[{"ddc":["000"],"date_updated":"2021-01-12T08:19:55Z","file_date_updated":"2020-09-21T13:57:34Z","department":[{"_id":"KrCh"}],"_id":"8533","status":"public","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"conference":{"start_date":"2020-08-24","end_date":"2020-08-28","location":"Prague, Czech Republic","name":"MFCS: Symposium on Mathematical Foundations of Computer Science"},"type":"conference","language":[{"iso":"eng"}],"file":[{"file_size":491374,"date_updated":"2020-09-21T13:57:34Z","creator":"dernst","file_name":"2020_LIPIcs_Chatterjee.pdf","date_created":"2020-09-21T13:57:34Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8550","checksum":"bbd7c4f55d45f2ff2a0a4ef0e10a77b1"}],"publication_status":"published","publication_identifier":{"isbn":["9783959771597"],"issn":["18688969"]},"ec_funded":1,"volume":170,"oa_version":"Published Version","abstract":[{"text":"Game of Life is a simple and elegant model to study dynamical system over networks. The model consists of a graph where every vertex has one of two types, namely, dead or alive. A configuration is a mapping of the vertices to the types. An update rule describes how the type of a vertex is updated given the types of its neighbors. In every round, all vertices are updated synchronously, which leads to a configuration update. While in general, Game of Life allows a broad range of update rules, we focus on two simple families of update rules, namely, underpopulation and overpopulation, that model several interesting dynamics studied in the literature. In both settings, a dead vertex requires at least a desired number of live neighbors to become alive. For underpopulation (resp., overpopulation), a live vertex requires at least (resp. at most) a desired number of live neighbors to remain alive. We study the basic computation problems, e.g., configuration reachability, for these two families of rules. For underpopulation rules, we show that these problems can be solved in polynomial time, whereas for overpopulation rules they are PSPACE-complete.","lang":"eng"}],"intvolume":" 170","month":"08","scopus_import":"1","alternative_title":["LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. “Simplified Game of Life: Algorithms and Complexity.” 45th International Symposium on Mathematical Foundations of Computer Science, vol. 170, 22:1-22:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.MFCS.2020.22.","ieee":"K. Chatterjee, R. Ibsen-Jensen, I. R. Jecker, and J. Svoboda, “Simplified game of life: Algorithms and complexity,” in 45th International Symposium on Mathematical Foundations of Computer Science, Prague, Czech Republic, 2020, vol. 170.","short":"K. Chatterjee, R. Ibsen-Jensen, I.R. Jecker, J. Svoboda, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ama":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. Simplified game of life: Algorithms and complexity. In: 45th International Symposium on Mathematical Foundations of Computer Science. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.MFCS.2020.22","apa":"Chatterjee, K., Ibsen-Jensen, R., Jecker, I. R., & Svoboda, J. (2020). Simplified game of life: Algorithms and complexity. In 45th International Symposium on Mathematical Foundations of Computer Science (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2020.22","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Ismael R Jecker, and Jakub Svoboda. “Simplified Game of Life: Algorithms and Complexity.” In 45th International Symposium on Mathematical Foundations of Computer Science, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.MFCS.2020.22.","ista":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. 2020. Simplified game of life: Algorithms and complexity. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 22:1-22:13."},"title":"Simplified game of life: Algorithms and complexity","article_processing_charge":"No","external_id":{"arxiv":["2007.02894"]},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen"},{"id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","first_name":"Ismael R","full_name":"Jecker, Ismael R","last_name":"Jecker"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda","full_name":"Svoboda, Jakub"}],"article_number":"22:1-22:13","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"publication":"45th International Symposium on Mathematical Foundations of Computer Science","day":"18","year":"2020","has_accepted_license":"1","date_created":"2020-09-20T22:01:36Z","date_published":"2020-08-18T00:00:00Z","doi":"10.4230/LIPIcs.MFCS.2020.22","acknowledgement":"Krishnendu Chatterjee: The research was partially supported by the Vienna Science and\r\nTechnology Fund (WWTF) Project ICT15-003.\r\nIsmaël Jecker: This project has received funding from the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1"},{"status":"public","conference":{"start_date":"2020-08-24","end_date":"2020-08-28","location":"Prague, Czech Republic","name":"MFCS: Symposium on Mathematical Foundations of Computer Science"},"tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"type":"conference","_id":"8534","department":[{"_id":"KrCh"}],"file_date_updated":"2020-09-21T14:17:08Z","ddc":["000"],"date_updated":"2021-01-12T08:19:56Z","intvolume":" 170","month":"08","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"A regular language L of finite words is composite if there are regular languages L₁,L₂,…,L_t such that L = ⋂_{i = 1}^t L_i and the index (number of states in a minimal DFA) of every language L_i is strictly smaller than the index of L. Otherwise, L is prime. Primality of regular languages was introduced and studied in [O. Kupferman and J. Mosheiff, 2015], where the complexity of deciding the primality of the language of a given DFA was left open, with a doubly-exponential gap between the upper and lower bounds. We study primality for unary regular languages, namely regular languages with a singleton alphabet. A unary language corresponds to a subset of ℕ, making the study of unary prime languages closer to that of primality in number theory. We show that the setting of languages is richer. In particular, while every composite number is the product of two smaller numbers, the number t of languages necessary to decompose a composite unary language induces a strict hierarchy. In addition, a primality witness for a unary language L, namely a word that is not in L but is in all products of languages that contain L and have an index smaller than L’s, may be of exponential length. Still, we are able to characterize compositionality by structural properties of a DFA for L, leading to a LogSpace algorithm for primality checking of unary DFAs.","lang":"eng"}],"ec_funded":1,"volume":170,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8552","checksum":"2dc9e2fad6becd4563aef3e27a473f70","file_size":597977,"date_updated":"2020-09-21T14:17:08Z","creator":"dernst","file_name":"2020_LIPIcsMFCS_Jecker.pdf","date_created":"2020-09-21T14:17:08Z"}],"publication_status":"published","publication_identifier":{"isbn":["9783959771597"],"issn":["18688969"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"51:1-51:12","title":"Unary prime languages","article_processing_charge":"No","author":[{"first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R","last_name":"Jecker"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"},{"last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas","first_name":"Nicolas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jecker, Ismael R., et al. “Unary Prime Languages.” 45th International Symposium on Mathematical Foundations of Computer Science, vol. 170, 51:1-51:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.MFCS.2020.51.","apa":"Jecker, I. R., Kupferman, O., & Mazzocchi, N. (2020). Unary prime languages. In 45th International Symposium on Mathematical Foundations of Computer Science (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2020.51","ama":"Jecker IR, Kupferman O, Mazzocchi N. Unary prime languages. In: 45th International Symposium on Mathematical Foundations of Computer Science. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.MFCS.2020.51","ieee":"I. R. Jecker, O. Kupferman, and N. Mazzocchi, “Unary prime languages,” in 45th International Symposium on Mathematical Foundations of Computer Science, Prague, Czech Republic, 2020, vol. 170.","short":"I.R. Jecker, O. Kupferman, N. Mazzocchi, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","chicago":"Jecker, Ismael R, Orna Kupferman, and Nicolas Mazzocchi. “Unary Prime Languages.” In 45th International Symposium on Mathematical Foundations of Computer Science, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.MFCS.2020.51.","ista":"Jecker IR, Kupferman O, Mazzocchi N. 2020. Unary prime languages. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 51:1-51:12."},"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","acknowledgement":"Ismaël Jecker: This project has received funding from the European Union’s Horizon\r\n2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No.\r\n754411. Nicolas Mazzocchi: PhD fellowship FRIA from the F.R.S.-FNRS.","date_created":"2020-09-20T22:01:36Z","date_published":"2020-08-18T00:00:00Z","doi":"10.4230/LIPIcs.MFCS.2020.51","publication":"45th International Symposium on Mathematical Foundations of Computer Science","day":"18","year":"2020","has_accepted_license":"1"},{"publication_identifier":{"eissn":["2199-6768"],"issn":["2199-675X"]},"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"We prove some recent experimental observations of Dan Reznik concerning periodic billiard orbits in ellipses. For example, the sum of cosines of the angles of a periodic billiard polygon remains constant in the 1-parameter family of such polygons (that exist due to the Poncelet porism). In our proofs, we use geometric and complex analytic methods.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2001.02934"}],"month":"09","date_updated":"2021-12-02T15:10:17Z","department":[{"_id":"HeEd"}],"_id":"8538","type":"journal_article","article_type":"original","status":"public","year":"2020","day":"09","publication":"European Journal of Mathematics","doi":"10.1007/s40879-020-00426-9","date_published":"2020-09-09T00:00:00Z","date_created":"2020-09-20T22:01:38Z","acknowledgement":" This paper would not be written if not for Dan Reznik’s curiosity and persistence; we are very grateful to him. We also thank R. Garcia and J. Koiller for interesting discussions. It is a pleasure to thank the Mathematical Institute of the University of Heidelberg for its stimulating atmosphere. ST thanks M. Bialy for interesting discussions and the Tel Aviv\r\nUniversity for its invariable hospitality. AA was supported by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). RS is supported by NSF Grant DMS-1807320. ST was supported by NSF grant DMS-1510055 and SFB/TRR 191.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"ieee":"A. Akopyan, R. Schwartz, and S. Tabachnikov, “Billiards in ellipses revisited,” European Journal of Mathematics. Springer Nature, 2020.","short":"A. Akopyan, R. Schwartz, S. Tabachnikov, European Journal of Mathematics (2020).","apa":"Akopyan, A., Schwartz, R., & Tabachnikov, S. (2020). Billiards in ellipses revisited. European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-020-00426-9","ama":"Akopyan A, Schwartz R, Tabachnikov S. Billiards in ellipses revisited. European Journal of Mathematics. 2020. doi:10.1007/s40879-020-00426-9","mla":"Akopyan, Arseniy, et al. “Billiards in Ellipses Revisited.” European Journal of Mathematics, Springer Nature, 2020, doi:10.1007/s40879-020-00426-9.","ista":"Akopyan A, Schwartz R, Tabachnikov S. 2020. Billiards in ellipses revisited. European Journal of Mathematics.","chicago":"Akopyan, Arseniy, Richard Schwartz, and Serge Tabachnikov. “Billiards in Ellipses Revisited.” European Journal of Mathematics. Springer Nature, 2020. https://doi.org/10.1007/s40879-020-00426-9."