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” In Proceedings of the 34th ACM Symposium on Applied Computing, Part F147772:374–81. ACM, 2019. https://doi.org/10.1145/3297280.3297319.","mla":"Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” Proceedings of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, 2019, pp. 374–81, doi:10.1145/3297280.3297319.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381."},"page":"374-381","abstract":[{"lang":"eng","text":"In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin."}],"type":"conference","pubrep_id":"1069","file":[{"checksum":"fbfbcd5a0c7a743862bfc3045539a614","date_created":"2019-05-06T12:09:27Z","date_updated":"2020-07-14T12:47:29Z","relation":"main_file","file_id":"6379","file_size":1023934,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_ACM_Chatterjee.pdf"}],"oa_version":"Submitted Version","_id":"6378","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["004"],"title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving"},{"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","year":"2019","date_created":"2019-03-25T10:13:25Z","date_updated":"2024-03-28T23:30:34Z","author":[{"last_name":"Wang","first_name":"Peixin","full_name":"Wang, Peixin"},{"first_name":"Hongfei","last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","full_name":"Fu, Hongfei"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Qin, Xudong","last_name":"Qin","first_name":"Xudong"},{"first_name":"Wenjun","last_name":"Shi","full_name":"Shi, Wenjun"}],"related_material":{"record":[{"id":"5457","status":"public","relation":"earlier_version"},{"id":"8934","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2020-07-14T12:47:20Z","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000523190300014"],"arxiv":["1902.04659"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2019-06-26","start_date":"2019-06-22","location":"Phoenix, AZ, United States","name":"PLDI: Conference on Programming Language Design and Implementation"},"doi":"10.1145/3314221.3314581","month":"06","ddc":["000"],"title":"Cost analysis of nondeterministic probabilistic programs","status":"public","_id":"6175","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","file_name":"paper.pdf","creator":"akafshda","content_type":"application/pdf","file_size":4051066,"file_id":"6176","relation":"main_file","checksum":"703a5e9b8c8587f2a44085ffd9a4db64","date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-25T10:11:22Z"}],"oa_version":"Submitted Version","type":"conference","abstract":[{"text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs,\r\nwhich aims at automated methods for analyzing the resource-usage of such programs.\r\nPrevious approaches for this problem could only handle nonnegative bounded costs.\r\nHowever, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols,\r\nboth positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the\r\nexpected accumulated cost of nondeterministic probabilistic programs.\r\nOur approach can handle (a) general positive and negative costs with bounded updates in\r\nvariables; and (b) nonnegative costs with general updates to variables.\r\nWe show that several natural examples which could not be\r\nhandled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no\r\nprevious approach for cost analysis of probabilistic programs could guarantee polynomial runtime.\r\nFinally, we show the effectiveness of our approach using experimental results on a variety of programs for which we efficiently synthesize tight resource-usage bounds.","lang":"eng"}],"page":"204-220","publication":"PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation","citation":{"ama":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. Cost analysis of nondeterministic probabilistic programs. In: PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2019:204-220. doi:10.1145/3314221.3314581","ista":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. 2019. Cost analysis of nondeterministic probabilistic programs. PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Conference on Programming Language Design and Implementation, 204–220.","apa":"Wang, P., Fu, H., Goharshady, A. K., Chatterjee, K., Qin, X., & Shi, W. (2019). Cost analysis of nondeterministic probabilistic programs. In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 204–220). Phoenix, AZ, United States: Association for Computing Machinery. https://doi.org/10.1145/3314221.3314581","ieee":"P. Wang, H. Fu, A. K. Goharshady, K. Chatterjee, X. Qin, and W. Shi, “Cost analysis of nondeterministic probabilistic programs,” in PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Phoenix, AZ, United States, 2019, pp. 204–220.","mla":"Wang, Peixin, et al. “Cost Analysis of Nondeterministic Probabilistic Programs.” PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–20, doi:10.1145/3314221.3314581.","short":"P. Wang, H. Fu, A.K. Goharshady, K. Chatterjee, X. Qin, W. Shi, in:, PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–220.","chicago":"Wang, Peixin, Hongfei Fu, Amir Kafshdar Goharshady, Krishnendu Chatterjee, Xudong Qin, and Wenjun Shi. “Cost Analysis of Nondeterministic Probabilistic Programs.” In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, 204–20. Association for Computing Machinery, 2019. https://doi.org/10.1145/3314221.3314581."},"date_published":"2019-06-08T00:00:00Z","keyword":["Program Cost Analysis","Program Termination","Probabilistic Programs","Martingales"],"scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"No"},{"type":"conference","abstract":[{"lang":"eng","text":"Smart contracts are programs that are stored and executed on the Blockchain and can receive, manage and transfer money (cryptocurrency units). Two important problems regarding smart contracts are formal analysis and compiler optimization. Formal analysis is extremely important, because smart contracts hold funds worth billions of dollars and their code is immutable after deployment. Hence, an undetected bug can cause significant financial losses. Compiler optimization is also crucial, because every action of a smart contract has to be executed by every node in the Blockchain network. Therefore, optimizations in compiling smart contracts can lead to significant savings in computation, time and energy.\r\n\r\nTwo classical approaches in program analysis and compiler optimization are intraprocedural and interprocedural analysis. In intraprocedural analysis, each function is analyzed separately, while interprocedural analysis considers the entire program. In both cases, the analyses are usually reduced to graph problems over the control flow graph (CFG) of the program. These graph problems are often computationally expensive. Hence, there has been ample research on exploiting structural properties of CFGs for efficient algorithms. One such well-studied property is the treewidth, which is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs of structured programs have treewidth at most 6, whereas the interprocedural treewidth cannot be bounded. This result has been used as a basis for many efficient intraprocedural analyses.\r\n\r\nIn this paper, we explore the idea of exploiting the treewidth of smart contracts for formal analysis and compiler optimization. First, similar to classical programs, we show that the intraprocedural treewidth of structured Solidity and Vyper smart contracts is at most 9. Second, for global analysis, we prove that the interprocedural treewidth of structured smart contracts is bounded by 10 and, in sharp contrast with classical programs, treewidth-based algorithms can be easily applied for interprocedural analysis. Finally, we supplement our theoretical results with experiments using a tool we implemented for computing treewidth of smart contracts and show that the treewidth is much lower in practice. We use 36,764 real-world Ethereum smart contracts as benchmarks and find that they have an average treewidth of at most 3.35 for the intraprocedural case and 3.65 for the interprocedural case.\r\n"}],"status":"public","title":"The treewidth of smart contracts","ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6490","oa_version":"Submitted Version","file":[{"file_name":"2019_ACM_Chatterjee.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6937138,"creator":"dernst","relation":"main_file","file_id":"7827","date_created":"2020-05-14T09:50:11Z","date_updated":"2020-07-14T12:47:32Z","checksum":"dddc20f6d9881f23b8755eb720ec9d6f"}],"pubrep_id":"1070","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","page":"400-408","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","citation":{"ama":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; :400-408. doi:10.1145/3297280.3297322","apa":"Chatterjee, K., Goharshady, A. K., & Goharshady, E. K. (n.d.). The treewidth of smart contracts. In Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772, pp. 400–408). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297322","ieee":"K. Chatterjee, A. K. Goharshady, and E. K. Goharshady, “The treewidth of smart contracts,” in Proceedings of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, vol. Part F147772, pp. 400–408.","ista":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. Proceedings of the 34th ACM Symposium on Applied Computing. SAC: Symposium on Applied Computing vol. Part F147772, 400–408.","short":"K. Chatterjee, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, n.d., pp. 400–408.","mla":"Chatterjee, Krishnendu, et al. “The Treewidth of Smart Contracts.” Proceedings of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, pp. 400–08, doi:10.1145/3297280.3297322.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “The Treewidth of Smart Contracts.” In Proceedings of the 34th ACM Symposium on Applied Computing, Part F147772:400–408. ACM, n.d. https://doi.org/10.1145/3297280.3297322."},"date_published":"2019-04-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:32Z","publication_status":"submitted","department":[{"_id":"KrCh"}],"publisher":"ACM","year":"2019","date_updated":"2024-03-28T23:30:34Z","date_created":"2019-05-26T21:59:15Z","volume":"Part F147772","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar"},{"full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady","first_name":"Ehsan Kafshdar"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"month":"04","publication_identifier":{"isbn":["9781450359337"]},"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000474685800052"]},"language":[{"iso":"eng"}],"conference":{"start_date":"2019-04-08","location":"Limassol, Cyprus","end_date":"2019-04-12","name":"SAC: Symposium on Applied Computing"},"doi":"10.1145/3297280.3297322"},{"date_published":"2019-11-01T00:00:00Z","article_type":"original","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Prateesh Goyal, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3363525.","short":"K. Chatterjee, A.K. Goharshady, P. Goyal, R. Ibsen-Jensen, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 41 (2019).","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 23, ACM, 2019, doi:10.1145/3363525.","apa":"Chatterjee, K., Goharshady, A. K., Goyal, P., Ibsen-Jensen, R., & Pavlogiannis, A. (2019). Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3363525","ieee":"K. Chatterjee, A. K. Goharshady, P. Goyal, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","ista":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. 2019. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 41(4), 23.","ama":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3363525"},"publication":"ACM Transactions on Programming Languages and Systems","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"file_name":"2019_ACMTransactions_Chatterjee.pdf","access_level":"open_access","file_size":667357,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8632","date_updated":"2020-10-08T12:58:10Z","date_created":"2020-10-08T12:58:10Z","checksum":"291cc86a07bd010d4815e177dac57b70","success":1}],"oa_version":"Submitted Version","intvolume":" 41","title":"Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth","status":"public","ddc":["000"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7158","issue":"4","abstract":[{"lang":"eng","text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, and so on. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, and so on. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in an important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect we consider is that the control flow graphs for most programs have constant treewidth.\r\n\r\nOur main contributions are simple and implementable algorithms that support multiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing but can answer subsequent queries significantly faster as compared to the current algorithmic solutions for interprocedural dataflow analysis. We have also implemented our algorithms and evaluated their performance for performing on-demand interprocedural dataflow analysis on various domains, such as for live variable analysis and reaching definitions, on a standard benchmark set. Our experimental results align with our theoretical statements and show that after a lightweight preprocessing, on-demand queries are answered much faster than the standard existing algorithmic approaches.