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Richard","last_name":"Schwartz","full_name":"Schwartz, Richard"},{"first_name":"Serge","last_name":"Tabachnikov","full_name":"Tabachnikov, Serge"}],"external_id":{"arxiv":["2001.02934"]},"article_processing_charge":"No","title":"Billiards in ellipses revisited","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"abstract":[{"text":"The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we reported that a substantial proportion of blood vessels in the adult brain sporadically occluded and regressed. Their regression proceeded through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels were found to be widespread in mouse, monkey and human brains. Both brief occlusions of the middle cerebral artery and lipopolysaccharide-mediated inflammation induced an increase of vessel regression. Blockage of leukocyte adhesion to endothelial cells alleviated LPS-induced vessel regression. We further revealed that blood vessel regression caused a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain.","lang":"eng"}],"acknowledgement":"The project was initiated in the Jan lab at UCSF. We thank Lily Jan and Yuh-Nung Jan’s generous support. We thank Liqun Luo’s lab for providing MADM-7 mice and Rolf A Brekken for VEGF-antibodies. Drs. Yuanquan Song (UPenn), Zhaozhu Hu (JHU), Ji Hu (ShanghaiTech), Yang Xiang (U. Mass), Hao Wang (Zhejiang U.) and Ruikang Wang (U. Washington) for critical input, colleagues at Children’s Research Institute, Departments of Neuroscience, Neurology and Neurotherapeutics, Pediatrics from UT Southwestern, and colleagues from the Jan lab for discussion. Dr. Bridget Samuels, Sean Morrison (UT Southwestern), and Nannan Lu (Zhejiang U.) for critical reading. We acknowledge the assistance of the CIBR Imaging core. We also thank UT Southwestern Live Cell Imaging Facility, a Shared Resource of the Harold C. Simmons Cancer Center, supported in part by an NCI Cancer Center Support Grant, P30 CA142543K. This work is supported by CIBR funds and the American Heart Association AWRP Summer 2016 Innovative Research Grant (17IRG33410377) to W-P.G.; National Natural Science Foundation of China (No.81370031) to Z.Z.;National Key Research and Development Program of China (2016YFE0125400)to F.H.;National Natural Science Foundations of China (No. 81473202) to Y.L.; National Natural Science Foundation of China (No.31600839) and Shenzhen Science and Technology Research Program (JCYJ20170818163320865) to B.P.; National Natural Science Foundation of China (No. 31800864) and Westlake University start-up funds to J-M. J. NIH R01NS088627 to W.L.J.; NIH: R01 AG020670 and RF1AG054111 to H.Z.; R01 NS088555 to A.M.S., and European Research Council No.725780 to S.H.;W-P.G. was a recipient of Bugher-American Heart Association Dan Adams Thinking Outside the Box Award.","oa_version":"Preprint","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.09.15.262782"}],"publisher":"Cold Spring Harbor Laboratory","month":"09","year":"2020","publication_status":"submitted","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"15","date_created":"2020-10-06T08:58:59Z","ec_funded":1,"date_published":"2020-09-15T00:00:00Z","doi":"10.1101/2020.09.15.262782","_id":"8616","type":"preprint","project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"status":"public","date_updated":"2021-01-12T08:20:19Z","citation":{"chicago":"Gao, Xiaofei, Jun-Liszt Li, Xingjun Chen, Bo Ci, Fei Chen, Nannan Lu, Bo Shen, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.09.15.262782.","ista":"Gao X, Li J-L, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J-M, Yi Y, Zhang S, Shi Y-C, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco DB, Lu Y, Yang S, Adams RH, Lindner V, Huang F, Wu L-J, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Su W, Bachoo RM, Ge W. Reduction of neuronal activity mediated by blood-vessel regression in the brain. bioRxiv, 10.1101/2020.09.15.262782.","mla":"Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.09.15.262782.","short":"X. Gao, J.-L. Li, X. Chen, B. Ci, F. Chen, N. Lu, B. Shen, L. Zheng, J.-M. Jia, Y. Yi, S. Zhang, Y.-C. Shi, K. Shi, N.E. Propson, Y. Huang, K. Poinsatte, Z. Zhang, Y. Yue, D.B. Bosco, Y. Lu, S. Yang, R.H. Adams, V. Lindner, F. Huang, L.-J. Wu, H. Zheng, F. Han, S. Hippenmeyer, A.M. Stowe, B. Peng, M. Margeta, X. Wang, Q. Liu, J. Körbelin, M. Trepel, H. Lu, B.O. Zhou, H. Zhao, W. Su, R.M. Bachoo, W. Ge, BioRxiv (n.d.).","ieee":"X. Gao et al., “Reduction of neuronal activity mediated by blood-vessel regression in the brain,” bioRxiv. Cold Spring Harbor Laboratory.","ama":"Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel regression in the brain. bioRxiv. doi:10.1101/2020.09.15.262782","apa":"Gao, X., Li, J.-L., Chen, X., Ci, B., Chen, F., Lu, N., … Ge, W. (n.d.). Reduction of neuronal activity mediated by blood-vessel regression in the brain. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.09.15.262782"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Gao, Xiaofei","last_name":"Gao","first_name":"Xiaofei"},{"first_name":"Jun-Liszt","last_name":"Li","full_name":"Li, Jun-Liszt"},{"last_name":"Chen","full_name":"Chen, Xingjun","first_name":"Xingjun"},{"first_name":"Bo","last_name":"Ci","full_name":"Ci, Bo"},{"first_name":"Fei","full_name":"Chen, Fei","last_name":"Chen"},{"first_name":"Nannan","full_name":"Lu, Nannan","last_name":"Lu"},{"first_name":"Bo","full_name":"Shen, Bo","last_name":"Shen"},{"full_name":"Zheng, Lijun","last_name":"Zheng","first_name":"Lijun"},{"first_name":"Jie-Min","last_name":"Jia","full_name":"Jia, Jie-Min"},{"first_name":"Yating","last_name":"Yi","full_name":"Yi, Yating"},{"full_name":"Zhang, Shiwen","last_name":"Zhang","first_name":"Shiwen"},{"full_name":"Shi, Ying-Chao","last_name":"Shi","first_name":"Ying-Chao"},{"first_name":"Kaibin","full_name":"Shi, Kaibin","last_name":"Shi"},{"full_name":"Propson, Nicholas E","last_name":"Propson","first_name":"Nicholas E"},{"last_name":"Huang","full_name":"Huang, Yubin","first_name":"Yubin"},{"last_name":"Poinsatte","full_name":"Poinsatte, Katherine","first_name":"Katherine"},{"last_name":"Zhang","full_name":"Zhang, Zhaohuan","first_name":"Zhaohuan"},{"first_name":"Yuanlei","last_name":"Yue","full_name":"Yue, Yuanlei"},{"full_name":"Bosco, Dale B","last_name":"Bosco","first_name":"Dale B"},{"first_name":"Ying-mei","full_name":"Lu, Ying-mei","last_name":"Lu"},{"first_name":"Shi-bing","full_name":"Yang, Shi-bing","last_name":"Yang"},{"last_name":"Adams","full_name":"Adams, Ralf H.","first_name":"Ralf H."},{"first_name":"Volkhard","last_name":"Lindner","full_name":"Lindner, Volkhard"},{"last_name":"Huang","full_name":"Huang, Fen","first_name":"Fen"},{"last_name":"Wu","full_name":"Wu, Long-Jun","first_name":"Long-Jun"},{"first_name":"Hui","last_name":"Zheng","full_name":"Zheng, Hui"},{"first_name":"Feng","full_name":"Han, Feng","last_name":"Han"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"first_name":"Ann M.","last_name":"Stowe","full_name":"Stowe, Ann M."},{"first_name":"Bo","last_name":"Peng","full_name":"Peng, Bo"},{"first_name":"Marta","full_name":"Margeta, Marta","last_name":"Margeta"},{"last_name":"Wang","full_name":"Wang, Xiaoqun","first_name":"Xiaoqun"},{"full_name":"Liu, Qiang","last_name":"Liu","first_name":"Qiang"},{"full_name":"Körbelin, Jakob","last_name":"Körbelin","first_name":"Jakob"},{"last_name":"Trepel","full_name":"Trepel, Martin","first_name":"Martin"},{"last_name":"Lu","full_name":"Lu, Hui","first_name":"Hui"},{"first_name":"Bo O.","last_name":"Zhou","full_name":"Zhou, Bo O."},{"last_name":"Zhao","full_name":"Zhao, Hu","first_name":"Hu"},{"last_name":"Su","full_name":"Su, Wenzhi","first_name":"Wenzhi"},{"full_name":"Bachoo, Robert M.","last_name":"Bachoo","first_name":"Robert M."},{"first_name":"Woo-ping","full_name":"Ge, Woo-ping","last_name":"Ge"}],"title":"Reduction of neuronal activity mediated by blood-vessel regression in the brain","department":[{"_id":"SiHi"}]},{"page":"36","date_published":"2020-10-21T00:00:00Z","doi":"10.5281/ZENODO.4109242","date_created":"2020-10-23T09:08:28Z","has_accepted_license":"1","publication_status":"published","year":"2020","file":[{"date_updated":"2020-10-23T09:29:45Z","file_size":2298363,"creator":"dernst","date_created":"2020-10-23T09:29:45Z","file_name":"2020_OANA_Mayer.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8696","checksum":"8eba912bb4b20b4f82f8010f2110461a","success":1}],"day":"21","language":[{"iso":"ger"}],"publisher":"OANA","oa":1,"month":"10","abstract":[{"text":"A look at international activities on Open Science reveals a broad spectrum from individual institutional policies to national action plans. The present Recommendations for a National Open Science Strategy in Austria are based on these international initiatives and present practical considerations for their coordinated implementation with regard to strategic developments in research, technology and innovation (RTI) in Austria until 2030. They are addressed to all relevant actors in the RTI system, in particular to Research Performing Organisations, Research Funding Organisations, Research Policy, memory institutions such as Libraries and Researchers. The recommendation paper was developed from 2018 to 2020 by the OANA working group \"Open Science Strategy\" and published for the first time in spring 2020 for a public consultation. The now available final version of the recommendation document, which contains feedback and comments from the consultation, is intended to provide an impetus for further discussion and implementation of Open Science in Austria and serves as a contribution and basis for a potential national Open Science Strategy in Austria. The document builds on the diverse expertise of the authors (academia, administration, library and archive, information technology, science policy, funding system, etc.) and reflects their personal experiences and opinions.","lang":"eng"},{"text":"Der Blick auf internationale Aktivitäten zu Open Science zeigt ein breites Spektrum von einzelnen institutionellen Policies bis hin zu nationalen Aktionsplänen. Die vorliegenden Empfehlungen für eine nationale Open Science Strategie in Österreich orientieren sich an diesen internationalen Initiativen und stellen praktische Überlegungen für ihre koordinierte Implementierung im Hinblick auf strategische Entwicklungen in Forschung, Technologie und Innovation (FTI) bis 2030 in Österreich dar. Dabei richten sie sich an alle relevanten Akteur*innen im FTI System, im Besonderen an Forschungsstätten, Forschungsförderer, Forschungspolitik, Gedächtnisinstitutionen wie Bibliotheken und Wissenschafter*innen. Das Empfehlungspapier wurde von 2018 bis 2020 von der OANA-Arbeitsgruppe \"Open Science Strategie\" entwickelt und im Frühling 2020 das erste Mal für eine öffentliche Konsultation veröffentlicht. Die nun vorliegende finale Version des Empfehlungsdokuments, die Feedback und Kommentare aus der Konsultation enthält, soll ein Anstoß für die weitere Diskussion und Umsetzung von Open Science in Österreich sein und als Beitrag und Grundlage einer potentiellen nationalen Open Science Strategie in Österreich dienen. Das Dokument baut auf der vielfältigen Expertise der Autor*innen auf (Wissenschaft, Administration, Bibliothek und Archiv, Informationstechnologie, Wissenschaftspolitik, Förderwesen etc.) und spiegelt deren persönliche Erfahrungen und Meinung wider.","lang":"ger"}],"oa_version":"Published Version","author":[{"first_name":"Katja","last_name":"Mayer","full_name":"Mayer, Katja"},{"first_name":"Katharina","last_name":"Rieck","full_name":"Rieck, Katharina"},{"full_name":"Reichmann, Stefan","last_name":"Reichmann","first_name":"Stefan"},{"last_name":"Danowski","full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick"},{"last_name":"Graschopf","full_name":"Graschopf, Anton","first_name":"Anton"},{"first_name":"Thomas","full_name":"König, Thomas","last_name":"König"},{"last_name":"Kraker","full_name":"Kraker, Peter","first_name":"Peter"},{"first_name":"Patrick","full_name":"Lehner, Patrick","last_name":"Lehner"},{"last_name":"Reckling","full_name":"Reckling, Falk","first_name":"Falk"},{"first_name":"Tony","last_name":"Ross-Hellauer","full_name":"Ross-Hellauer, Tony"},{"full_name":"Spichtinger, Daniel","last_name":"Spichtinger","first_name":"Daniel"},{"first_name":"Michalis","last_name":"Tzatzanis","full_name":"Tzatzanis, Michalis"},{"full_name":"Schürz, Stefanie","last_name":"Schürz","first_name":"Stefanie"}],"article_processing_charge":"No","file_date_updated":"2020-10-23T09:29:45Z","title":"Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria","department":[{"_id":"E-Lib"}],"citation":{"mla":"Mayer, Katja, et al. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA, 2020, doi:10.5281/ZENODO.4109242.","short":"K. Mayer, K. Rieck, S. Reichmann, P. Danowski, A. Graschopf, T. König, P. Kraker, P. Lehner, F. Reckling, T. Ross-Hellauer, D. Spichtinger, M. Tzatzanis, S. Schürz, Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria, OANA, 2020.","ieee":"K. Mayer et al., Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA, 2020.","ama":"Mayer K, Rieck K, Reichmann S, et al. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA; 2020. doi:10.5281/ZENODO.4109242","apa":"Mayer, K., Rieck, K., Reichmann, S., Danowski, P., Graschopf, A., König, T., … Schürz, S. (2020). Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA. https://doi.org/10.5281/ZENODO.4109242","chicago":"Mayer, Katja, Katharina Rieck, Stefan Reichmann, Patrick Danowski, Anton Graschopf, Thomas König, Peter Kraker, et al. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA, 2020. https://doi.org/10.5281/ZENODO.4109242.","ista":"Mayer K, Rieck K, Reichmann S, Danowski P, Graschopf A, König T, Kraker P, Lehner P, Reckling F, Ross-Hellauer T, Spichtinger D, Tzatzanis M, Schürz S. 2020. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria, OANA, 36p."},"date_updated":"2020-10-23T09:34:40Z","ddc":["020"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"working_paper","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"8695"},{"article_processing_charge":"No","author":[{"orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick","last_name":"Danowski","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Ferus","full_name":"Ferus, Andreas"},{"first_name":"Anna-Laetitia","full_name":"Hikl, Anna-Laetitia","last_name":"Hikl"},{"last_name":"McNeill","full_name":"McNeill, Gerda","first_name":"Gerda"},{"first_name":"Clemens","last_name":"Miniberger","full_name":"Miniberger, Clemens"},{"full_name":"Reding, Steve","last_name":"Reding","first_name":"Steve"},{"full_name":"Zarka, Tobias","last_name":"Zarka","first_name":"Tobias"},{"first_name":"Michael","full_name":"Zojer, Michael","last_name":"Zojer"}],"title":"„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B","citation":{"mla":"Danowski, Patrick, et al. “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 2, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 278–84, doi:10.31263/voebm.v73i2.3941.","ama":"Danowski P, Ferus A, Hikl A-L, et al. „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(2):278-284. doi:10.31263/voebm.v73i2.3941","apa":"Danowski, P., Ferus, A., Hikl, A.-L., McNeill, G., Miniberger, C., Reding, S., … Zojer, M. (2020). „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i2.3941","ieee":"P. Danowski et al., “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 2. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 278–284, 2020.","short":"P. Danowski, A. Ferus, A.-L. Hikl, G. McNeill, C. Miniberger, S. Reding, T. Zarka, M. Zojer, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 278–284.","chicago":"Danowski, Patrick, Andreas Ferus, Anna-Laetitia Hikl, Gerda McNeill, Clemens Miniberger, Steve Reding, Tobias Zarka, and Michael Zojer. “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i2.3941.","ista":"Danowski P, Ferus A, Hikl A-L, McNeill G, Miniberger C, Reding S, Zarka T, Zojer M. 2020. „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(2), 278–284."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"278-284","date_created":"2020-10-25T23:01:19Z","date_published":"2020-07-14T00:00:00Z","doi":"10.31263/voebm.v73i2.3941","year":"2020","has_accepted_license":"1","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","day":"14","oa":1,"quality_controlled":"1","publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","file_date_updated":"2020-10-27T16:27:25Z","department":[{"_id":"E-Lib"}],"date_updated":"2021-01-12T08:20:40Z","ddc":["020"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"8706","issue":"2","volume":73,"publication_status":"published","publication_identifier":{"eissn":["10222588"]},"language":[{"iso":"ger"}],"file":[{"date_created":"2020-10-27T16:27:25Z","file_name":"2020_VOEB_Danowski.pdf","creator":"kschuh","date_updated":"2020-10-27T16:27:25Z","file_size":960317,"checksum":"37443c34d91d5bdbeb38c78b14792537","file_id":"8714","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 73","month":"07","abstract":[{"lang":"eng","text":"As part of the Austrian Transition to Open Access (AT2OA) project, subproject TP1-B is working on designing a monitoring solution for the output of Open Access publications in Austria. This report on a potential Open Access monitoring approach in Austria is one of the results of these efforts and can serve as a basis for discussion on an international level."},{"text":"Als Teil des Hochschulraumstrukturmittel-Projekts Austrian Transition to Open Access (AT2OA) befasst sich das Teilprojekt TP1-B mit der Konzeption einer Monitoring-Lösung für den Open Access-Publikationsoutput in Österreich. Der nun vorliegende Bericht zu einem potentiellen Open Access-Monitoring in Österreich ist eines der Ergebnisse dieser Bemühungen und kann als Grundlage einer Diskussion auf internationaler Ebene dienen.","lang":"ger"}],"oa_version":"Published Version"},{"citation":{"mla":"Laukoter, Susanne, et al. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” STAR Protocols, vol. 1, no. 3, 100215, Elsevier, 2020, doi:10.1016/j.xpro.2020.100215.","apa":"Laukoter, S., Amberg, N., Pauler, F., & Hippenmeyer, S. (2020). Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2020.100215","ama":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 2020;1(3). doi:10.1016/j.xpro.2020.100215","ieee":"S. Laukoter, N. Amberg, F. Pauler, and S. Hippenmeyer, “Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy,” STAR Protocols, vol. 1, no. 3. Elsevier, 2020.","short":"S. Laukoter, N. Amberg, F. Pauler, S. Hippenmeyer, STAR Protocols 1 (2020).","chicago":"Laukoter, Susanne, Nicole Amberg, Florian Pauler, and Simon Hippenmeyer. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” STAR Protocols. Elsevier, 2020. https://doi.org/10.1016/j.xpro.2020.100215.","ista":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. 2020. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 1(3), 100215."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Laukoter, Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","last_name":"Amberg"},{"last_name":"Pauler","full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["33377108"]},"title":"Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy","article_number":"100215","project":[{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"},{"call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2020","day":"18","publication":"STAR Protocols","doi":"10.1016/j.xpro.2020.100215","date_published":"2020-12-18T00:00:00Z","date_created":"2020-12-30T10:17:07Z","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). N.A received support from the FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2021-01-12T08:21:36Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2021-01-07T15:57:27Z","_id":"8978","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","publication_identifier":{"issn":["2666-1667"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2021-01-07T15:57:27Z","file_size":4031449,"date_created":"2021-01-07T15:57:27Z","file_name":"2020_STARProtocols_Laukoter.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f1e9a433e9cb0f41f7b6df6b76db1f6e","file_id":"8996","success":1}],"language":[{"iso":"eng"}],"volume":1,"issue":"3","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b)."}],"pmid":1,"oa_version":"Published Version","month":"12","intvolume":" 1"},{"_id":"9103","status":"public","conference":{"end_date":"2020-12-18","location":"Jeju Islang, Korea (South)","start_date":"2020-12-14","name":"CDC: Conference on Decision and Control"},"type":"conference","date_updated":"2021-02-09T09:20:58Z","department":[{"_id":"ToHe"}],"oa_version":"Preprint","abstract":[{"text":"We introduce LRT-NG, a set of techniques and an associated toolset that computes a reachtube (an over-approximation of the set of reachable states over a given time horizon) of a nonlinear dynamical system. LRT-NG significantly advances the state-of-the-art Langrangian Reachability and its associated tool LRT. From a theoretical perspective, LRT-NG is superior to LRT in three ways. First, it uses for the first time an analytically computed metric for the propagated ball which is proven to minimize the ball’s volume. We emphasize that the metric computation is the centerpiece of all bloating-based techniques. Secondly, it computes the next reachset as the intersection of two balls: one based on the Cartesian metric and the other on the new metric. While the two metrics were previously considered opposing approaches, their joint use considerably tightens the reachtubes. Thirdly, it avoids the \"wrapping effect\" associated with the validated integration of the center of the reachset, by optimally absorbing the interval approximation in the radius of the next ball. From a tool-development perspective, LRT-NG is superior to LRT in two ways. First, it is a standalone tool that no longer relies on CAPD. This required the implementation of the Lohner method and a Runge-Kutta time-propagation method. Secondly, it has an improved interface, allowing the input model and initial conditions to be provided as external input files. Our experiments on a comprehensive set of benchmarks, including two Neural ODEs, demonstrates LRT-NG’s superior performance compared to LRT, CAPD, and Flow*.","lang":"eng"}],"intvolume":" 2020","month":"12","main_file_link":[{"url":"https://arxiv.org/abs/2012.07458","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781728174471"],"issn":["07431546"]},"volume":2020,"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Gruenbacher S, Cyranka J, Lechner M, Islam MA, Smolka SA, Grosu R. Lagrangian reachtubes: The next generation. In: Proceedings of the 59th IEEE Conference on Decision and Control. Vol 2020. IEEE; 2020:1556-1563. doi:10.1109/CDC42340.2020.9304042","apa":"Gruenbacher, S., Cyranka, J., Lechner, M., Islam, M. A., Smolka, S. A., & Grosu, R. (2020). Lagrangian reachtubes: The next generation. In Proceedings of the 59th IEEE Conference on Decision and Control (Vol. 2020, pp. 1556–1563). Jeju Islang, Korea (South): IEEE. https://doi.org/10.1109/CDC42340.2020.9304042","ieee":"S. Gruenbacher, J. Cyranka, M. Lechner, M. A. Islam, S. A. Smolka, and R. Grosu, “Lagrangian reachtubes: The next generation,” in Proceedings of the 59th IEEE Conference on Decision and Control, Jeju Islang, Korea (South), 2020, vol. 2020, pp. 1556–1563.","short":"S. Gruenbacher, J. Cyranka, M. Lechner, M.A. Islam, S.A. Smolka, R. Grosu, in:, Proceedings of the 59th IEEE Conference on Decision and Control, IEEE, 2020, pp. 1556–1563.","mla":"Gruenbacher, Sophie, et al. “Lagrangian Reachtubes: The next Generation.” Proceedings of the 59th IEEE Conference on Decision and Control, vol. 2020, IEEE, 2020, pp. 1556–63, doi:10.1109/CDC42340.2020.9304042.","ista":"Gruenbacher S, Cyranka J, Lechner M, Islam MA, Smolka SA, Grosu R. 2020. Lagrangian reachtubes: The next generation. Proceedings of the 59th IEEE Conference on Decision and Control. CDC: Conference on Decision and Control vol. 2020, 1556–1563.","chicago":"Gruenbacher, Sophie, Jacek Cyranka, Mathias Lechner, Md Ariful Islam, Scott A. Smolka, and Radu Grosu. “Lagrangian Reachtubes: The next Generation.” In Proceedings of the 59th IEEE Conference on Decision and Control, 2020:1556–63. IEEE, 2020. https://doi.org/10.1109/CDC42340.2020.9304042."},"title":"Lagrangian reachtubes: The next generation","article_processing_charge":"No","external_id":{"arxiv":["2012.07458"]},"author":[{"first_name":"Sophie","full_name":"Gruenbacher, Sophie","last_name":"Gruenbacher"},{"first_name":"Jacek","full_name":"Cyranka, Jacek","last_name":"Cyranka"},{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"first_name":"Md Ariful","full_name":"Islam, Md Ariful","last_name":"Islam"},{"full_name":"Smolka, Scott A.","last_name":"Smolka","first_name":"Scott A."},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"}],"acknowledgement":"The authors would like to thank Ramin Hasani and Guillaume Berger for intellectual discussions about the research which lead to the generation of new ideas. ML was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Smolka’s research was supported by NSF grants CPS-1446832 and CCF-1918225. Gruenbacher is funded by FWF project W1255-N23. JC was partially supported by NAWA Polish Returns grant\r\nPPN/PPO/2018/1/00029.