\r\n"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1145/3363525","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000564108400004"]},"oa":1,"publication_identifier":{"issn":["0164-0925"]},"month":"11","volume":41,"date_updated":"2024-03-28T23:30:34Z","date_created":"2019-12-09T08:33:33Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Goyal, Prateesh","first_name":"Prateesh","last_name":"Goyal"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"}],"publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2019","ec_funded":1,"file_date_updated":"2020-10-08T12:58:10Z","article_number":"23"},{"date_created":"2019-11-13T08:33:43Z","date_updated":"2024-03-28T23:30:34Z","volume":41,"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"}],"related_material":{"record":[{"id":"639","status":"public","relation":"earlier_version"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"ACM","year":"2019","ec_funded":1,"article_number":"20","language":[{"iso":"eng"}],"doi":"10.1145/3339984","quality_controlled":"1","isi":1,"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"external_id":{"arxiv":["1705.00317"],"isi":["000564108400001"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}],"month":"10","oa_version":"Preprint","status":"public","title":"Non-polynomial worst-case analysis of recursive programs","intvolume":" 41","_id":"7014","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving\r\nworst-case bounds of non-deterministic recursive programs. Ranking functions\r\nare sound and complete for proving termination and worst-case bounds of\r\nnonrecursive programs. First, we apply ranking functions to recursion,\r\nresulting in measure functions. We show that measure functions provide a sound\r\nand complete approach to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second contribution is the synthesis of measure functions in\r\nnonpolynomial forms. We show that non-polynomial measure functions with\r\nlogarithm and exponentiation can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$ is not an integer. We present\r\nexperimental results to demonstrate that our approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii) Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that $r$ is not an integer and\r\nclose to the best-known bounds for the respective algorithms."}],"issue":"4","type":"journal_article","date_published":"2019-10-01T00:00:00Z","article_type":"original","publication":"ACM Transactions on Programming Languages and Systems","citation":{"ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3339984","ista":"Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 41(4), 20.","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2019). Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3339984","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis of recursive programs,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","mla":"Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 20, ACM, 2019, doi:10.1145/3339984.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages and Systems 41 (2019).","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3339984."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"department":[{"_id":"BjHo"}],"publisher":"ASME","publication_status":"published","year":"2019","volume":141,"date_created":"2019-05-26T21:59:13Z","date_updated":"2024-03-28T23:30:36Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7258"}]},"author":[{"full_name":"Kühnen, Jakob","last_name":"Kühnen","first_name":"Jakob","orcid":"0000-0003-4312-0179","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scarselli, Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","first_name":"Davide","last_name":"Scarselli"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"article_number":"111105","ec_funded":1,"project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.07625"}],"external_id":{"arxiv":["1809.07625"],"isi":["000487748600005"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"doi":"10.1115/1.4043494","publication_identifier":{"issn":["00982202"],"eissn":["1528901X"]},"month":"11","intvolume":" 141","title":"Relaminarization of pipe flow by means of 3D-printed shaped honeycombs","status":"public","_id":"6486","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow."}],"article_type":"original","citation":{"ista":"Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.","apa":"Kühnen, J., Scarselli, D., & Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. ASME. https://doi.org/10.1115/1.4043494","ieee":"J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” Journal of Fluids Engineering, vol. 141, no. 11. ASME, 2019.","ama":"Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 2019;141(11). doi:10.1115/1.4043494","chicago":"Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering. ASME, 2019. https://doi.org/10.1115/1.4043494.","mla":"Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering, vol. 141, no. 11, 111105, ASME, 2019, doi:10.1115/1.4043494.","short":"J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019)."},"publication":"Journal of Fluids Engineering","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"abstract":[{"text":"Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","status":"public","title":"Relaminarising pipe flow by wall movement","intvolume":" 867","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6228","day":"25","article_processing_charge":"No","scopus_import":"1","date_published":"2019-05-25T00:00:00Z","page":"934-948","publication":"Journal of Fluid Mechanics","citation":{"chicago":"Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2019.191.","short":"D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.","mla":"Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:10.1017/jfm.2019.191.","apa":"Scarselli, D., Kühnen, J., & Hof, B. (2019). Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2019.191","ieee":"D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” Journal of Fluid Mechanics, vol. 867. Cambridge University Press, pp. 934–948, 2019.","ista":"Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948.","ama":"Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 2019;867:934-948. doi:10.1017/jfm.2019.191"},"ec_funded":1,"date_created":"2019-04-07T21:59:14Z","date_updated":"2024-03-28T23:30:36Z","volume":867,"author":[{"orcid":"0000-0001-5227-4271","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","first_name":"Davide","full_name":"Scarselli, Davide"},{"first_name":"Jakob","last_name":"Kühnen","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7258"}],"link":[{"url":"https://doi.org/10.1017/jfm.2019.191","relation":"supplementary_material"}]},"publication_status":"published","publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"year":"2019","month":"05","publication_identifier":{"eissn":["14697645"],"issn":["00221120"]},"language":[{"iso":"eng"}],"doi":"10.1017/jfm.2019.191","isi":1,"quality_controlled":"1","project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"name":"Eliminating turbulence in oil pipelines","call_identifier":"H2020","grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000462606100001"],"arxiv":["1807.05357"]},"main_file_link":[{"url":"https://arxiv.org/abs/1807.05357","open_access":"1"}],"oa":1},{"month":"06","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"doi":"10.1104/pp.19.00201","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.19.00201"}],"oa":1,"external_id":{"pmid":["30936248"],"isi":["000470086100045"]},"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"ec_funded":1,"author":[{"full_name":"Oochi, A","first_name":"A","last_name":"Oochi"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","first_name":"Jakub","last_name":"Hajny","full_name":"Hajny, Jakub"},{"last_name":"Fukui","first_name":"K","full_name":"Fukui, K"},{"full_name":"Nakao, Y","first_name":"Y","last_name":"Nakao"},{"full_name":"Gallei, Michelle C","first_name":"Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"full_name":"Quareshy, M","last_name":"Quareshy","first_name":"M"},{"full_name":"Takahashi, K","first_name":"K","last_name":"Takahashi"},{"first_name":"T","last_name":"Kinoshita","full_name":"Kinoshita, T"},{"last_name":"Harborough","first_name":"SR","full_name":"Harborough, SR"},{"first_name":"S","last_name":"Kepinski","full_name":"Kepinski, S"},{"full_name":"Kasahara, H","last_name":"Kasahara","first_name":"H"},{"full_name":"Napier, RM","first_name":"RM","last_name":"Napier"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"first_name":"KI","last_name":"Hayashi","full_name":"Hayashi, KI"}],"related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"8822"}]},"date_updated":"2024-03-28T23:30:38Z","date_created":"2019-04-09T08:38:20Z","volume":180,"year":"2019","acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.).","pmid":1,"publication_status":"published","publisher":"ASPB","department":[{"_id":"JiFr"}],"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","publication":"Plant Physiology","citation":{"ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165. doi:10.1104/pp.19.00201","ieee":"A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019.","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201","ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165.","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165.","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:10.1104/pp.19.00201.","chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201."},"article_type":"original","page":"1152-1165","abstract":[{"lang":"eng","text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport."}],"issue":"2","type":"journal_article","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6260","title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","status":"public","intvolume":" 180"},{"scopus_import":"1","day":"30","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"1463-1479.e18","publication":"Cell","citation":{"ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” Cell, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.030","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 2019;177(6):1463-1479.e18. doi:10.1016/j.cell.2019.04.030","chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.030.","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:10.1016/j.cell.2019.04.030.","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18."},"date_published":"2019-05-30T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation."}],"issue":"6","ddc":["570"],"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","status":"public","intvolume":" 177","_id":"6508","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"creator":"dernst","file_size":3356292,"content_type":"application/pdf","file_name":"2019_Cell_Shamipour_accepted.pdf","access_level":"open_access","date_updated":"2020-10-21T07:22:34Z","date_created":"2020-10-21T07:22:34Z","success":1,"checksum":"aea43726d80e35ce3885073a5f05c3e3","file_id":"8686","relation":"main_file"}],"month":"05","publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"}],"oa":1,"external_id":{"isi":["000469415100013"],"pmid":["31080065"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.04.030","open_access":"1"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2019.04.030","file_date_updated":"2020-10-21T07:22:34Z","ec_funded":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"year":"2019","acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","pmid":1,"date_updated":"2024-03-28T23:30:39Z","date_created":"2019-06-02T21:59:12Z","volume":177,"author":[{"full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kardos, Roland","last_name":"Kardos","first_name":"Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xue, Shi-lei","first_name":"Shi-lei","last_name":"Xue","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8350"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/"}]}},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"doi":"10.1016/j.cell.2019.10.006","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000493898000012"],"pmid":["31675500"]},"oa":1,"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"month":"10","volume":179,"date_updated":"2024-03-28T23:30:39Z","date_created":"2019-11-12T12:51:06Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","description":"News auf IST Website","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"7186"},{"status":"public","relation":"dissertation_contains","id":"8350"}]},"author":[{"last_name":"Schwayer","first_name":"Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia"},{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"},{"last_name":"Pranjic-Ferscha","first_name":"Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","full_name":"Pranjic-Ferscha, Kornelija"},{"last_name":"Schauer","first_name":"Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra"},{"first_name":"M","last_name":"Balda","full_name":"Balda, M"},{"full_name":"Tada, M","first_name":"M","last_name":"Tada"},{"first_name":"K","last_name":"Matter","full_name":"Matter, K"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"department":[{"_id":"CaHe"},{"_id":"BjHo"}],"publisher":"Cell Press","publication_status":"published","pmid":1,"year":"2019","ec_funded":1,"file_date_updated":"2020-10-21T07:09:45Z","date_published":"2019-10-31T00:00:00Z","page":"937-952.e18","article_type":"original","citation":{"mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:10.1016/j.cell.2019.10.006.