\r\n","oa":1,"publisher":"IEEE","quality_controlled":"1","publication":"Proceedings of the 59th IEEE Conference on Decision and Control","day":"14","year":"2020","date_created":"2021-02-07T23:01:14Z","doi":"10.1109/CDC42340.2020.9304042","date_published":"2020-12-14T00:00:00Z","page":"1556-1563"},{"volume":33,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2002.07867","open_access":"1"}],"month":"07","intvolume":" 33","abstract":[{"text":"Recent works have shown that gradient descent can find a global minimum for over-parameterized neural networks where the widths of all the hidden layers scale polynomially with N (N being the number of training samples). In this paper, we prove that, for deep networks, a single layer of width N following the input layer suffices to ensure a similar guarantee. In particular, all the remaining layers are allowed to have constant widths, and form a pyramidal topology. We show an application of our result to the widely used LeCun’s initialization and obtain an over-parameterization requirement for the single wide layer of order N2.\r\n","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"MaMo"}],"date_updated":"2022-01-04T09:24:41Z","type":"conference","conference":{"start_date":"2020-12-06","location":"Vancouver, Canada","end_date":"2020-12-12","name":"NeurIPS: Neural Information Processing Systems"},"status":"public","_id":"9221","page":"11961–11972","date_published":"2020-07-07T00:00:00Z","date_created":"2021-03-03T12:06:02Z","year":"2020","day":"07","publication":"34th Conference on Neural Information Processing Systems","publisher":"Curran Associates","quality_controlled":"1","oa":1,"acknowledgement":"The authors would like to thank Jan Maas, Mahdi Soltanolkotabi, and Daniel Soudry for the helpful discussions, Marius Kloft, Matthias Hein and Quoc Dinh Tran for proofreading portions of a prior version of this paper, and James Martens for a clarification concerning LeCun’s initialization. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. Q. Nguyen was partially supported by the German Research Foundation (DFG) award KL 2698/2-1.","author":[{"first_name":"Quynh","full_name":"Nguyen, Quynh","last_name":"Nguyen"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"external_id":{"arxiv":["2002.07867"]},"article_processing_charge":"No","title":"Global convergence of deep networks with one wide layer followed by pyramidal topology","citation":{"ieee":"Q. Nguyen and M. Mondelli, “Global convergence of deep networks with one wide layer followed by pyramidal topology,” in 34th Conference on Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 11961–11972.","short":"Q. Nguyen, M. Mondelli, in:, 34th Conference on Neural Information Processing Systems, Curran Associates, 2020, pp. 11961–11972.","apa":"Nguyen, Q., & Mondelli, M. (2020). Global convergence of deep networks with one wide layer followed by pyramidal topology. In 34th Conference on Neural Information Processing Systems (Vol. 33, pp. 11961–11972). Vancouver, Canada: Curran Associates.","ama":"Nguyen Q, Mondelli M. Global convergence of deep networks with one wide layer followed by pyramidal topology. In: 34th Conference on Neural Information Processing Systems. Vol 33. Curran Associates; 2020:11961–11972.","mla":"Nguyen, Quynh, and Marco Mondelli. “Global Convergence of Deep Networks with One Wide Layer Followed by Pyramidal Topology.” 34th Conference on Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 11961–11972.","ista":"Nguyen Q, Mondelli M. 2020. Global convergence of deep networks with one wide layer followed by pyramidal topology. 34th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 11961–11972.","chicago":"Nguyen, Quynh, and Marco Mondelli. “Global Convergence of Deep Networks with One Wide Layer Followed by Pyramidal Topology.” In 34th Conference on Neural Information Processing Systems, 33:11961–11972. Curran Associates, 2020."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}]},{"date_created":"2021-05-23T22:01:45Z","date_published":"2020-07-12T00:00:00Z","page":"5533-5543","publication":"37th International Conference on Machine Learning, ICML 2020","day":"12","year":"2020","has_accepted_license":"1","oa":1,"quality_controlled":"1","title":"Inducing and exploiting activation sparsity for fast neural network inference","article_processing_charge":"No","author":[{"first_name":"Mark","last_name":"Kurtz","full_name":"Kurtz, Mark"},{"last_name":"Kopinsky","full_name":"Kopinsky, Justin","first_name":"Justin"},{"first_name":"Rati","full_name":"Gelashvili, Rati","last_name":"Gelashvili"},{"last_name":"Matveev","full_name":"Matveev, Alexander","first_name":"Alexander"},{"first_name":"John","last_name":"Carr","full_name":"Carr, John"},{"first_name":"Michael","full_name":"Goin, Michael","last_name":"Goin"},{"first_name":"William","full_name":"Leiserson, William","last_name":"Leiserson"},{"full_name":"Moore, Sage","last_name":"Moore","first_name":"Sage"},{"first_name":"Bill","full_name":"Nell, Bill","last_name":"Nell"},{"first_name":"Nir","full_name":"Shavit, Nir","last_name":"Shavit"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Kurtz et al., “Inducing and exploiting activation sparsity for fast neural network inference,” in 37th International Conference on Machine Learning, ICML 2020, Online, 2020, vol. 119, pp. 5533–5543.","short":"M. Kurtz, J. Kopinsky, R. Gelashvili, A. Matveev, J. Carr, M. Goin, W. Leiserson, S. Moore, B. Nell, N. Shavit, D.-A. Alistarh, in:, 37th International Conference on Machine Learning, ICML 2020, 2020, pp. 5533–5543.","ama":"Kurtz M, Kopinsky J, Gelashvili R, et al. Inducing and exploiting activation sparsity for fast neural network inference. In: 37th International Conference on Machine Learning, ICML 2020. Vol 119. ; 2020:5533-5543.","apa":"Kurtz, M., Kopinsky, J., Gelashvili, R., Matveev, A., Carr, J., Goin, M., … Alistarh, D.-A. (2020). Inducing and exploiting activation sparsity for fast neural network inference. In 37th International Conference on Machine Learning, ICML 2020 (Vol. 119, pp. 5533–5543). Online.","mla":"Kurtz, Mark, et al. “Inducing and Exploiting Activation Sparsity for Fast Neural Network Inference.” 37th International Conference on Machine Learning, ICML 2020, vol. 119, 2020, pp. 5533–43.","ista":"Kurtz M, Kopinsky J, Gelashvili R, Matveev A, Carr J, Goin M, Leiserson W, Moore S, Nell B, Shavit N, Alistarh D-A. 2020. Inducing and exploiting activation sparsity for fast neural network inference. 37th International Conference on Machine Learning, ICML 2020. ICML: International Conference on Machine Learning vol. 119, 5533–5543.","chicago":"Kurtz, Mark, Justin Kopinsky, Rati Gelashvili, Alexander Matveev, John Carr, Michael Goin, William Leiserson, et al. “Inducing and Exploiting Activation Sparsity for Fast Neural Network Inference.” In 37th International Conference on Machine Learning, ICML 2020, 119:5533–43, 2020."},"volume":119,"language":[{"iso":"eng"}],"file":[{"file_name":"2020_PMLR_Kurtz.pdf","date_created":"2021-05-25T09:51:36Z","creator":"kschuh","file_size":741899,"date_updated":"2021-05-25T09:51:36Z","success":1,"checksum":"2aaaa7d7226e49161311d91627cf783b","file_id":"9421","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_identifier":{"issn":["2640-3498"]},"intvolume":" 119","month":"07","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Optimizing convolutional neural networks for fast inference has recently become an extremely active area of research. One of the go-to solutions in this context is weight pruning, which aims to reduce computational and memory footprint by removing large subsets of the connections in a neural network. Surprisingly, much less attention has been given to exploiting sparsity in the activation maps, which tend to be naturally sparse in many settings thanks to the structure of rectified linear (ReLU) activation functions. In this paper, we present an in-depth analysis of methods for maximizing the sparsity of the activations in a trained neural network, and show that, when coupled with an efficient sparse-input convolution algorithm, we can leverage this sparsity for significant performance gains. To induce highly sparse activation maps without accuracy loss, we introduce a new regularization technique, coupled with a new threshold-based sparsification method based on a parameterized activation function called Forced-Activation-Threshold Rectified Linear Unit (FATReLU). We examine the impact of our methods on popular image classification models, showing that most architectures can adapt to significantly sparser activation maps without any accuracy loss. Our second contribution is showing that these these compression gains can be translated into inference speedups: we provide a new algorithm to enable fast convolution operations over networks with sparse activations, and show that it can enable significant speedups for end-to-end inference on a range of popular models on the large-scale ImageNet image classification task on modern Intel CPUs, with little or no retraining cost. "}],"file_date_updated":"2021-05-25T09:51:36Z","department":[{"_id":"DaAl"}],"ddc":["000"],"date_updated":"2023-02-23T13:57:24Z","status":"public","conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2020-07-18","location":"Online","start_date":"2020-07-12"},"type":"conference","_id":"9415"},{"date_published":"2020-03-11T00:00:00Z","date_created":"2022-01-25T15:50:00Z","day":"11","publication":"8th International Conference on Learning Representations","has_accepted_license":"1","year":"2020","quality_controlled":"1","publisher":"ICLR","oa":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein Award).\r\n","title":"Learning representations for binary-classification without backpropagation","author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lechner, Mathias. “Learning Representations for Binary-Classification without Backpropagation.” In 8th International Conference on Learning Representations. ICLR, 2020.","ista":"Lechner M. 2020. Learning representations for binary-classification without backpropagation. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","mla":"Lechner, Mathias. “Learning Representations for Binary-Classification without Backpropagation.” 8th International Conference on Learning Representations, ICLR, 2020.","ieee":"M. Lechner, “Learning representations for binary-classification without backpropagation,” in 8th International Conference on Learning Representations, Virtual ; Addis Ababa, Ethiopia, 2020.","short":"M. Lechner, in:, 8th International Conference on Learning Representations, ICLR, 2020.","ama":"Lechner M. Learning representations for binary-classification without backpropagation. In: 8th International Conference on Learning Representations. ICLR; 2020.","apa":"Lechner, M. (2020). Learning representations for binary-classification without backpropagation. In 8th International Conference on Learning Representations. Virtual ; Addis Ababa, Ethiopia: ICLR."},"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","file":[{"file_id":"10677","checksum":"ea13d42dd4541ddb239b6a75821fd6c9","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-01-26T07:35:17Z","file_name":"iclr_2020.pdf","date_updated":"2022-01-26T07:35:17Z","file_size":249431,"creator":"mlechner"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"03","scopus_import":"1","main_file_link":[{"url":"https://openreview.net/forum?id=Bke61krFvS","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The family of feedback alignment (FA) algorithms aims to provide a more biologically motivated alternative to backpropagation (BP), by substituting the computations that are unrealistic to be implemented in physical brains. While FA algorithms have been shown to work well in practice, there is a lack of rigorous theory proofing their learning capabilities. Here we introduce the first feedback alignment algorithm with provable learning guarantees. In contrast to existing work, we do not require any assumption about the size or depth of the network except that it has a single output neuron, i.e., such as for binary classification tasks. We show that our FA algorithm can deliver its theoretical promises in practice, surpassing the learning performance of existing FA methods and matching backpropagation in binary classification tasks. Finally, we demonstrate the limits of our FA variant when the number of output neurons grows beyond a certain quantity."}],"file_date_updated":"2022-01-26T07:35:17Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-04-03T07:33:40Z","status":"public","type":"conference","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"conference":{"name":"ICLR: International Conference on Learning Representations","location":"Virtual ; Addis Ababa, Ethiopia","end_date":"2020-05-01","start_date":"2020-04-26"},"_id":"10672"},{"article_processing_charge":"No","external_id":{"arxiv":["2007.06705"]},"author":[{"last_name":"Henderson","orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M","first_name":"Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"title":"Unsupervised object-centric video generation and decomposition in 3D","citation":{"ista":"Henderson PM, Lampert C. 2020. Unsupervised object-centric video generation and decomposition in 3D. 34th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 3106–3117.","chicago":"Henderson, Paul M, and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” In 34th Conference on Neural Information Processing Systems, 33:3106–3117. Curran Associates, 2020.","apa":"Henderson, P. M., & Lampert, C. (2020). Unsupervised object-centric video generation and decomposition in 3D. In 34th Conference on Neural Information Processing Systems (Vol. 33, pp. 3106–3117). Vancouver, Canada: Curran Associates.","ama":"Henderson PM, Lampert C. Unsupervised object-centric video generation and decomposition in 3D. In: 34th Conference on Neural Information Processing Systems. Vol 33. Curran Associates; 2020:3106–3117.","ieee":"P. M. Henderson and C. Lampert, “Unsupervised object-centric video generation and decomposition in 3D,” in 34th Conference on Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 3106–3117.","short":"P.M. Henderson, C. Lampert, in:, 34th Conference on Neural Information Processing Systems, Curran Associates, 2020, pp. 3106–3117.","mla":"Henderson, Paul M., and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” 34th Conference on Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 3106–3117."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3106–3117","date_created":"2020-07-31T16:59:19Z","date_published":"2020-07-07T00:00:00Z","year":"2020","publication":"34th Conference on Neural Information Processing Systems","day":"07","oa":1,"publisher":"Curran Associates","quality_controlled":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources\r\nprovided by Scientific Computing (SciComp). PH is employed part-time by Blackford Analysis, but\r\nthey did not support this project in any way.","department":[{"_id":"ChLa"}],"date_updated":"2023-04-25T09:49:58Z","conference":{"end_date":"2020-12-12","location":"Vancouver, Canada","start_date":"2020-12-06","name":"NeurIPS: Neural Information Processing Systems"},"type":"conference","status":"public","_id":"8188","volume":33,"publication_status":"published","publication_identifier":{"isbn":["9781713829546"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06705"}],"intvolume":" 33","month":"07","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that\r\ngives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to\r\ngenerate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on\r\ndepth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking.","lang":"eng"}],"oa_version":"Preprint"},{"_id":"7474","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2020-02-19","location":"Klosterneuburg, Austria","end_date":"2020-02-21","name":"AHPC: Austrian High-Performance-Computing Meeting"},"type":"book_editor","status":"public","date_updated":"2023-05-16T07:48:28Z","ddc":["000"],"department":[{"_id":"ScienComp"}],"file_date_updated":"2020-07-14T12:47:59Z","abstract":[{"text":"This booklet is a collection of abstracts presented at the AHPC conference.","lang":"eng"}],"oa_version":"Published Version","place":"Klosterneuburg, Austria","month":"02","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-004-6"]},"language":[{"iso":"eng"}],"file":[{"checksum":"49798edb9e57bbd6be18362d1d7b18a9","file_id":"7504","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-02-19T06:53:38Z","file_name":"BOOKLET_AHPC2020.final.pdf","creator":"schloegl","date_updated":"2020-07-14T12:47:59Z","file_size":90899507}],"citation":{"mla":"Schlögl, Alois, et al., editors. Austrian High-Performance-Computing Meeting (AHPC2020). IST Austria, 2020, doi:10.15479/AT:ISTA:7474.","short":"A. Schlögl, J. Kiss, S. Elefante, eds., Austrian High-Performance-Computing Meeting (AHPC2020), IST Austria, Klosterneuburg, Austria, 2020.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, Eds., Austrian High-Performance-Computing meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020.","ama":"Schlögl A, Kiss J, Elefante S, eds. Austrian High-Performance-Computing Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria; 2020. doi:10.15479/AT:ISTA:7474","apa":"Schlögl, A., Kiss, J., & Elefante, S. (Eds.). (2020). Austrian High-Performance-Computing meeting (AHPC2020). Presented at the AHPC: Austrian High-Performance-Computing Meeting, Klosterneuburg, Austria: IST Austria. https://doi.org/10.15479/AT:ISTA:7474","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante, eds. Austrian High-Performance-Computing Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:7474.","ista":"Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","title":"Austrian High-Performance-Computing meeting (AHPC2020)","editor":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100"},{"full_name":"Kiss, Janos","last_name":"Kiss","first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"quality_controlled":"1","publisher":"IST Austria","year":"2020","has_accepted_license":"1","day":"19","page":"72","date_created":"2020-02-11T07:59:04Z","date_published":"2020-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:7474"},{"publication":"International Conference on Tools and Algorithms for the Construction and Analysis of Systems","day":"17","year":"2020","has_accepted_license":"1","date_created":"2020-05-10T22:00:49Z","date_published":"2020-04-17T00:00:00Z","doi":"10.1007/978-3-030-45237-7_5","page":"79-97","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Giacobbe, T.A. Henzinger, M. Lechner, in:, International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2020, pp. 79–97.","ieee":"M. Giacobbe, T. A. Henzinger, and M. Lechner, “How many bits does it take to quantize your neural network?,” in International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Dublin, Ireland, 2020, vol. 12079, pp. 79–97.","ama":"Giacobbe M, Henzinger TA, Lechner M. How many bits does it take to quantize your neural network? In: International Conference on Tools and Algorithms for the Construction and Analysis of Systems. Vol 12079. Springer Nature; 2020:79-97. doi:10.1007/978-3-030-45237-7_5","apa":"Giacobbe, M., Henzinger, T. A., & Lechner, M. (2020). How many bits does it take to quantize your neural network? In International Conference on Tools and Algorithms for the Construction and Analysis of Systems (Vol. 12079, pp. 79–97). Dublin, Ireland: Springer Nature. https://doi.org/10.1007/978-3-030-45237-7_5","mla":"Giacobbe, Mirco, et al. “How Many Bits Does It Take to Quantize Your Neural Network?” International Conference on Tools and Algorithms for the Construction and Analysis of Systems, vol. 12079, Springer Nature, 2020, pp. 79–97, doi:10.1007/978-3-030-45237-7_5.","ista":"Giacobbe M, Henzinger TA, Lechner M. 2020. How many bits does it take to quantize your neural network? International Conference on Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 12079, 79–97.","chicago":"Giacobbe, Mirco, Thomas A Henzinger, and Mathias Lechner. “How Many Bits Does It Take to Quantize Your Neural Network?” In International Conference on Tools and Algorithms for the Construction and Analysis of Systems, 12079:79–97. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45237-7_5."},"title":"How many bits does it take to quantize your neural network?","article_processing_charge":"No","author":[{"last_name":"Giacobbe","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco","first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f19905a42891fe5ce93d69143fa3f6fb","file_id":"7893","creator":"dernst","date_updated":"2020-07-14T12:48:03Z","file_size":2744030,"date_created":"2020-05-26T12:48:15Z","file_name":"2020_TACAS_Giacobbe.pdf"}],"publication_status":"published","publication_identifier":{"isbn":["9783030452360"],"eissn":["16113349"],"issn":["03029743"]},"volume":12079,"related_material":{"record":[{"id":"11362","status":"public","relation":"dissertation_contains"}]},"oa_version":"Published Version","abstract":[{"text":"Quantization converts neural networks into low-bit fixed-point computations which can be carried out by efficient integer-only hardware, and is standard practice for the deployment of neural networks on real-time embedded devices. However, like their real-numbered counterpart, quantized networks are not immune to malicious misclassification caused by adversarial attacks. We investigate how quantization affects a network’s robustness to adversarial attacks, which is a formal verification question. We show that neither robustness nor non-robustness are monotonic with changing the number of bits for the representation and, also, neither are preserved by quantization from a real-numbered network. For this reason, we introduce a verification method for quantized neural networks which, using SMT solving over bit-vectors, accounts for their exact, bit-precise semantics. We built a tool and analyzed the effect of quantization on a classifier for the MNIST dataset. We demonstrate that, compared to our method, existing methods for the analysis of real-numbered networks often derive false conclusions about their quantizations, both when determining robustness and when detecting attacks, and that existing methods for quantized networks often miss attacks. Furthermore, we applied our method beyond robustness, showing how the number of bits in quantization enlarges the gender bias of a predictor for students’ grades.","lang":"eng"}],"intvolume":" 12079","month":"04","scopus_import":1,"alternative_title":["LNCS"],"ddc":["000"],"date_updated":"2023-06-23T07:01:11Z","file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"ToHe"}],"_id":"7808","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2020-04-25","location":"Dublin, Ireland","end_date":"2020-04-30","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"type":"conference"},{"status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Zürich, Switzerland","end_date":"2020-06-26","start_date":"2020-06-22","name":"SoCG: Symposium on Computational Geometry"},"_id":"7952","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:48:06Z","ddc":["510"],"date_updated":"2023-08-02T06:49:16Z","month":"06","intvolume":" 164","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f: ℝ^d → ℝ^(d-n). A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently fine triangulation 𝒯. This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary. "}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"9649"}]},"volume":164,"ec_funded":1,"file":[{"creator":"dernst","file_size":1009739,"date_updated":"2020-07-14T12:48:06Z","file_name":"2020_LIPIcsSoCG_Boissonnat.pdf","date_created":"2020-06-17T10:13:34Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7969","checksum":"38cbfa4f5d484d267a35d44d210df044"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-95977-143-6"],"issn":["1868-8969"]},"publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_number":"20:1-20:18","title":"The topological correctness of PL-approximations of isomanifolds","author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Boissonnat, Jean-Daniel, and Mathijs Wintraecken. “The Topological Correctness of PL-Approximations of Isomanifolds.” 36th International Symposium on Computational Geometry, vol. 164, 20:1-20:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.SoCG.2020.20.","apa":"Boissonnat, J.-D., & Wintraecken, M. (2020). The topological correctness of PL-approximations of isomanifolds. In 36th International Symposium on Computational Geometry (Vol. 164). Zürich, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2020.20","ama":"Boissonnat J-D, Wintraecken M. The topological correctness of PL-approximations of isomanifolds. In: 36th International Symposium on Computational Geometry. Vol 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.SoCG.2020.20","ieee":"J.