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006.","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18. doi:10.1016/j.cell.2019.10.006","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","ieee":"C. Schwayer et al., “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006"},"publication":"Cell","has_accepted_license":"1","article_processing_charge":"No","day":"31","scopus_import":"1","oa_version":"Submitted Version","file":[{"file_size":8805878,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_Cell_Schwayer_accepted.pdf","checksum":"33dac4bb77ee630e2666e936b4d57980","success":1,"date_updated":"2020-10-21T07:09:45Z","date_created":"2020-10-21T07:09:45Z","relation":"main_file","file_id":"8684"}],"intvolume":" 179","ddc":["570"],"status":"public","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7001","issue":"4","type":"journal_article"},{"file":[{"relation":"source_file","file_id":"6950","checksum":"00d100d6468e31e583051e0a006b640c","date_updated":"2020-10-17T22:30:03Z","date_created":"2019-10-15T05:28:42Z","access_level":"closed","embargo_to":"open_access","file_name":"Kopf_PhD_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":74735267,"creator":"akopf"},{"date_created":"2019-10-15T05:28:47Z","date_updated":"2020-10-17T22:30:03Z","checksum":"5d1baa899993ae6ca81aebebe1797000","embargo":"2020-10-16","file_id":"6951","relation":"main_file","creator":"akopf","file_size":52787224,"content_type":"application/pdf","file_name":"Kopf_PhD_Thesis1.pdf","access_level":"open_access"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"The implication of cytoskeletal dynamics on leukocyte migration","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6891","abstract":[{"text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2019-07-24T00:00:00Z","page":"171","citation":{"mla":"Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6891.","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:10.15479/AT:ISTA:6891","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","apa":"Kopf, A. (2019). The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6891","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019."},"day":"24","article_processing_charge":"No","has_accepted_license":"1","keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"date_created":"2019-09-19T08:19:44Z","date_updated":"2023-10-18T08:49:17Z","author":[{"full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","first_name":"Aglaja","last_name":"Kopf"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/feeling-like-a-cell/"}],"record":[{"id":"6328","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"15"},{"relation":"part_of_dissertation","status":"public","id":"6877"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiSi"}],"year":"2019","file_date_updated":"2020-10-17T22:30:03Z","degree_awarded":"PhD","supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6891","project":[{"call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"}],"oa":1,"month":"07","publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]}},{"month":"04","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"265FAEBA-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000465594200050"],"pmid":["30944468"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1038/s41586-019-1087-5","ec_funded":1,"publisher":"Springer Nature","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"publication_status":"published","pmid":1,"year":"2019","volume":568,"date_created":"2019-04-17T06:52:28Z","date_updated":"2024-03-28T23:30:40Z","related_material":{"record":[{"id":"14697","relation":"dissertation_contains","status":"public"},{"id":"6891","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"full_name":"Renkawitz, Jörg","first_name":"Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369"},{"orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","first_name":"Aglaja","full_name":"Kopf, Aglaja"},{"full_name":"Stopp, Julian A","last_name":"Stopp","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"de Vries","first_name":"Ingrid","full_name":"de Vries, Ingrid"},{"full_name":"Driscoll, Meghan K.","first_name":"Meghan K.","last_name":"Driscoll"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"first_name":"Erik S.","last_name":"Welf","full_name":"Welf, Erik S."},{"first_name":"Gaudenz","last_name":"Danuser","full_name":"Danuser, Gaudenz"},{"full_name":"Fiolka, Reto","first_name":"Reto","last_name":"Fiolka"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"scopus_import":"1","article_processing_charge":"No","day":"25","page":"546-550","article_type":"letter_note","citation":{"short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.","mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature, vol. 568, Springer Nature, 2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5.","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 2019;568:546-550. doi:10.1038/s41586-019-1087-5","ieee":"J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” Nature, vol. 568. Springer Nature, pp. 546–550, 2019.","apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5","ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550."},"publication":"Nature","date_published":"2019-04-25T00:00:00Z","type":"journal_article","abstract":[{"text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion.","lang":"eng"}],"intvolume":" 568","status":"public","title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6328","oa_version":"Submitted Version"},{"pmid":1,"year":"2019","department":[{"_id":"MiSi"}],"publisher":"Elsevier","publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6891"}]},"author":[{"last_name":"Kopf","first_name":"Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"volume":179,"date_created":"2019-09-15T22:00:46Z","date_updated":"2024-03-28T23:30:40Z","external_id":{"isi":["000486618500011"],"pmid":["31539498"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.cell.2019.08.047","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"month":"09","_id":"6877","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 179","title":"The neural crest pitches in to remove apoptotic debris","status":"public","oa_version":"None","type":"journal_article","issue":"1","citation":{"ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell. 2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047","ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53.","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","apa":"Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047","mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047.","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047."},"publication":"Cell","page":"51-53","article_type":"original","date_published":"2019-09-19T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"19"},{"status":"public","title":"Memo1 tiles the radial glial cell grid","intvolume":" 103","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6830","oa_version":"Published Version","type":"journal_article","issue":"5","article_type":"letter_note","page":"750-752","publication":"Neuron","citation":{"chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752.","apa":"Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021"},"date_published":"2019-09-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Elsevier","year":"2019","pmid":1,"date_updated":"2024-03-28T23:30:42Z","date_created":"2019-08-25T22:00:50Z","volume":103,"author":[{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7902"}]},"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.021","open_access":"1"}],"external_id":{"isi":["000484400200002"],"pmid":["31487522"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2019.08.021","month":"09","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]}},{"publication_identifier":{"eissn":["1422-0067"]},"month":"07","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000477041100221"],"pmid":["31284661"]},"language":[{"iso":"eng"}],"doi":"10.3390/ijms20133337","article_number":"3337","ec_funded":1,"file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"JiFr"}],"publisher":"MDPI","publication_status":"published","pmid":1,"year":"2019","volume":20,"date_created":"2019-07-11T12:00:32Z","date_updated":"2024-03-28T23:30:44Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10083"}]},"author":[{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"07","article_type":"original","citation":{"chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337.","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337","ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337.","ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337"},"publication":"International Journal of Molecular Sciences","date_published":"2019-07-07T00:00:00Z","type":"journal_article","issue":"13","abstract":[{"lang":"eng","text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation."}],"intvolume":" 20","ddc":["580"],"status":"public","title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6627","file":[{"checksum":"dd9d1cbb933a72ceb666c9667890ac51","date_created":"2019-07-17T06:17:15Z","date_updated":"2020-07-14T12:47:34Z","relation":"main_file","file_id":"6645","content_type":"application/pdf","file_size":3330291,"creator":"dernst","access_level":"open_access","file_name":"2019_JournalMolecularScience_Adamowski.pdf"}],"oa_version":"Published Version"},{"language":[{"iso":"eng"}],"doi":"10.1145/3355089.3356576","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000498397300007"]},"oa":1,"publication_identifier":{"issn":["0730-0301"]},"month":"11","volume":38,"date_updated":"2024-03-28T23:30:47Z","date_created":"2019-11-26T14:22:09Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12897"}]},"author":[{"full_name":"Hafner, Christian","first_name":"Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schumacher","first_name":"Christian","full_name":"Schumacher, Christian"},{"full_name":"Knoop, Espen","first_name":"Espen","last_name":"Knoop"},{"full_name":"Auzinger, Thomas","first_name":"Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"},{"full_name":"Bächer, Moritz","first_name":"Moritz","last_name":"Bächer"}],"publisher":"ACM","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:49Z","article_number":"157","date_published":"2019-11-06T00:00:00Z","article_type":"original","citation":{"ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576."},"publication":"ACM Transactions on Graphics","article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"xcad_sup_mat_siga19.pdf","creator":"bbickel","content_type":"application/pdf","file_size":1673176,"title":"X-CAD Supplemental Material","file_id":"7119","relation":"supplementary_material","checksum":"56a2fb019adcb556d2b022f5e5acb68c","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:24:26Z"},{"checksum":"5f29d76aceb5102e766cbab9b17d776e","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:24:27Z","relation":"main_file","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file_id":"7120","content_type":"application/pdf","file_size":14563618,"creator":"bbickel","access_level":"open_access","description":"This is the author's version of the work.","file_name":"XCAD_authors_version.pdf"},{"checksum":"0d31e123286cbec9e28b2001c2bb0d55","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:27:37Z","relation":"main_file","file_id":"7121","content_type":"video/mp4","file_size":259979129,"creator":"bbickel","access_level":"open_access","file_name":"XCAD_video.mp4"}],"intvolume":" 38","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","ddc":["000"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7117","issue":"6","abstract":[{"lang":"eng","text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models."}],"type":"journal_article"},{"oa_version":"Published Version","file":[{"file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","access_level":"open_access","creator":"cigler","file_size":12597663,"content_type":"application/pdf","embargo":"2020-05-02","file_id":"6373","relation":"main_file","date_created":"2019-05-03T11:54:52Z","date_updated":"2021-02-11T11:17:13Z","checksum":"c0085d47c58c9cbcab1b0a783480f6da"},{"date_updated":"2020-07-14T12:47:28Z","date_created":"2019-05-03T11:54:54Z","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","relation":"source_file","file_id":"6374","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":34644426,"creator":"cigler","embargo_to":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","access_level":"closed"}],"ddc":["576","579"],"status":"public","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","_id":"6371","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2019-05-03T00:00:00Z","page":"152","citation":{"short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria."},"article_processing_charge":"No","has_accepted_license":"1","day":"03","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"date_created":"2019-05-03T11:55:51Z","date_updated":"2024-02-21T13:45:52Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"67"},{"status":"public","relation":"popular_science","id":"5585"}]},"author":[{"full_name":"Igler, Claudia","first_name":"Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2019","file_date_updated":"2021-02-11T11:17:13Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"doi":"10.15479/AT:ISTA:6371","project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"05"},{"scopus_import":"1","article_processing_charge":"No","day":"22","citation":{"chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502.","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019.","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502"},"publication":"Physical Review Letters","date_published":"2019-03-22T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations.","lang":"eng"}],"intvolume":" 122","title":"Transition to turbulence in particle laden flows","status":"public","_id":"6189","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"month":"03","isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1809.06358"],"isi":["000461922000006"]},"main_file_link":[{"url":"https://arxiv.org/abs/1809.06358","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.122.114502","article_number":"114502","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","year":"2019","volume":122,"date_created":"2019-03-31T21:59:12Z","date_updated":"2024-03-28T23:30:48Z","related_material":{"record":[{"id":"9728","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"469E6004-F248-11E8-B48F-1D18A9856A87","last_name":"Agrawal","first_name":"Nishchal","full_name":"Agrawal, Nishchal"},{"full_name":"Choueiri, George H","first_name":"George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"}]},{"type":"journal_article","abstract":[{"text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied.","lang":"eng"}],"issue":"3","_id":"10286","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Evaluation and monitoring of free running oscillators serving as source of randomness","ddc":["000"],"intvolume":" 2018","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_IACR_Allini.pdf","creator":"cchlebak","file_size":955755,"content_type":"application/pdf","file_id":"10289","relation":"main_file","success":1,"checksum":"b816b848f046c48a8357700d9305dce5","date_created":"2021-11-15T10:27:29Z","date_updated":"2021-11-15T10:27:29Z"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","citation":{"chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242.","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242"},"article_type":"original","page":"214-242","date_published":"2018-01-01T00:00:00Z","file_date_updated":"2021-11-15T10:27:29Z","year":"2018","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"International Association for Cryptologic Research","author":[{"full_name":"Allini, Elie Noumon","first_name":"Elie Noumon","last_name":"Allini"},{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski"},{"first_name":"Oto","last_name":"Petura","full_name":"Petura, Oto"},{"full_name":"Bernard, Florent","last_name":"Bernard","first_name":"Florent"},{"full_name":"Laban, Marek","first_name":"Marek","last_name":"Laban"},{"first_name":"Viktor","last_name":"Fischer","full_name":"Fischer, Viktor"}],"date_updated":"2021-11-15T10:48:49Z","date_created":"2021-11-14T23:01:25Z","volume":2018,"month":"01","publication_identifier":{"eissn":["2569-2925"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.13154/tches.v2018.i3.214-242","language":[{"iso":"eng"}]},{"issue":"2","abstract":[{"text":"Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 12","status":"public","title":"A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10362","article_processing_charge":"No","day":"19","keyword":["general physics and astronomy"],"scopus_import":"1","date_published":"2018-01-19T00:00:00Z","page":"1508-1518","article_type":"original","citation":{"chicago":"Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano. American Chemical Society, 2018. https://doi.org/10.1021/acsnano.7b08044.","mla":"Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano, vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:10.1021/acsnano.7b08044.","short":"P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley, A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518.","ista":"Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 12(2), 1508–1518.","apa":"Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley, D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.7b08044","ieee":"P. D. E. Fisher et al., “A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement,” ACS Nano, vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.","ama":"Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 2018;12(2):1508-1518. doi:10.1021/acsnano.7b08044"},"publication":"ACS Nano","extern":"1","volume":12,"date_updated":"2021-11-26T15:57:02Z","date_created":"2021-11-26T15:15:00Z","author":[{"full_name":"Fisher, Patrick D. Ellis","first_name":"Patrick D. Ellis","last_name":"Fisher"},{"full_name":"Shen, Qi","last_name":"Shen","first_name":"Qi"},{"full_name":"Akpinar, Bernice","last_name":"Akpinar","first_name":"Bernice"},{"first_name":"Luke K.","last_name":"Davis","full_name":"Davis, Luke K."},{"last_name":"Chung","first_name":"Kenny Kwok Hin","full_name":"Chung, Kenny Kwok Hin"},{"last_name":"Baddeley","first_name":"David","full_name":"Baddeley, David"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Thomas J.","last_name":"Melia","full_name":"Melia, Thomas J."},{"first_name":"Bart W.","last_name":"Hoogenboom","full_name":"Hoogenboom, Bart W."},{"full_name":"Lin, Chenxiang","last_name":"Lin","first_name":"Chenxiang"},{"first_name":"C. Patrick","last_name":"Lusk","full_name":"Lusk, C. Patrick"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2018","acknowledgement":"We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1, and EP/M028100/1).","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1021/acsnano.7b08044","quality_controlled":"1","external_id":{"pmid":["29350911"]}},{"publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"month":"03","doi":"10.1038/s41557-018-0023-x","language":[{"iso":"eng"}],"external_id":{"pmid":["29581486"]},"quality_controlled":"1","extern":"1","author":[{"full_name":"Cohen, Samuel I. A.","first_name":"Samuel I. A.","last_name":"Cohen"},{"first_name":"Risto","last_name":"Cukalevski","full_name":"Cukalevski, Risto"},{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Mattias","last_name":"Törnquist","full_name":"Törnquist, Mattias"},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"full_name":"Buell, Alexander K.","last_name":"Buell","first_name":"Alexander K."},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"}],"volume":10,"date_created":"2021-11-26T12:41:38Z","date_updated":"2021-11-26T15:14:00Z","pmid":1,"acknowledgement":"We thank B. Jönsson and I. André for helpful discussions. We acknowledge financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge (S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden (S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust (A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases (C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).","year":"2018","publisher":"Springer Nature","publication_status":"published","article_processing_charge":"No","day":"26","scopus_import":"1","keyword":["general chemical engineering","general chemistry"],"date_published":"2018-03-26T00:00:00Z","citation":{"chicago":"Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić, Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell, Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry. Springer Nature, 2018. https://doi.org/10.1038/s41557-018-0023-x.","mla":"Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry, vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:10.1038/s41557-018-0023-x.","short":"S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M. Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry 10 (2018) 523–531.","ista":"Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 10(5), 523–531.","apa":"Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist, M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-018-0023-x","ieee":"S. I. A. Cohen et al., “Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide,” Nature Chemistry, vol. 10, no. 5. Springer Nature, pp. 523–531, 2018.","ama":"Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 2018;10(5):523-531. doi:10.1038/s41557-018-0023-x"},"publication":"Nature Chemistry","page":"523-531","article_type":"original","issue":"5","abstract":[{"text":"Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.","lang":"eng"}],"type":"journal_article","oa_version":"None","_id":"10360","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 10","title":"Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide","status":"public"},{"pmid":1,"year":"2018","acknowledgement":"We acknowledge support from the Schiff Foundation (A.J.D.), the Royal Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC (T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several useful discussions.","publisher":"American Chemical Society","publication_status":"published","author":[{"last_name":"Dear","first_name":"Alexander J.","full_name":"Dear, Alexander J."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela"},{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}],"volume":122,"date_updated":"2021-11-26T12:40:02Z","date_created":"2021-11-26T11:55:12Z","extern":"1","external_id":{"pmid":["30336667"]},"quality_controlled":"1","doi":"10.1021/acs.jpcb.8b07805","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"month":"10","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10357","intvolume":" 122","title":"Statistical mechanics of globular oligomer formation by protein molecules","status":"public","oa_version":"None","type":"journal_article","issue":"49","abstract":[{"text":"The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements.","lang":"eng"}],"citation":{"ieee":"A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles, “Statistical mechanics of globular oligomer formation by protein molecules,” The Journal of Physical Chemistry B, vol. 122, no. 49. American Chemical Society, pp. 11721–11730, 2018.","apa":"Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., & Knowles, T. P. J. (2018). Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.8b07805","ista":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 122(49), 11721–11730.","ama":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 2018;122(49):11721-11730. doi:10.1021/acs.jpcb.8b07805","chicago":"Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M. Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B. American Chemical Society, 2018. https://doi.org/10.1021/acs.jpcb.8b07805.","short":"A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal of Physical Chemistry B 122 (2018) 11721–11730.","mla":"Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B, vol. 122, no. 49, American Chemical Society, 2018, pp. 11721–30, doi:10.1021/acs.jpcb.8b07805."},"publication":"The Journal of Physical Chemistry B","page":"11721-11730","article_type":"original","date_published":"2018-10-18T00:00:00Z","scopus_import":"1","keyword":["materials chemistry"],"article_processing_charge":"No","day":"18"},{"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.10147"}],"external_id":{"pmid":["29667410"]},"oa":1,"quality_controlled":"1","doi":"10.1021/acs.nanolett.8b00786","language":[{"iso":"eng"}],"extern":"1","pmid":1,"year":"2018","acknowledgement":"We acknowledge discussions with Giuseppe Battaglia as well as support from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.). We thank Claudia Flandoli for help with Figure 1.","publisher":"American Chemical Society","publication_status":"published","author":[{"full_name":"Curk, Tine","last_name":"Curk","first_name":"Tine"},{"last_name":"Wirnsberger","first_name":"Peter","full_name":"Wirnsberger, Peter"},{"last_name":"Dobnikar","first_name":"Jure","full_name":"Dobnikar, Jure"},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"},{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"volume":18,"date_updated":"2021-11-26T15:14:08Z","date_created":"2021-11-26T12:15:47Z","scopus_import":"1","keyword":["mechanical engineering","condensed matter physics"],"article_processing_charge":"No","day":"18","citation":{"chicago":"Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b00786.","mla":"Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56, doi:10.1021/acs.nanolett.8b00786.","short":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters 18 (2018) 5350–5356.","ista":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.","apa":"Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., & Šarić, A. (2018). Controlling cargo trafficking in multicomponent membranes. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b00786","ieee":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling cargo trafficking in multicomponent membranes,” Nano Letters, vol. 18, no. 9. American Chemical Society, pp. 5350–5356, 2018.","ama":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 2018;18(9):5350-5356. doi:10.1021/acs.nanolett.8b00786"},"publication":"Nano Letters","page":"5350-5356","article_type":"original","date_published":"2018-04-18T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"text":"Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10359","intvolume":" 18","status":"public","title":"Controlling cargo trafficking in multicomponent membranes","oa_version":"Preprint"},{"date_published":"2018-05-24T00:00:00Z","citation":{"ama":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 2018;116(21-22):3055-3065. doi:10.1080/00268976.2018.1474280","ista":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 116(21–22), 3055–3065.","ieee":"T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P. J. Knowles, “Reaction rate theory for supramolecular kinetics: application to protein aggregation,” Molecular Physics, vol. 116, no. 21–22. Taylor & Francis, pp. 3055–3065, 2018.","apa":"Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., & Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2018.1474280","mla":"Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics, vol. 116, no. 21–22, Taylor & Francis, 2018, pp. 3055–65, doi:10.1080/00268976.2018.1474280.","short":"T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles, Molecular Physics 116 (2018) 3055–3065.","chicago":"Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics. Taylor & Francis, 2018. https://doi.org/10.1080/00268976.2018.1474280."},"publication":"Molecular Physics","page":"3055-3065","article_type":"original","article_processing_charge":"No","day":"24","scopus_import":"1","keyword":["physical chemistry"],"oa_version":"Preprint","_id":"10358","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 116","title":"Reaction rate theory for supramolecular kinetics: application to protein aggregation","status":"public","issue":"21-22","abstract":[{"lang":"eng","text":"Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements."}],"type":"journal_article","doi":"10.1080/00268976.2018.1474280","language":[{"iso":"eng"}],"external_id":{"arxiv":["1803.04851"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.04851"}],"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["0026-8976"],"eissn":["1362-3028"]},"month":"05","author":[{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"first_name":"Lucie X.","last_name":"Liu","full_name":"Liu, Lucie X."},{"full_name":"Curk, Samo","last_name":"Curk","first_name":"Samo"},{"full_name":"Bolhuis, Peter G.","last_name":"Bolhuis","first_name":"Peter G."},{"full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."}],"volume":116,"date_updated":"2021-11-26T12:39:58Z","date_created":"2021-11-26T12:08:02Z","acknowledgement":"We thank Claudia Flandoli for the help with illustrations.","year":"2018","publisher":"Taylor & Francis","publication_status":"published","extern":"1"},{"extern":"1","publication_status":"published","publisher":"Annual Reviews","acknowledgement":"We acknowledge support from the Swiss National Science Foundation (T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.); the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt (337969).","year":"2018","pmid":1,"date_created":"2021-11-26T12:52:12Z","date_updated":"2021-11-26T15:58:19Z","volume":69,"author":[{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Habchi","first_name":"Johnny","full_name":"Habchi, Johnny"},{"full_name":"Chia, Sean","first_name":"Sean","last_name":"Chia"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."}],"month":"02","publication_identifier":{"eissn":["1545-1593"],"issn":["0066-426X"]},"quality_controlled":"1","external_id":{"pmid":["29490200"]},"language":[{"iso":"eng"}],"doi":"10.1146/annurev-physchem-050317-021322","type":"journal_article","abstract":[{"text":"Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.","lang":"eng"}],"issue":"1","status":"public","title":"Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation","intvolume":" 69","_id":"10361","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","keyword":["physical and theoretical chemistry"],"scopus_import":"1","day":"28","article_processing_charge":"No","article_type":"original","page":"273-298","publication":"Annual Review of Physical Chemistry","citation":{"chicago":"Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry. Annual Reviews, 2018. https://doi.org/10.1146/annurev-physchem-050317-021322.","short":"T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.","mla":"Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:10.1146/annurev-physchem-050317-021322.","apa":"Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo, M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. Annual Reviews. https://doi.org/10.1146/annurev-physchem-050317-021322","ieee":"T. C. T. Michaels et al., “Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation,” Annual Review of Physical Chemistry, vol. 69, no. 1. Annual Reviews, pp. 273–298, 2018.","ista":"Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 69(1), 273–298.","ama":"Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 2018;69(1):273-298. doi:10.1146/annurev-physchem-050317-021322"},"date_published":"2018-02-28T00:00:00Z"},{"type":"journal_article","issue":"22","abstract":[{"text":"Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4.","lang":"eng"}],"intvolume":" 121","status":"public","title":"Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10626","oa_version":"Preprint","keyword":["general physics and astronomy"],"scopus_import":"1","article_processing_charge":"No","day":"28","article_type":"original","citation":{"ista":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 121(22), 226801.","apa":"Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., & Young, A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.226801","ieee":"H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young, “Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices,” Physical Review Letters, vol. 121, no. 22. American Physical Society, 2018.","ama":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 2018;121(22). doi:10.1103/physrevlett.121.226801","chicago":"Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.226801.","mla":"Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters, vol. 121, no. 22, 226801, American Physical Society, 2018, doi:10.1103/physrevlett.121.226801.","short":"H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young, Physical Review Letters 121 (2018)."},"publication":"Physical Review Letters","date_published":"2018-11-28T00:00:00Z","article_number":"226801","extern":"1","publisher":"American Physical Society","publication_status":"published","year":"2018","acknowledgement":"We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for discussing their unpublished data and for sharing the stack inversion technique. The authors acknowledge further discussions of the results with I. Sodemann, M. Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Prize Fellowship in Science of the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard Foundation.","volume":121,"date_created":"2022-01-14T12:15:47Z","date_updated":"2022-01-14T13:48:35Z","author":[{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy"},{"full_name":"Zhou, H.","last_name":"Zhou","first_name":"H."},{"full_name":"Spanton, E. M.","first_name":"E. M.","last_name":"Spanton"},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"last_name":"Watanabe","first_name":"K.","full_name":"Watanabe, K."},{"last_name":"Young","first_name":"A. F.","full_name":"Young, A. F."}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"11","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.04199"}],"external_id":{"arxiv":["1805.04199"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.121.226801"},{"oa_version":"Preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10627","status":"public","title":"Imaging phase slip dynamics in micron-size superconducting rings","intvolume":" 97","abstract":[{"lang":"eng","text":"We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures."}],"issue":"18","type":"journal_article","date_published":"2018-05-08T00:00:00Z","publication":"Physical Review B","citation":{"chicago":"Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.184501.","short":"H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).","mla":"Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B, vol. 97, no. 18, 184501, American Physical Society, 2018, doi:10.1103/physrevb.97.184501.","ieee":"H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in micron-size superconducting rings,” Physical Review B, vol. 97, no. 18. American Physical Society, 2018.","apa":"Polshyn, H., Naibert, T. R., & Budakian, R. (2018). Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.184501","ista":"Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 97(18), 184501.","ama":"Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 2018;97(18). doi:10.1103/physrevb.97.184501"},"article_type":"original","day":"08","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"},{"full_name":"Naibert, Tyler R.","last_name":"Naibert","first_name":"Tyler R."},{"full_name":"Budakian, Raffi","first_name":"Raffi","last_name":"Budakian"}],"date_created":"2022-01-14T13:48:47Z","date_updated":"2022-01-14T13:58:24Z","volume":97,"acknowledgement":"We are grateful to Nadya Mason for useful discussions. This work was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649, the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.\r\n","year":"2018","publication_status":"published","publisher":"American Physical Society","extern":"1","article_number":"184501","doi":"10.1103/physrevb.97.184501","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1703.08184"]},"main_file_link":[{"url":"https://arxiv.org/abs/1703.08184","open_access":"1"}],"quality_controlled":"1","month":"05","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]}},{"publication_status":"published","publisher":"EasyChair","department":[{"_id":"KrCh"}],"year":"2018","acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","date_updated":"2022-07-29T09:24:31Z","date_created":"2022-03-18T12:46:32Z","volume":57,"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvořák, Wolfgang","first_name":"Wolfgang","last_name":"Dvořák"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"file_date_updated":"2022-05-17T07:51:08Z","ec_funded":1,"quality_controlled":"1","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"external_id":{"arxiv":["1909.04983"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","location":"Awassa, Ethiopia","start_date":"2018-11-17","end_date":"2018-11-21"},"doi":"10.29007/5z5k","month":"10","publication_identifier":{"issn":["2398-7340"]},"status":"public","title":"Quasipolynomial set-based symbolic algorithms for parity games","ddc":["000"],"intvolume":" 57","_id":"10883","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","file":[{"access_level":"open_access","file_name":"2018_EPiCs_Chatterjee.pdf","content_type":"application/pdf","file_size":720893,"creator":"dernst","relation":"main_file","file_id":"11392","checksum":"1229aa8640bd6db610c85decf2265480","success":1,"date_updated":"2022-05-17T07:51:08Z","date_created":"2022-05-17T07:51:08Z"}],"oa_version":"Published Version","alternative_title":["EPiC Series in Computing"],"type":"conference","abstract":[{"lang":"eng","text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space."}],"page":"233-253","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k"},"date_published":"2018-10-23T00:00:00Z","scopus_import":"1","day":"23","article_processing_charge":"No","has_accepted_license":"1"},{"type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. We show that there is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models we give a construction of this polytope as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models. "}],"publist_id":"6284","issue":"1","status":"public","title":"Generalized permutohedra from probabilistic graphical models","publication_status":"published","publisher":"SIAM","intvolume":" 32","_id":"1092","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2018","date_updated":"2021-01-12T06:48:13Z","date_created":"2018-12-11T11:50:06Z","oa_version":"Preprint","volume":32,"author":[{"full_name":"Mohammadi, Fatemeh","id":"2C29581E-F248-11E8-B48F-1D18A9856A87","first_name":"Fatemeh","last_name":"Mohammadi"},{"first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"},{"last_name":"Wang","first_name":"Charles","full_name":"Wang, Charles"},{"full_name":"Yu, Josephine","first_name":"Josephine","last_name":"Yu"}],"month":"01","day":"01","quality_controlled":"1","page":"64-93","publication":"SIAM Journal on Discrete Mathematics","citation":{"mla":"Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics, vol. 32, no. 1, SIAM, 2018, pp. 64–93, doi:10.1137/16M107894X.","short":"F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics 32 (2018) 64–93.","chicago":"Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics. SIAM, 2018. https://doi.org/10.1137/16M107894X.","ama":"Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 2018;32(1):64-93. doi:10.1137/16M107894X","ista":"Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93.","ieee":"F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from probabilistic graphical models,” SIAM Journal on Discrete Mathematics, vol. 32, no. 1. SIAM, pp. 64–93, 2018.","apa":"Mohammadi, F., Uhler, C., Wang, C., & Yu, J. (2018). Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. SIAM. https://doi.org/10.1137/16M107894X"},"main_file_link":[{"url":"https://arxiv.org/abs/1606.01814","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1137/16M107894X","date_published":"2018-01-01T00:00:00Z"},{"ec_funded":1,"publist_id":"8045","publisher":"Springer","department":[{"_id":"RoSe"}],"publication_status":"published","year":"2018","volume":270,"date_created":"2018-12-11T11:44:08Z","date_updated":"2021-01-12T06:48:16Z","author":[{"full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","last_name":"Leopold","first_name":"Nikolai K"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"}],"month":"10","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10843"}],"external_id":{"arxiv":["1806.10843"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-01602-9_9","conference":{"location":"Munich, Germany","start_date":"2017-03-30","end_date":"2017-04-01","name":"MaLiQS: Macroscopic Limits of Quantum Systems"},"type":"conference","abstract":[{"lang":"eng","text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm."}],"intvolume":" 270","title":"Mean-field limits of particles in interaction with quantised radiation fields","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11","oa_version":"Preprint","scopus_import":1,"day":"27","page":"185 - 214","citation":{"chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9"},"date_published":"2018-10-27T00:00:00Z"},{"doi":"10.1101/gad.315523.118","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["30228202"]},"main_file_link":[{"url":"https://doi.org/10.1101/gad.315523.118","open_access":"1"}],"quality_controlled":"1","publication_identifier":{"issn":["0890-9369","1549-5477"]},"month":"09","author":[{"last_name":"McCloskey","first_name":"Asako","full_name":"McCloskey, Asako"},{"last_name":"Ibarra","first_name":"Arkaitz","full_name":"Ibarra, Arkaitz"},{"last_name":"HETZER","first_name":"Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W"}],"volume":32,"date_updated":"2022-07-18T08:32:32Z","date_created":"2022-04-07T07:45:30Z","pmid":1,"year":"2018","publisher":"Cold Spring Harbor Laboratory","publication_status":"published","extern":"1","date_published":"2018-09-18T00:00:00Z","citation":{"short":"A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331.","mla":"McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118.","chicago":"McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development. Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118.","ama":"McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331. doi:10.1101/gad.315523.118","apa":"McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118","ieee":"A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of nuclear pore complexes per cell nucleus,” Genes & Development, vol. 32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018.","ista":"McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331."},"publication":"Genes & Development","page":"1321-1331","article_type":"original","article_processing_charge":"No","day":"18","scopus_import":"1","keyword":["Developmental Biology","Genetics"],"oa_version":"Published Version","_id":"11063","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","intvolume":" 32","title":"Tpr regulates the total number of nuclear pore complexes per cell nucleus","status":"public","issue":"19-20","abstract":[{"text":"The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.","lang":"eng"}],"type":"journal_article"},{"language":[{"iso":"eng"}],"doi":"10.1186/s13059-018-1599-6","quality_controlled":"1","external_id":{"pmid":["30567591"]},"main_file_link":[{"url":"https://doi.org/10.1186/s13059-018-1599-6","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["1474-760X"]},"month":"12","volume":19,"date_created":"2022-04-07T07:45:40Z","date_updated":"2022-07-18T08:32:34Z","author":[{"full_name":"Fleischer, Jason G.","last_name":"Fleischer","first_name":"Jason G."},{"full_name":"Schulte, Roberta","last_name":"Schulte","first_name":"Roberta"},{"full_name":"Tsai, Hsiao H.","first_name":"Hsiao H.","last_name":"Tsai"},{"full_name":"Tyagi, Swati","last_name":"Tyagi","first_name":"Swati"},{"last_name":"Ibarra","first_name":"Arkaitz","full_name":"Ibarra, Arkaitz"},{"first_name":"Maxim N.","last_name":"Shokhirev","full_name":"Shokhirev, Maxim N."},{"full_name":"Huang, Ling","last_name":"Huang","first_name":"Ling"},{"last_name":"HETZER","first_name":"Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W"},{"last_name":"Navlakha","first_name":"Saket","full_name":"Navlakha, Saket"}],"publisher":"BioMed Central","publication_status":"published","pmid":1,"year":"2018","extern":"1","article_number":"221","date_published":"2018-12-20T00:00:00Z","article_type":"original","citation":{"short":"J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev, L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018).","mla":"Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology, vol. 19, 221, BioMed Central, 2018, doi:10.1186/s13059-018-1599-6.","chicago":"Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1599-6.","ama":"Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 2018;19. doi:10.1186/s13059-018-1599-6","apa":"Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1599-6","ieee":"J. G. Fleischer et al., “Predicting age from the transcriptome of human dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018.","ista":"Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 19, 221."},"publication":"Genome Biology","article_processing_charge":"No","day":"20","scopus_import":"1","oa_version":"Published Version","intvolume":" 19","title":"Predicting age from the transcriptome of human dermal fibroblasts","status":"public","_id":"11064","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","abstract":[{"text":"Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients.","lang":"eng"}],"type":"journal_article"},{"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: formation / dark ages / reionization / first stars / techniques: spectroscopic / intergalactic medium"],"scopus_import":"1","article_processing_charge":"No","day":"19","article_type":"original","citation":{"apa":"Matthee, J. J., Sobral, D., Gronke, M., Paulino-Afonso, A., Stefanon, M., & Röttgering, H. (2018). Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833528","ieee":"J. J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, and H. Röttgering, “Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe,” Astronomy & Astrophysics, vol. 619. EDP Sciences, 2018.","ista":"Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. 2018. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 619, A136.","ama":"Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 2018;619. doi:10.1051/0004-6361/201833528","chicago":"Matthee, Jorryt J, David Sobral, Max Gronke, Ana Paulino-Afonso, Mauro Stefanon, and Huub Röttgering. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201833528.","short":"J.J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, H. Röttgering, Astronomy & Astrophysics 619 (2018).","mla":"Matthee, Jorryt J., et al. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics, vol. 619, A136, EDP Sciences, 2018, doi:10.1051/0004-6361/201833528."},"publication":"Astronomy & Astrophysics","date_published":"2018-11-19T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Distant luminous Lyman-α emitters (LAEs) are excellent targets for spectroscopic observations of galaxies in the epoch of reionisation (EoR). We present deep high-resolution (R = 5000) VLT/X-shooter observations, along with an extensive collection of photometric data of COLA1, a proposed double peaked LAE at z = 6.6. We rule out the possibility that COLA1’s emission line is an [OII] doublet at z = 1.475 on the basis of i) the asymmetric red line-profile and flux ratio of the peaks (blue/red=0.31 ± 0.03) and ii) an unphysical [OII]/Hα ratio ([OII]/Hα > 22). We show that COLA1’s observed B-band flux is explained by a faint extended foreground LAE, for which we detect Lyα and [OIII] at z = 2.142. We thus conclude that COLA1 is a real double-peaked LAE at z = 6.593, the first discovered at z > 6. COLA1 is UV luminous (M1500 = −21.6 ± 0.3), has a high equivalent width (EW0,Lyα = 120−40+50 Å) and very compact Lyα emission (r50,Lyα = 0.33−0.04+0.07 kpc). Relatively weak inferred Hβ+[OIII] line-emission from Spitzer/IRAC indicates an extremely low metallicity of Z < 1/20 Z⊙ or reduced strength of nebular lines due to high escape of ionising photons. The small Lyα peak separation of 220 ± 20 km s−1 implies a low HI column density and an ionising photon escape fraction of ≈15 − 30%, providing the first direct evidence that such galaxies contribute actively to the reionisation of the Universe at z > 6. Based on simple estimates, we find that COLA1 could have provided just enough photons to reionise its own ≈0.3 pMpc (2.3 cMpc) bubble, allowing the blue Lyα line to be observed. However, we also discuss alternative scenarios explaining the detected double peaked nature of COLA1. Our results show that future high-resolution observations of statistical samples of double peaked LAEs at z > 5 are a promising probe of the occurrence of ionised regions around galaxies in the EoR."}],"intvolume":" 619","status":"public","title":"Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11508","oa_version":"Published Version","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"month":"11","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.11621"}],"oa":1,"external_id":{"arxiv":["1805.11621"]},"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/201833528","article_number":"A136","extern":"1","publisher":"EDP Sciences","publication_status":"published","acknowledgement":"JM acknowledges the award of a Huygens PhD fellowship from Leiden University. MG acknowledges support from NASA grant NNX17AK58G. APA, PhD::SPACE fellow, acknowledges support from the FCT through the fellowship PD/BD/52706/2014. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 294.A-5018, 098.A-0819, 099.A-0254 and 0100.A-0213. We are grateful for the excellent data-sets from the COSMOS and UltraVISTA survey teams. This research was supported by the Munich Institute for Astro- and Particle Physics (MIAPP) of the DFG cluster of excellence “Origin and Structure of the Universe”. We thank the referee for their comments that improved the paper. We also thank Christoph Behrens, Len Cowie, Koki Kakiichi, Peter Laursen, Charlotte Mason, Eros Vanzella, Lewis Weinberger and Johannes Zabl for discussions. We have benefited from the public available programming language Python, including the numpy, matplotlib, scipy and astropy packages (Hunter 2007; Astropy Collaboration 2013), the astronomical imaging tools Swarp (Bertin 2010) and ds9 and the Topcat analysis tool (Taylor 2013).","year":"2018","volume":619,"date_created":"2022-07-06T11:14:23Z","date_updated":"2022-07-19T09:32:08Z","author":[{"full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"full_name":"Gronke, Max","first_name":"Max","last_name":"Gronke"},{"full_name":"Paulino-Afonso, Ana","first_name":"Ana","last_name":"Paulino-Afonso"},{"full_name":"Stefanon, Mauro","first_name":"Mauro","last_name":"Stefanon"},{"first_name":"Huub","last_name":"Röttgering","full_name":"Röttgering, Huub"}]},{"abstract":[{"lang":"eng","text":"We investigate the clustering properties of ∼7000 H β + [O III] and [O II] narrowband-selected emitters at z ∼ 0.8–4.7 from the High-z Emission Line Survey. We find clustering lengths, r0, of 1.5–4.0 h−1 Mpc and minimum dark matter halo masses of 1010.7–12.1 M⊙ for our z = 0.8–3.2 H β + [O III] emitters and r0 ∼ 2.0–8.3 h−1 Mpc and halo masses of 1011.5–12.6 M⊙ for our z = 1.5–4.7 [O II] emitters. We find r0 to strongly increase both with increasing line luminosity and redshift. By taking into account the evolution of the characteristic line luminosity, L⋆(z), and using our model predictions of halo mass given r0, we find a strong, redshift-independent increasing trend between L/L⋆(z) and minimum halo mass. The faintest H β + [O III] emitters are found to reside in 109.5 M⊙ haloes and the brightest emitters in 1013.0 M⊙ haloes. For [O II] emitters, the faintest emitters are found in 1010.5 M⊙ haloes and the brightest emitters in 1012.6 M⊙ haloes. A redshift-independent stellar mass dependency is also observed where the halo mass increases from 1011 to 1012.5 M⊙ for stellar masses of 108.5 to 1011.5 M⊙, respectively. We investigate the interdependencies of these trends by repeating our analysis in a Lline−Mstar grid space for our most populated samples (H β + [O III] z = 0.84 and [O II] z = 1.47) and find that the line luminosity dependency is stronger than the stellar mass dependency on halo mass. For L > L⋆ emitters at all epochs, we find a relatively flat trend with halo masses of 1012.5–13 M⊙, which may be due to quenching mechanisms in massive haloes that is consistent with a transitional halo mass predicted by models."}],"issue":"3","type":"journal_article","oa_version":"Published Version","_id":"11549","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass","status":"public","intvolume":" 478","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: haloes","galaxies: high-redshift","galaxies: star formation","cosmology: observations","large-scale structure of Universe"],"date_published":"2018-08-01T00:00:00Z","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"chicago":"Khostovan, A A, D Sobral, B Mobasher, P N Best, I Smail, Jorryt J Matthee, B Darvish, H Nayyeri, S Hemmati, and J P Stott. “The Clustering of H β + [O III] and [O II] Emitters since z ∼ 5: Dependencies with Line Luminosity and Stellar Mass.