-D. Boissonnat and M. Wintraecken, “The topological correctness of PL-approximations of isomanifolds,” in 36th International Symposium on Computational Geometry, Zürich, Switzerland, 2020, vol. 164.","short":"J.-D. Boissonnat, M. Wintraecken, in:, 36th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","chicago":"Boissonnat, Jean-Daniel, and Mathijs Wintraecken. “The Topological Correctness of PL-Approximations of Isomanifolds.” In 36th International Symposium on Computational Geometry, Vol. 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.SoCG.2020.20.","ista":"Boissonnat J-D, Wintraecken M. 2020. The topological correctness of PL-approximations of isomanifolds. 36th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 164, 20:1-20:18."},"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"doi":"10.4230/LIPIcs.SoCG.2020.20","date_published":"2020-06-01T00:00:00Z","date_created":"2020-06-09T07:24:11Z","day":"01","publication":"36th International Symposium on Computational Geometry","has_accepted_license":"1","year":"2020"},{"date_updated":"2023-08-04T08:51:07Z","ddc":["510"],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:06Z","_id":"7990","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2020-06-22","location":"Zürich, Switzerland","end_date":"2020-06-26"},"type":"conference","status":"public","publication_status":"published","publication_identifier":{"isbn":["9783959771436"],"issn":["18688969"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:06Z","file_size":793187,"date_created":"2020-06-23T06:37:27Z","file_name":"2020_LIPIcsSoCG_Wagner.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8003","checksum":"3f6925be5f3dcdb3b14cab92f410edf7"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"12129"}]},"volume":164,"abstract":[{"text":"Given a finite point set P in general position in the plane, a full triangulation is a maximal straight-line embedded plane graph on P. A partial triangulation on P is a full triangulation of some subset P' of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge, removes a non-extreme point of degree 3, or adds a point in P ⧵ P' as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The goal of this paper is to investigate the structure of this graph, with emphasis on its connectivity. For sets P of n points in general position, we show that the bistellar flip graph is (n-3)-connected, thereby answering, for sets in general position, an open questions raised in a book (by De Loera, Rambau, and Santos) and a survey (by Lee and Santos) on triangulations. This matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points and projecting the lower convex hull), where (n-3)-connectivity has been known since the late 1980s through the secondary polytope (Gelfand, Kapranov, Zelevinsky) and Balinski’s Theorem. Our methods also yield the following results (see the full version [Wagner and Welzl, 2020]): (i) The bistellar flip graph can be covered by graphs of polytopes of dimension n-3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n-3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations are regular iff the trivial subdivision has height n-3 in the partial order of partial subdivisions. (iv) There are arbitrarily large sets P with non-regular partial triangulations, while every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular partial triangulations (answering a question by F. Santos in the unexpected direction).","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 164","month":"06","citation":{"ama":"Wagner U, Welzl E. Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips). In: 36th International Symposium on Computational Geometry. Vol 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.SoCG.2020.67","apa":"Wagner, U., & Welzl, E. (2020). Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips). In 36th International Symposium on Computational Geometry (Vol. 164). Zürich, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2020.67","short":"U. Wagner, E. Welzl, in:, 36th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"U. Wagner and E. Welzl, “Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips),” in 36th International Symposium on Computational Geometry, Zürich, Switzerland, 2020, vol. 164.","mla":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane (Part II: Bistellar Flips).” 36th International Symposium on Computational Geometry, vol. 164, 67:1-67:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.SoCG.2020.67.","ista":"Wagner U, Welzl E. 2020. Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips). 36th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 164, 67:1-67:16.","chicago":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane (Part II: Bistellar Flips).” In 36th International Symposium on Computational Geometry, Vol. 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.SoCG.2020.67."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2003.13557"]},"article_processing_charge":"No","author":[{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"},{"full_name":"Welzl, Emo","last_name":"Welzl","first_name":"Emo"}],"title":"Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)","article_number":"67:1 - 67:16","year":"2020","has_accepted_license":"1","publication":"36th International Symposium on Computational Geometry","day":"01","date_created":"2020-06-22T09:14:19Z","doi":"10.4230/LIPIcs.SoCG.2020.67","date_published":"2020-06-01T00:00:00Z","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1"},{"_id":"7807","status":"public","type":"conference","conference":{"end_date":"2020-01-08","location":"Salt Lake City, UT, United States","start_date":"2020-01-05","name":"SODA: Symposium on Discrete Algorithms"},"date_updated":"2023-08-04T08:51:07Z","department":[{"_id":"UlWa"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In a straight-line embedded triangulation of a point set P in the plane, removing an inner edge and—provided the resulting quadrilateral is convex—adding the other diagonal is called an edge flip. The (edge) flip graph has all triangulations as vertices, and a pair of triangulations is adjacent if they can be obtained from each other by an edge flip. The goal of this paper is to contribute to a better understanding of the flip graph, with an emphasis on its connectivity.\r\nFor sets in general position, it is known that every triangulation allows at least edge flips (a tight bound) which gives the minimum degree of any flip graph for n points. We show that for every point set P in general position, the flip graph is at least -vertex connected. Somewhat more strongly, we show that the vertex connectivity equals the minimum degree occurring in the flip graph, i.e. the minimum number of flippable edges in any triangulation of P, provided P is large enough. Finally, we exhibit some of the geometry of the flip graph by showing that the flip graph can be covered by 1-skeletons of polytopes of dimension (products of associahedra).\r\nA corresponding result ((n – 3)-vertex connectedness) can be shown for the bistellar flip graph of partial triangulations, i.e. the set of all triangulations of subsets of P which contain all extreme points of P. This will be treated separately in a second part."}],"month":"01","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611975994.172"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781611975994"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"12129","relation":"later_version"}]},"volume":"2020-January","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Wagner U, Welzl E. 2020. Connectivity of triangulation flip graphs in the plane (Part I: Edge flips). Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2020–January, 2823–2841.","chicago":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane (Part I: Edge Flips).” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 2020–January:2823–41. SIAM, 2020. https://doi.org/10.1137/1.9781611975994.172.","ieee":"U. Wagner and E. Welzl, “Connectivity of triangulation flip graphs in the plane (Part I: Edge flips),” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Salt Lake City, UT, United States, 2020, vol. 2020–January, pp. 2823–2841.","short":"U. Wagner, E. Welzl, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2020, pp. 2823–2841.","ama":"Wagner U, Welzl E. Connectivity of triangulation flip graphs in the plane (Part I: Edge flips). In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2020-January. SIAM; 2020:2823-2841. doi:10.1137/1.9781611975994.172","apa":"Wagner, U., & Welzl, E. (2020). Connectivity of triangulation flip graphs in the plane (Part I: Edge flips). In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2020–January, pp. 2823–2841). Salt Lake City, UT, United States: SIAM. https://doi.org/10.1137/1.9781611975994.172","mla":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane (Part I: Edge Flips).” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2020–January, SIAM, 2020, pp. 2823–41, doi:10.1137/1.9781611975994.172."},"title":"Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)","author":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"},{"full_name":"Welzl, Emo","last_name":"Welzl","first_name":"Emo"}],"article_processing_charge":"No","external_id":{"arxiv":["2003.13557"]},"publisher":"SIAM","quality_controlled":"1","oa":1,"day":"01","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","year":"2020","date_published":"2020-01-01T00:00:00Z","doi":"10.1137/1.9781611975994.172","date_created":"2020-05-10T22:00:48Z","page":"2823-2841"},{"oa_version":"Published Version","abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"month":"09","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.r4xgxd29n","open_access":"1"}],"publisher":"Dryad","day":"22","year":"2020","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-23T16:48:27Z","doi":"10.5061/DRYAD.R4XGXD29N","related_material":{"record":[{"id":"8708","status":"public","relation":"used_in_publication"}]},"date_published":"2020-09-22T00:00:00Z","_id":"13073","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"mla":"Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N.","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N."},"date_updated":"2023-08-04T11:04:11Z","department":[{"_id":"NiBa"}],"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","article_processing_charge":"No","author":[{"last_name":"Simon","full_name":"Simon, Alexis","first_name":"Alexis"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"full_name":"El Ayari, Tahani","last_name":"El Ayari","first_name":"Tahani"},{"first_name":"Cathy","full_name":"Liautard-Haag, Cathy","last_name":"Liautard-Haag"},{"first_name":"Petr","full_name":"Strelkov, Petr","last_name":"Strelkov"},{"first_name":"John","full_name":"Welch, John","last_name":"Welch"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}]},{"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"first_name":"Stephanie","last_name":"Arnoux","full_name":"Arnoux, Stephanie"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"},{"first_name":"Christopher","last_name":"Sauvage","full_name":"Sauvage, Christopher"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD","chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD.","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD."},"date_updated":"2023-08-04T11:19:26Z","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","_id":"13065","date_created":"2023-05-23T16:30:20Z","related_material":{"link":[{"url":"https://github.com/starnoux/arnoux_et_al_2019","relation":"software"}],"record":[{"status":"public","id":"8928","relation":"used_in_publication"}]},"doi":"10.5061/DRYAD.Q2BVQ83HD","date_published":"2020-10-19T00:00:00Z","day":"19","year":"2020","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available."}]},{"related_material":{"record":[{"relation":"later_version","status":"public","id":"9047"}]},"volume":"2020-June","language":[{"iso":"eng"}],"publication_identifier":{"issn":["21578095"],"isbn":["9781728164328"]},"publication_status":"published","month":"06","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1909.04892","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N 1−1/µ ), where N is the block length and µ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 and 1."}],"department":[{"_id":"MaMo"}],"date_updated":"2023-08-07T13:36:24Z","status":"public","type":"conference","conference":{"location":"Los Angeles, CA, United States","end_date":"2020-06-26","start_date":"2020-06-21","name":"ISIT: Internation Symposium on Information Theory"},"_id":"8536","date_published":"2020-06-01T00:00:00Z","doi":"10.1109/ISIT44484.2020.9174141","date_created":"2020-09-20T22:01:37Z","day":"01","publication":"IEEE International Symposium on Information Theory - Proceedings","year":"2020","quality_controlled":"1","publisher":"IEEE","oa":1,"acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162 and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei.","title":"Simplified successive cancellation decoding of polar codes has sublinear latency","author":[{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"},{"first_name":"Seyyed Ali","last_name":"Hashemi","full_name":"Hashemi, Seyyed Ali"},{"first_name":"John","full_name":"Cioffi, John","last_name":"Cioffi"},{"full_name":"Goldsmith, Andrea","last_name":"Goldsmith","first_name":"Andrea"}],"external_id":{"arxiv":["1909.04892"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John Cioffi, and Andrea Goldsmith. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” In IEEE International Symposium on Information Theory - Proceedings, Vol. 2020–June. IEEE, 2020. https://doi.org/10.1109/ISIT44484.2020.9174141.","ista":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. 2020. Simplified successive cancellation decoding of polar codes has sublinear latency. IEEE International Symposium on Information Theory - Proceedings. ISIT: Internation Symposium on Information Theory vol. 2020–June, 401–406.","mla":"Mondelli, Marco, et al. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” IEEE International Symposium on Information Theory - Proceedings, vol. 2020–June, 401–406, IEEE, 2020, doi:10.1109/ISIT44484.2020.9174141.","apa":"Mondelli, M., Hashemi, S. A., Cioffi, J., & Goldsmith, A. (2020). Simplified successive cancellation decoding of polar codes has sublinear latency. In IEEE International Symposium on Information Theory - Proceedings (Vol. 2020–June). Los Angeles, CA, United States: IEEE. https://doi.org/10.1109/ISIT44484.2020.9174141","ama":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. 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Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems. Journal of Statistical Physics. 178(2), 319–378.","chicago":"Carlen, Eric A., and Jan Maas. “Non-Commutative Calculus, Optimal Transport and Functional Inequalities in Dissipative Quantum Systems.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-019-02434-w.","short":"E.A. Carlen, J. Maas, Journal of Statistical Physics 178 (2020) 319–378.","ieee":"E. A. Carlen and J. Maas, “Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems,” Journal of Statistical Physics, vol. 178, no. 2. Springer Nature, pp. 319–378, 2020.","apa":"Carlen, E. A., & Maas, J. (2020). Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-019-02434-w","ama":"Carlen EA, Maas J. 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We develop a non-nommutative differential calculus that allows us to obtain non-commutative Ricci curvature bounds, logarithmic Sobolev inequalities, transport-entropy inequalities, andspectral gap estimates.","lang":"eng"}],"oa_version":"Published Version","issue":"2","related_material":{"link":[{"url":"https://doi.org/10.1007/s10955-020-02671-4","relation":"erratum"}]},"volume":178,"ec_funded":1,"publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"publication_status":"published","file":[{"checksum":"7b04befbdc0d4982c0ee945d25d19872","file_id":"7209","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_JourStatistPhysics_Carlen.pdf","date_created":"2019-12-23T12:03:09Z","file_size":905538,"date_updated":"2020-07-14T12:47:28Z","creator":"dernst"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6358","file_date_updated":"2020-07-14T12:47:28Z","department":[{"_id":"JaMa"}],"date_updated":"2023-08-17T13:49:40Z","ddc":["500"]},{"volume":2256,"ec_funded":1,"publication_identifier":{"issn":["00758434"],"isbn":["9783030360191"],"eissn":["16179692"],"eisbn":["9783030360207"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1808.07350","open_access":"1"}],"month":"06","intvolume":" 2256","abstract":[{"lang":"eng","text":"We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean space, motivated by the famous theorem of Gromov about the waist of radially symmetric Gaussian measures. In particular, it turns our possible to extend Gromov’s original result to the case of not necessarily radially symmetric Gaussian measure. We also provide examples of measures having no t-neighborhood waist property, including a rather wide class\r\nof compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2.\r\nWe use a simpler form of Gromov’s pancake argument to produce some estimates of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for reader’s convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian\r\nmeasures."}],"oa_version":"Preprint","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"date_updated":"2023-08-17T13:48:31Z","type":"book_chapter","status":"public","series_title":"LNM","_id":"74","page":"1-27","doi":"10.1007/978-3-030-36020-7_1","date_published":"2020-06-21T00:00:00Z","date_created":"2018-12-11T11:44:29Z","isi":1,"year":"2020","day":"21","publication":"Geometric Aspects of Functional Analysis","quality_controlled":"1","publisher":"Springer Nature","oa":1,"author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"}],"article_processing_charge":"No","external_id":{"isi":["000557689300003"],"arxiv":["1808.07350"]},"editor":[{"first_name":"Bo'az","full_name":"Klartag, Bo'az","last_name":"Klartag"},{"first_name":"Emanuel","last_name":"Milman","full_name":"Milman, Emanuel"}],"title":"Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures","citation":{"chicago":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” In Geometric Aspects of Functional Analysis, edited by Bo’az Klartag and Emanuel Milman, 2256:1–27. 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In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.\r\n","lang":"eng"}],"intvolume":" 374","month":"03","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Optimal Upper Bound for the Correlation Energy of a Fermi Gas in the Mean-Field Regime.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03505-5.","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2020. Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. Communications in Mathematical Physics. 374, 2097–2150.","mla":"Benedikter, Niels P., et al. “Optimal Upper Bound for the Correlation Energy of a Fermi Gas in the Mean-Field Regime.” Communications in Mathematical Physics, vol. 374, Springer Nature, 2020, pp. 2097–2150, doi:10.1007/s00220-019-03505-5.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Communications in Mathematical Physics 374 (2020) 2097–2150.","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime,” Communications in Mathematical Physics, vol. 374. Springer Nature, pp. 2097–2150, 2020.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. 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Partial coherence and frustration in self-organizing spherical grids. Hippocampus. 30(4), 302–313.","chicago":"Stella, Federico, Eugenio Urdapilleta, Yifan Luo, and Alessandro Treves. “Partial Coherence and Frustration in Self-Organizing Spherical Grids.” Hippocampus. Wiley, 2020. https://doi.org/10.1002/hipo.23144.","short":"F. Stella, E. Urdapilleta, Y. Luo, A. Treves, Hippocampus 30 (2020) 302–313.","ieee":"F. Stella, E. Urdapilleta, Y. Luo, and A. Treves, “Partial coherence and frustration in self-organizing spherical grids,” Hippocampus, vol. 30, no. 4. Wiley, pp. 302–313, 2020.","ama":"Stella F, Urdapilleta E, Luo Y, Treves A. Partial coherence and frustration in self-organizing spherical grids. Hippocampus. 2020;30(4):302-313. doi:10.1002/hipo.23144","apa":"Stella, F., Urdapilleta, E., Luo, Y., & Treves, A. (2020). Partial coherence and frustration in self-organizing spherical grids. Hippocampus. Wiley. https://doi.org/10.1002/hipo.23144","mla":"Stella, Federico, et al. “Partial Coherence and Frustration in Self-Organizing Spherical Grids.” Hippocampus, vol. 30, no. 4, Wiley, 2020, pp. 302–13, doi:10.1002/hipo.23144."},"doi":"10.1002/hipo.23144","date_published":"2020-04-01T00:00:00Z","date_created":"2019-08-11T21:59:24Z","page":"302-313","day":"01","publication":"Hippocampus","isi":1,"has_accepted_license":"1","year":"2020","quality_controlled":"1","publisher":"Wiley","oa":1,"file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"JoCs"}],"ddc":["570"],"date_updated":"2023-08-17T13:53:14Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6796","volume":30,"issue":"4","file":[{"file_id":"6800","checksum":"7b54d22bfbfc0d1188a9ea24d985bfb2","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_Hippocampus_Stella.pdf","date_created":"2019-08-12T07:53:33Z","file_size":2370658,"date_updated":"2020-07-14T12:47:40Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10981063"],"issn":["10509631"]},"publication_status":"published","month":"04","intvolume":" 30","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses.","lang":"eng"}]},{"citation":{"chicago":"Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation Games.” Theoretical Computer Science. Elsevier, 2020. https://doi.org/10.1016/j.tcs.2019.06.031.","ista":"Avni G, Henzinger TA, Kupferman O. 2020. Dynamic resource allocation games. Theoretical Computer Science. 807, 42–55.","mla":"Avni, Guy, et al. “Dynamic Resource Allocation Games.” Theoretical Computer Science, vol. 807, Elsevier, 2020, pp. 42–55, doi:10.1016/j.tcs.2019.06.031.","apa":"Avni, G., Henzinger, T. A., & Kupferman, O. (2020). Dynamic resource allocation games. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2019.06.031","ama":"Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. Theoretical Computer Science. 2020;807:42-55. doi:10.1016/j.tcs.2019.06.031","ieee":"G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” Theoretical Computer Science, vol. 807. Elsevier, pp. 42–55, 2020.","short":"G. Avni, T.A. Henzinger, O. Kupferman, Theoretical Computer Science 807 (2020) 42–55."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"external_id":{"isi":["000512219400004"]},"article_processing_charge":"No","title":"Dynamic resource allocation games","project":[{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"06","publication":"Theoretical Computer Science","page":"42-55","doi":"10.1016/j.tcs.2019.06.031","date_published":"2020-02-06T00:00:00Z","date_created":"2019-08-04T21:59:20Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2023-08-17T13:52:49Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-09T06:31:22Z","_id":"6761","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"issn":["03043975"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8639","checksum":"e86635417f45eb2cd75778f91382f737","creator":"dernst","file_size":1413001,"date_updated":"2020-10-09T06:31:22Z","file_name":"2020_TheoreticalCS_Avni.pdf","date_created":"2020-10-09T06:31:22Z"}],"language":[{"iso":"eng"}],"volume":807,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1341"}]},"abstract":[{"lang":"eng","text":"In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability."}],"oa_version":"Submitted Version","scopus_import":"1","month":"02","intvolume":" 807"},{"_id":"6593","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-17T13:51:18Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"VlKo"}],"abstract":[{"lang":"eng","text":"We consider the monotone variational inequality problem in a Hilbert space and describe a projection-type method with inertial terms under the following properties: (a) The method generates a strongly convergent iteration sequence; (b) The method requires, at each iteration, only one projection onto the feasible set and two evaluations of the operator; (c) The method is designed for variational inequality for which the underline operator is monotone and uniformly continuous; (d) The method includes an inertial term. The latter is also shown to speed up the convergence in our numerical results. A comparison with some related methods is given and indicates that the new method is promising."}],"oa_version":"Submitted Version","scopus_import":"1","month":"05","intvolume":" 84","publication_identifier":{"issn":["1017-1398"],"eissn":["1572-9265"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6927","checksum":"bb1a1eb3ebb2df380863d0db594673ba","file_size":359654,"date_updated":"2020-07-14T12:47:34Z","creator":"kschuh","file_name":"ExtragradientMethodPaper.pdf","date_created":"2019-10-01T13:14:10Z"}],"language":[{"iso":"eng"}],"volume":84,"ec_funded":1,"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"citation":{"short":"Y. Shehu, X.