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty925.","mla":"Khostovan, A. A., et al. “The Clustering of H β + [O III] and [O II] Emitters since z ∼ 5: Dependencies with Line Luminosity and Stellar Mass.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 3, Oxford University Press, 2018, pp. 2999–3015, doi:10.1093/mnras/sty925.","short":"A.A. Khostovan, D. Sobral, B. Mobasher, P.N. Best, I. Smail, J.J. Matthee, B. Darvish, H. Nayyeri, S. Hemmati, J.P. Stott, Monthly Notices of the Royal Astronomical Society 478 (2018) 2999–3015.","ista":"Khostovan AA, Sobral D, Mobasher B, Best PN, Smail I, Matthee JJ, Darvish B, Nayyeri H, Hemmati S, Stott JP. 2018. The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. 478(3), 2999–3015.","ieee":"A. A. Khostovan et al., “The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 3. Oxford University Press, pp. 2999–3015, 2018.","apa":"Khostovan, A. A., Sobral, D., Mobasher, B., Best, P. N., Smail, I., Matthee, J. J., … Stott, J. P. (2018). The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty925","ama":"Khostovan AA, Sobral D, Mobasher B, et al. The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. 2018;478(3):2999-3015. doi:10.1093/mnras/sty925"},"article_type":"original","page":"2999-3015","extern":"1","author":[{"full_name":"Khostovan, A A","first_name":"A A","last_name":"Khostovan"},{"last_name":"Sobral","first_name":"D","full_name":"Sobral, D"},{"last_name":"Mobasher","first_name":"B","full_name":"Mobasher, B"},{"full_name":"Best, P N","first_name":"P N","last_name":"Best"},{"last_name":"Smail","first_name":"I","full_name":"Smail, I"},{"last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"full_name":"Darvish, B","first_name":"B","last_name":"Darvish"},{"last_name":"Nayyeri","first_name":"H","full_name":"Nayyeri, H"},{"full_name":"Hemmati, S","first_name":"S","last_name":"Hemmati"},{"last_name":"Stott","first_name":"J P","full_name":"Stott, J P"}],"date_updated":"2022-08-19T06:53:39Z","date_created":"2022-07-08T11:48:48Z","volume":478,"acknowledgement":"We thank the anonymous referee for their useful comments and suggestions that improved this study. AAK thanks Anahita Alavi and Irene Shivaei for useful discussion in the making of this paper. AAK acknowledges that this work was supported by NASA Headquarters under the NASA Earth and Space Science Fellowship Program – Grant NNX16AO92H. DS acknowledges financial support from the Netherlands Organization for Scientific Research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. PNB is grateful for support from STFC via grant STM001229/1. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Grant DUSTYGAL (321334), and a Royal Society/Wolfson Merit award. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G.","year":"2018","publication_status":"published","publisher":"Oxford University Press","month":"08","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"doi":"10.1093/mnras/sty925","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1705.01101"}],"external_id":{"arxiv":["1705.01101"]},"quality_controlled":"1"},{"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1802.10102"]},"main_file_link":[{"url":"https://arxiv.org/abs/1802.10102","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1093/mnras/sty782","month":"06","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","publisher":"Oxford University Press","acknowledgement":"We thank the anonymous reviewer for their timely and constructive comments that greatly helped us to improve the manuscript. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science Foundation, grant number 1716907. IRS acknowledges support from the ERC Advanced Grant DUSTYGAL (321334), STFC (ST/P000541/1), and a Royal Society/Wolfson Merit Award. PNB is grateful for support from STFC via grant ST/M001229/1. We thank Anne Verhamme, Kimihiko Nakajima, Ryan Trainor, Sangeeta Malhotra, Max Gronke, James Rhoads, Fang Xia An, Matthew Hayes, Takashi Kojima, Mark Dijkstra, and Anne Jaskot for many helpful and engaging discussions, particularly during the SnowCLAW Ly α workshop. We thank Bruno Ribeiro, Stephane Charlot, and Joseph Caruana for comments on the manuscript. The authors would also like to thank Ingrid Tengs, Meg Singleton, Ali Khostovan, and Sara Perez for participating in part of the observations. We also thank Joao Calhau, Leah Morabito, Sergio Santos, and Aayush Saxena for their assistance with the narrow-band observations which allowed to select some of the sour ces. Based on observations obtained with the William Herschel Telescope, program: W16AN004; the Very Large Telescope, programs: 098.A-0819 & 099.A-0254; and the Keck II telescope, program: C267D. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 294.A-5039, 092.A-0786, 093.A-0561, 097.A-0943, 098.A-0819, 099.A-0254 and 179.A-2005. The authors acknowledge the award of service time (SW2014b20) on the WHT. WHT and its service programme are operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. The authors would also like to thank all the extremely helpful observatory staff that have greatly contributed towards our observations, particularly Fiona Riddick, Lilian Dominguez, Florencia Jimenez, and Ian Skillen. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY & SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2013). This research has made use of the VizieR catalogue access tool, CDS, Strasbourg, France.","year":"2018","date_created":"2022-07-12T07:18:02Z","date_updated":"2022-08-19T07:01:08Z","volume":477,"author":[{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee"},{"last_name":"Darvish","first_name":"Behnam","full_name":"Darvish, Behnam"},{"full_name":"Smail, Ian","first_name":"Ian","last_name":"Smail"},{"last_name":"Best","first_name":"Philip N","full_name":"Best, Philip N"},{"full_name":"Alegre, Lara","first_name":"Lara","last_name":"Alegre"},{"full_name":"Röttgering, Huub","first_name":"Huub","last_name":"Röttgering"},{"last_name":"Mobasher","first_name":"Bahram","full_name":"Mobasher, Bahram"},{"full_name":"Paulino-Afonso, Ana","last_name":"Paulino-Afonso","first_name":"Ana"},{"full_name":"Stroe, Andra","first_name":"Andra","last_name":"Stroe"},{"full_name":"Oteo, Iván","first_name":"Iván","last_name":"Oteo"}],"extern":"1","article_type":"original","page":"2817-2840","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"mla":"Sobral, David, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2, Oxford University Press, 2018, pp. 2817–40, doi:10.1093/mnras/sty782.","short":"D. Sobral, J.J. Matthee, B. Darvish, I. Smail, P.N. Best, L. Alegre, H. Röttgering, B. Mobasher, A. Paulino-Afonso, A. Stroe, I. Oteo, Monthly Notices of the Royal Astronomical Society 477 (2018) 2817–2840.","chicago":"Sobral, David, Jorryt J Matthee, Behnam Darvish, Ian Smail, Philip N Best, Lara Alegre, Huub Röttgering, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty782.","ama":"Sobral D, Matthee JJ, Darvish B, et al. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 2018;477(2):2817-2840. doi:10.1093/mnras/sty782","ista":"Sobral D, Matthee JJ, Darvish B, Smail I, Best PN, Alegre L, Röttgering H, Mobasher B, Paulino-Afonso A, Stroe A, Oteo I. 2018. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 477(2), 2817–2840.","apa":"Sobral, D., Matthee, J. J., Darvish, B., Smail, I., Best, P. N., Alegre, L., … Oteo, I. (2018). The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty782","ieee":"D. Sobral et al., “The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN,” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2. Oxford University Press, pp. 2817–2840, 2018."},"date_published":"2018-06-01T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","galaxies: starburst","cosmology: observations"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN","intvolume":" 477","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11557","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Deep narrow-band surveys have revealed a large population of faint Ly α emitters (LAEs) in the distant Universe, but relatively little is known about the most luminous sources (LLyα≳1042.7 erg s−1; LLyα≳L∗Lyα). Here we present the spectroscopic follow-up of 21 luminous LAEs at z ∼ 2–3 found with panoramic narrow-band surveys over five independent extragalactic fields (≈4 × 106 Mpc3 surveyed at z ∼ 2.2 and z ∼ 3.1). We use WHT/ISIS, Keck/DEIMOS, and VLT/X-SHOOTER to study these sources using high ionization UV lines. Luminous LAEs at z ∼ 2–3 have blue UV slopes (β=−2.0+0.3−0.1) and high Ly α escape fractions (50+20−15 per cent) and span five orders of magnitude in UV luminosity (MUV ≈ −19 to −24). Many (70 per cent) show at least one high ionization rest-frame UV line such as C IV, N V, C III], He II or O III], typically blue-shifted by ≈100–200 km s−1 relative to Ly α. Their Ly α profiles reveal a wide variety of shapes, including significant blue-shifted components and widths from 200 to 4000 km s−1. Overall, 60 ± 11 per cent appear to be active galactic nucleus (AGN) dominated, and at LLyα > 1043.3 erg s−1 and/or MUV < −21.5 virtually all LAEs are AGNs with high ionization parameters (log U = 0.6 ± 0.5) and with metallicities of ≈0.5 − 1 Z⊙. Those lacking signatures of AGNs (40 ± 11 per cent) have lower ionization parameters (logU=−3.0+1.6−0.9 and log ξion = 25.4 ± 0.2) and are apparently metal-poor sources likely powered by young, dust-poor ‘maximal’ starbursts. Our results show that luminous LAEs at z ∼ 2–3 are a diverse population and that 2×L∗Lyα and 2×M∗UV mark a sharp transition in the nature of LAEs, from star formation dominated to AGN dominated."}],"issue":"2"},{"oa_version":"Preprint","_id":"11558","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6","intvolume":" 476","abstract":[{"lang":"eng","text":"We present and explore deep narrow- and medium-band data obtained with the Subaru and the Isaac Newton Telescopes in the ∼2 deg2 COSMOS field. We use these data as an extremely wide, low-resolution (R ∼ 20–80) Integral Field Unit survey to slice through the COSMOS field and obtain a large sample of ∼4000 Ly α emitters (LAEs) from z ∼ 2 to 6 in 16 redshift slices (SC4K). We present new Ly α luminosity functions (LFs) covering a comoving volume of ∼108 Mpc3. SC4K extensively complements ultradeep surveys, jointly covering over 4 dex in Ly α luminosity and revealing a global (2.5 < z < 6) synergy LF with α=−1.93+0.12−0.12, log10Φ∗Lyα=−3.45+0.22−0.29 Mpc−3, and log10L∗Lyα=42.93+0.15−0.11 erg s−1. The Schechter component of the Ly α LF reveals a factor ∼5 rise in L∗Lyα and a ∼7 × decline in Φ∗Lyα from z ∼ 2 to 6. The data reveal an extra power-law (or Schechter) component above LLy α ≈ 1043.3 erg s−1 at z ∼ 2.2–3.5 and we show that it is partially driven by X-ray and radio active galactic nucleus (AGN), as their Ly α LF resembles the excess. The power-law component vanishes and/or is below our detection limits above z > 3.5, likely linked with the evolution of the AGN population. The Ly α luminosity density rises by a factor ∼2 from z ∼ 2 to 3 but is then found to be roughly constant (1.1+0.2−0.2×1040 erg s−1 Mpc−3) to z ∼ 6, despite the ∼0.7 dex drop in ultraviolet (UV) luminosity density. The Ly α/UV luminosity density ratio rises from 4 ± 1 per cent to 30 ± 6 per cent from z ∼ 2.2 to 6. Our results imply a rise of a factor of ≈2 in the global ionization efficiency (ξion) and a factor ≈4 ± 1 in the Ly α escape fraction from z ∼ 2 to 6, hinting for evolution in both the typical burstiness/stellar populations and even more so in the typical interstellar medium conditions allowing Ly α photons to escape."}],"issue":"4","type":"journal_article","date_published":"2018-06-01T00:00:00Z","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"ama":"Sobral D, Santos S, Matthee JJ, et al. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 2018;476(4):4725-4752. doi:10.1093/mnras/sty378","ista":"Sobral D, Santos S, Matthee JJ, Paulino-Afonso A, Ribeiro B, Calhau J, Khostovan AA. 2018. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 476(4), 4725–4752.","ieee":"D. Sobral et al., “Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6,” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4. Oxford University Press, pp. 4725–4752, 2018.","apa":"Sobral, D., Santos, S., Matthee, J. J., Paulino-Afonso, A., Ribeiro, B., Calhau, J., & Khostovan, A. A. (2018). Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty378","mla":"Sobral, David, et al. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4, Oxford University Press, 2018, pp. 4725–52, doi:10.1093/mnras/sty378.","short":"D. Sobral, S. Santos, J.J. Matthee, A. Paulino-Afonso, B. Ribeiro, J. Calhau, A.A. Khostovan, Monthly Notices of the Royal Astronomical Society 476 (2018) 4725–4752.","chicago":"Sobral, David, Sérgio Santos, Jorryt J Matthee, Ana Paulino-Afonso, Bruno Ribeiro, João Calhau, and Ali A Khostovan. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty378."},"article_type":"original","page":"4725-4752","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: formation","galaxies: high-redshift","galaxies: luminosity function","mass function","galaxies: statistics"],"author":[{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"last_name":"Santos","first_name":"Sérgio","full_name":"Santos, Sérgio"},{"full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Paulino-Afonso, Ana","first_name":"Ana","last_name":"Paulino-Afonso"},{"full_name":"Ribeiro, Bruno","last_name":"Ribeiro","first_name":"Bruno"},{"full_name":"Calhau, João","first_name":"João","last_name":"Calhau"},{"first_name":"Ali A","last_name":"Khostovan","full_name":"Khostovan, Ali A"}],"date_updated":"2022-08-19T07:04:45Z","date_created":"2022-07-12T10:41:08Z","volume":476,"year":"2018","acknowledgement":"We thank the anonymous referee for their constructive comments that helped us improve the manuscript. DS acknowledges the hospitality of the IAC and a Severo Ochoa visiting grant. SS and JC acknowledge studentships from the Lancaster University. JM acknowledges a Huygens PhD fellowship from Leiden University. APA acknowledges financial support from the Science and Technology Foundation (FCT, Portugal) through research grants UID/FIS/04434/2013 and fellowship PD/BD/52706/2014. The authors thank Alyssa Drake, Kimihiko Nakajima, Yuichi Harikane, Max Gronke, Irene Shivaei, Helmut Dannerbauer, Huub Rottgering, ¨ Marius Eide, and Masami Ouchi for many engaging and stimulating discussions. We also thank Sara Perez, Alex Bennett, and Tom Rose for their involvement in the early stages of this project. Based on data products from observations made with European Southern Observatory (ESO) Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 097.A 0943,\r\n098.A-0819, 099.A-0254, and 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. Based on observations using the WFC on the 2.5 m INT, as part of programmes 2013AN002, 2013BN008, 2014AC88, 2014AN002, 2014BN006, 2014BC118, and 2016AN001. The INT is operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. This work is based in part on data products produced at TERAPIX available at the Canadian Astronomy Data Centre as part of the Canada–France– Hawaii Telescope Legacy Survey (CFHTLS), a collaborative project of NRC and CNRS.\r\nWe are grateful to the CFHTLS, COSMOS-UltraVISTA, and COSMOS survey teams. We are also unmeasurably thankful to the pioneering and continuous work from previous Ly α surveys’ teams. Without these previous Ly α and the wider reach legacy surveys, this research would have been impossible. We also thank the VUDS team for making available spectroscopic redshifts from data obtained with VIMOS at the European Southern Observatory Very Large Telescope, Paranal, Chile, under Large Programme 185.A-0791. Finally, the authors acknowledge the unique value of the publicly available programming language PYTHON, including the NUMPY and SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2005). We publicly release a catalogue with all LAEs used in this paper (SC4K), so it can be freely explored by the community (see five example entries in Table A1).","publication_status":"published","publisher":"Oxford University Press","extern":"1","doi":"10.1093/mnras/sty378","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1712.04451","open_access":"1"}],"external_id":{"arxiv":["1712.04451"]},"quality_controlled":"1","month":"06","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]}},{"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1093/mnras/sty1088","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1712.03985"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.03985"}],"extern":"1","volume":478,"date_updated":"2022-08-19T06:58:06Z","date_created":"2022-07-11T08:05:42Z","author":[{"first_name":"S","last_name":"Carniani","full_name":"Carniani, S"},{"last_name":"Maiolino","first_name":"R","full_name":"Maiolino, R"},{"full_name":"Amorin, R","last_name":"Amorin","first_name":"R"},{"last_name":"Pentericci","first_name":"L","full_name":"Pentericci, L"},{"last_name":"Pallottini","first_name":"A","full_name":"Pallottini, A"},{"last_name":"Ferrara","first_name":"A","full_name":"Ferrara, A"},{"full_name":"Willott, C J","first_name":"C J","last_name":"Willott"},{"last_name":"Smit","first_name":"R","full_name":"Smit, R"},{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"first_name":"D","last_name":"Sobral","full_name":"Sobral, D"},{"last_name":"Santini","first_name":"P","full_name":"Santini, P"},{"last_name":"Castellano","first_name":"M","full_name":"Castellano, M"},{"full_name":"De Barros, S","last_name":"De Barros","first_name":"S"},{"last_name":"Fontana","first_name":"A","full_name":"Fontana, A"},{"last_name":"Grazian","first_name":"A","full_name":"Grazian, A"},{"last_name":"Guaita","first_name":"L","full_name":"Guaita, L"}],"publisher":"Oxford University Press","publication_status":"published","year":"2018","acknowledgement":"This paper makes use of the following ALMA data:\r\nADS/JAO.ALMA#2012.1.00719.S, ADS/JAO.ALMA#2012.A.00040.S,\r\nADS/JAO.ALMA#2013.A.00433.S, ADS/JAO.ALMA#2011.0.00115.S,\r\nADS/JAO.ALMA#2012.1.00033.S, ADS/JAO.ALMA#2012.1.00523.S,\r\nADS/JAO.ALMA#2013.1.00815.S, ADS/JAO.ALMA#2015.1.00834.S.,\r\nADS/JAO.ALMA#2015.1.01105.S, AND ADS/JAO.ALMA#2016.1.01240.S\r\nwhich can be retrieved from the ALMA data archive:\r\nhttps://almascience.eso.org/ alma-data/archive. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. We are grateful to G. Jones to for providing his [C II] flux maps. RM and SC acknowledge support by the Science and Technology Facilities Council (STFC). RM acknowledges ERC Advanced Grant 695671 ‘QUENCH’. AF acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120.","article_processing_charge":"No","day":"01","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","galaxies: formation"],"scopus_import":"1","date_published":"2018-07-01T00:00:00Z","page":"1170-1184","article_type":"original","citation":{"ista":"Carniani S, Maiolino R, Amorin R, Pentericci L, Pallottini A, Ferrara A, Willott CJ, Smit R, Matthee JJ, Sobral D, Santini P, Castellano M, De Barros S, Fontana A, Grazian A, Guaita L. 2018. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 478(1), 1170–1184.","ieee":"S. Carniani et al., “Kiloparsec-scale gaseous clumps and star formation at z = 5–7,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1. Oxford University Press, pp. 1170–1184, 2018.","apa":"Carniani, S., Maiolino, R., Amorin, R., Pentericci, L., Pallottini, A., Ferrara, A., … Guaita, L. (2018). Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty1088","ama":"Carniani S, Maiolino R, Amorin R, et al. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 2018;478(1):1170-1184. doi:10.1093/mnras/sty1088","chicago":"Carniani, S, R Maiolino, R Amorin, L Pentericci, A Pallottini, A Ferrara, C J Willott, et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty1088.","mla":"Carniani, S., et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1, Oxford University Press, 2018, pp. 1170–84, doi:10.1093/mnras/sty1088.","short":"S. Carniani, R. Maiolino, R. Amorin, L. Pentericci, A. Pallottini, A. Ferrara, C.J. Willott, R. Smit, J.J. Matthee, D. Sobral, P. Santini, M. Castellano, S. De Barros, A. Fontana, A. Grazian, L. Guaita, Monthly Notices of the Royal Astronomical Society 478 (2018) 1170–1184."},"publication":"Monthly Notices of the Royal Astronomical Society","issue":"1","abstract":[{"text":"We investigate the morphology of the [C II] emission in a sample of ‘normal’ star-forming galaxies at 5 < z < 7.2 in relation to their UV (rest-frame) counterpart. We use new Atacama Large Millimetre/submillimetre Array (ALMA) observations of galaxies at z ∼ 6–7, as well as a careful re-analysis of archival ALMA data. In total 29 galaxies were analysed, 21 of which are detected in [C II]. For several of the latter the [C II] emission breaks into multiple components. Only a fraction of these [C II] components, if any, is associated with the primary UV systems, while the bulk of the [C II] emission is associated either with fainter UV components, or not associated with any UV counterpart at the current limits. By taking into account the presence of all these components, we find that the L[CII]–SFR (star formation rate) relation at early epochs is fully consistent with the local relation, but it has a dispersion of 0.48 ± 0.07 dex, which is about two times larger than observed locally. We also find that the deviation from the local L[CII]–SFR relation has a weak anticorrelation with the EW(Ly α). The morphological analysis also reveals that [C II] emission is generally much more extended than the UV emission. As a consequence, these primordial galaxies are characterized by a [C II] surface brightness generally much lower than expected from the local Σ[CII]−ΣSFR relation. These properties are likely a consequence of a combination of different effects, namely gas metallicity, [C II] emission from obscured star-forming regions, strong variations of the ionization parameter, and circumgalactic gas in accretion or ejected by these primeval galaxies.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 478","status":"public","title":"Kiloparsec-scale gaseous clumps and star formation at z = 5–7","_id":"11555","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"text":"Observations show that star-forming galaxies reside on a tight 3D plane between mass, gas-phase metallicity, and star formation rate (SFR), which can be explained by the interplay between metal-poor gas inflows, SFR and outflows. However, different metals are released on different time-scales, which may affect the slope of this relation. Here, we use central, star-forming galaxies with Mstar = 109.0–10.5 M⊙ from the EAGLE hydrodynamical simulation to examine 3D relations between mass, SFR, and chemical enrichment using absolute and relative C, N, O, and Fe abundances. We show that the scatter is smaller when gas-phase α-enhancement is used rather than metallicity. A similar plane also exists for stellar α-enhancement, implying that present-day specific SFRs are correlated with long time-scale star formation histories. Between z = 0 and 1, the α-enhancement plane is even more insensitive to redshift than the plane using metallicity. However, it evolves at z > 1 due to lagging iron yields. At fixed mass, galaxies with higher SFRs have star formation histories shifted towards late times, are more α-enhanced, and this α-enhancement increases with redshift as observed. These findings suggest that relations between physical properties inferred from observations may be affected by systematic variations in α-enhancements.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Preprint","status":"public","title":"Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement","intvolume":" 479","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11584","day":"01","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: abundances","galaxies: evolution","galaxies: formation","galaxies: star formation"],"scopus_import":"1","date_published":"2018-09-01T00:00:00Z","article_type":"original","page":"L34 - L39","publication":"Monthly Notices of the Royal Astronomical Society: Letters","citation":{"ista":"Matthee JJ, Schaye J. 2018. Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. 479(1), L34–L39.","apa":"Matthee, J. J., & Schaye, J. (2018). Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. Oxford University Press. https://doi.org/10.1093/mnrasl/sly093","ieee":"J. J. Matthee and J. Schaye, “Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement,” Monthly Notices of the Royal Astronomical Society: Letters, vol. 479, no. 1. Oxford University Press, pp. L34–L39, 2018.","ama":"Matthee JJ, Schaye J. Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. 2018;479(1):L34-L39. doi:10.1093/mnrasl/sly093","chicago":"Matthee, Jorryt J, and Joop Schaye. “Star-Forming Galaxies Are Predicted to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.” Monthly Notices of the Royal Astronomical Society: Letters. Oxford University Press, 2018. https://doi.org/10.1093/mnrasl/sly093.","mla":"Matthee, Jorryt J., and Joop Schaye. “Star-Forming Galaxies Are Predicted to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.” Monthly Notices of the Royal Astronomical Society: Letters, vol. 479, no. 1, Oxford University Press, 2018, pp. L34–39, doi:10.1093/mnrasl/sly093.","short":"J.J. Matthee, J. Schaye, Monthly Notices of the Royal Astronomical Society: Letters 479 (2018) L34–L39."},"extern":"1","date_updated":"2022-08-19T08:35:45Z","date_created":"2022-07-14T12:49:47Z","volume":479,"author":[{"last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"last_name":"Schaye","first_name":"Joop","full_name":"Schaye, Joop"}],"publication_status":"published","publisher":"Oxford University Press","acknowledgement":"We thank the anonymous referee for their constructive comments. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Jarle Brinchmann, Rob Crain and David Sobral for discussions. We acknowledge the use of the TOPCAT software (Taylor 2013) for assisting in rapid exploration of multidimensional data sets and the use of PYTHON and its NUMPY, MATPLOTLIB, and PANDAS packages.","year":"2018","month":"09","publication_identifier":{"eissn":["1745-3933"],"issn":["1745-3925"]},"language":[{"iso":"eng"}],"doi":"10.1093/mnrasl/sly093","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.06786","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1802.06786"]}}]