-H. Li, Q.-L. Dong, Numerical Algorithms 84 (2020) 365–388.","ieee":"Y. Shehu, X.-H. Li, and Q.-L. Dong, “An efficient projection-type method for monotone variational inequalities in Hilbert spaces,” Numerical Algorithms, vol. 84. Springer Nature, pp. 365–388, 2020.","apa":"Shehu, Y., Li, X.-H., & Dong, Q.-L. (2020). An efficient projection-type method for monotone variational inequalities in Hilbert spaces. Numerical Algorithms. Springer Nature. https://doi.org/10.1007/s11075-019-00758-y","ama":"Shehu Y, Li X-H, Dong Q-L. An efficient projection-type method for monotone variational inequalities in Hilbert spaces. Numerical Algorithms. 2020;84:365-388. doi:10.1007/s11075-019-00758-y","mla":"Shehu, Yekini, et al. “An Efficient Projection-Type Method for Monotone Variational Inequalities in Hilbert Spaces.” Numerical Algorithms, vol. 84, Springer Nature, 2020, pp. 365–88, doi:10.1007/s11075-019-00758-y.","ista":"Shehu Y, Li X-H, Dong Q-L. 2020. An efficient projection-type method for monotone variational inequalities in Hilbert spaces. Numerical Algorithms. 84, 365–388.","chicago":"Shehu, Yekini, Xiao-Huan Li, and Qiao-Li Dong. “An Efficient Projection-Type Method for Monotone Variational Inequalities in Hilbert Spaces.” Numerical Algorithms. Springer Nature, 2020. https://doi.org/10.1007/s11075-019-00758-y."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"},{"full_name":"Li, Xiao-Huan","last_name":"Li","first_name":"Xiao-Huan"},{"full_name":"Dong, Qiao-Li","last_name":"Dong","first_name":"Qiao-Li"}],"external_id":{"isi":["000528979000015"]},"article_processing_charge":"No","title":"An efficient projection-type method for monotone variational inequalities in Hilbert spaces","acknowledgement":"The research of this author is supported by the ERC grant at the IST.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Numerical Algorithms","page":"365-388","date_published":"2020-05-01T00:00:00Z","doi":"10.1007/s11075-019-00758-y","date_created":"2019-06-27T20:09:33Z"},{"project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"title":"Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens","article_processing_charge":"No","external_id":{"pmid":["31344404"],"isi":["000525860400005"]},"author":[{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","last_name":"Jahr","full_name":"Jahr, Wiebke"},{"last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Jahr, Wiebke, Philipp Velicky, and Johann G Danzl. “Strategies to Maximize Performance in STimulated Emission Depletion (STED) Nanoscopy of Biological Specimens.” Methods. Elsevier, 2020. https://doi.org/10.1016/j.ymeth.2019.07.019.","ista":"Jahr W, Velicky P, Danzl JG. 2020. Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. Methods. 174(3), 27–41.","mla":"Jahr, Wiebke, et al. “Strategies to Maximize Performance in STimulated Emission Depletion (STED) Nanoscopy of Biological Specimens.” Methods, vol. 174, no. 3, Elsevier, 2020, pp. 27–41, doi:10.1016/j.ymeth.2019.07.019.","ama":"Jahr W, Velicky P, Danzl JG. Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. Methods. 2020;174(3):27-41. doi:10.1016/j.ymeth.2019.07.019","apa":"Jahr, W., Velicky, P., & Danzl, J. G. (2020). Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. Methods. Elsevier. https://doi.org/10.1016/j.ymeth.2019.07.019","short":"W. Jahr, P. Velicky, J.G. Danzl, Methods 174 (2020) 27–41.","ieee":"W. Jahr, P. Velicky, and J. G. Danzl, “Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens,” Methods, vol. 174, no. 3. Elsevier, pp. 27–41, 2020."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","date_created":"2019-08-12T16:36:32Z","doi":"10.1016/j.ymeth.2019.07.019","date_published":"2020-03-01T00:00:00Z","page":"27-41","publication":"Methods","day":"01","year":"2020","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"6808","department":[{"_id":"JoDa"}],"date_updated":"2023-08-17T13:59:57Z","intvolume":" 174","month":"03","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100895/"}],"scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions."}],"volume":174,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1046-2023"]}},{"publication_identifier":{"eissn":["16153383"],"issn":["16153375"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":20,"abstract":[{"lang":"eng","text":"This paper presents two algorithms. The first decides the existence of a pointed homotopy between given simplicial maps 𝑓,𝑔:𝑋→𝑌, and the second computes the group [𝛴𝑋,𝑌]∗ of pointed homotopy classes of maps from a suspension; in both cases, the target Y is assumed simply connected. More generally, these algorithms work relative to 𝐴⊆𝑋."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.2337"}],"month":"04","intvolume":" 20","date_updated":"2023-08-17T13:50:44Z","department":[{"_id":"UlWa"}],"_id":"6563","article_type":"original","type":"journal_article","status":"public","isi":1,"year":"2020","day":"01","publication":"Foundations of Computational Mathematics","page":"311-330","date_published":"2020-04-01T00:00:00Z","doi":"10.1007/s10208-019-09419-x","date_created":"2019-06-16T21:59:14Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"ista":"Filakovský M, Vokřínek L. 2020. Are two given maps homotopic? An algorithmic viewpoint. Foundations of Computational Mathematics. 20, 311–330.","chicago":"Filakovský, Marek, and Lukas Vokřínek. “Are Two given Maps Homotopic? An Algorithmic Viewpoint.” Foundations of Computational Mathematics. Springer Nature, 2020. https://doi.org/10.1007/s10208-019-09419-x.","ieee":"M. Filakovský and L. Vokřínek, “Are two given maps homotopic? An algorithmic viewpoint,” Foundations of Computational Mathematics, vol. 20. Springer Nature, pp. 311–330, 2020.","short":"M. Filakovský, L. Vokřínek, Foundations of Computational Mathematics 20 (2020) 311–330.","ama":"Filakovský M, Vokřínek L. Are two given maps homotopic? An algorithmic viewpoint. Foundations of Computational Mathematics. 2020;20:311-330. doi:10.1007/s10208-019-09419-x","apa":"Filakovský, M., & Vokřínek, L. (2020). Are two given maps homotopic? An algorithmic viewpoint. Foundations of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-019-09419-x","mla":"Filakovský, Marek, and Lukas Vokřínek. “Are Two given Maps Homotopic? An Algorithmic Viewpoint.” Foundations of Computational Mathematics, vol. 20, Springer Nature, 2020, pp. 311–30, doi:10.1007/s10208-019-09419-x."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Filakovský","full_name":"Filakovský, Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"},{"first_name":"Lukas","full_name":"Vokřínek, Lukas","last_name":"Vokřínek"}],"article_processing_charge":"No","external_id":{"arxiv":["1312.2337"],"isi":["000522437400004"]},"title":"Are two given maps homotopic? An algorithmic viewpoint","project":[{"call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory"}]},{"publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1007/s11263-019-01219-8","date_published":"2020-04-01T00:00:00Z","date_created":"2019-10-17T13:38:20Z","page":"835-854","day":"01","publication":"International Journal of Computer Vision","has_accepted_license":"1","isi":1,"year":"2020","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"title":"Learning single-image 3D reconstruction by generative modelling of shape, pose and shading","author":[{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M","last_name":"Henderson","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445"},{"last_name":"Ferrari","full_name":"Ferrari, Vittorio","first_name":"Vittorio"}],"external_id":{"isi":["000491042100002"],"arxiv":["1901.06447"]},"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"P.M. Henderson, V. Ferrari, International Journal of Computer Vision 128 (2020) 835–854.","ieee":"P. M. Henderson and V. Ferrari, “Learning single-image 3D reconstruction by generative modelling of shape, pose and shading,” International Journal of Computer Vision, vol. 128. Springer Nature, pp. 835–854, 2020.","apa":"Henderson, P. M., & Ferrari, V. (2020). Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01219-8","ama":"Henderson PM, Ferrari V. Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. International Journal of Computer Vision. 2020;128:835-854. doi:10.1007/s11263-019-01219-8","mla":"Henderson, Paul M., and Vittorio Ferrari. “Learning Single-Image 3D Reconstruction by Generative Modelling of Shape, Pose and Shading.” International Journal of Computer Vision, vol. 128, Springer Nature, 2020, pp. 835–54, doi:10.1007/s11263-019-01219-8.","ista":"Henderson PM, Ferrari V. 2020. Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. International Journal of Computer Vision. 128, 835–854.","chicago":"Henderson, Paul M, and Vittorio Ferrari. “Learning Single-Image 3D Reconstruction by Generative Modelling of Shape, Pose and Shading.” International Journal of Computer Vision. Springer Nature, 2020. https://doi.org/10.1007/s11263-019-01219-8."},"month":"04","intvolume":" 128","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn.","lang":"eng"}],"volume":128,"file":[{"date_updated":"2020-07-14T12:47:46Z","file_size":2243134,"creator":"dernst","date_created":"2019-10-25T10:28:29Z","file_name":"2019_CompVision_Henderson.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"a0f05dd4f5f64e4f713d8d9d4b5b1e3f","file_id":"6973"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6952","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:47:46Z","ddc":["004"],"date_updated":"2023-08-17T14:01:16Z"},{"volume":57,"issue":"2","publication_identifier":{"issn":["0893-7648"],"eissn":["1559-1182"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035206/"}],"month":"02","intvolume":" 57","abstract":[{"lang":"eng","text":"Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality."}],"oa_version":"Submitted Version","pmid":1,"department":[{"_id":"SaSi"}],"date_updated":"2023-08-17T14:05:48Z","article_type":"original","type":"journal_article","status":"public","_id":"7033","page":"1070–1084","date_published":"2020-02-01T00:00:00Z","doi":"10.1007/s12035-019-01783-7","date_created":"2019-11-18T14:18:39Z","isi":1,"year":"2020","day":"01","publication":"Molecular Neurobiology","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This work was supported by National Eye Institute grants R01 EY012223 (RWN), R01 EY030123 (RWN), T32 EY027721 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), and a Vision Science Core grant P30 EY016665 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), an unrestricted funding grant from Research to Prevent Blindness (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), the Frederick A. Davis Endowment (RWN), and the Mr. and Mrs. George Taylor Foundation (RWN).","author":[{"full_name":"Donahue, RJ","last_name":"Donahue","first_name":"RJ"},{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085"},{"last_name":"Grosser","full_name":"Grosser, JA","first_name":"JA"},{"first_name":"RW","full_name":"Nickells, RW","last_name":"Nickells"}],"external_id":{"pmid":["31673950"],"isi":["000493754200001"]},"article_processing_charge":"No","title":"BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage","citation":{"ista":"Donahue R, Maes ME, Grosser J, Nickells R. 2020. BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. 57(2), 1070–1084.","chicago":"Donahue, RJ, Margaret E Maes, JA Grosser, and RW Nickells. “BAX-Depleted Retinal Ganglion Cells Survive and Become Quiescent Following Optic Nerve Damage.” Molecular Neurobiology. Springer Nature, 2020. https://doi.org/10.1007/s12035-019-01783-7.","apa":"Donahue, R., Maes, M. E., Grosser, J., & Nickells, R. (2020). BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. Springer Nature. https://doi.org/10.1007/s12035-019-01783-7","ama":"Donahue R, Maes ME, Grosser J, Nickells R. BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. 2020;57(2):1070–1084. doi:10.1007/s12035-019-01783-7","ieee":"R. Donahue, M. E. Maes, J. Grosser, and R. Nickells, “BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage,” Molecular Neurobiology, vol. 57, no. 2. Springer Nature, pp. 1070–1084, 2020.","short":"R. Donahue, M.E. Maes, J. Grosser, R. Nickells, Molecular Neurobiology 57 (2020) 1070–1084.","mla":"Donahue, RJ, et al. “BAX-Depleted Retinal Ganglion Cells Survive and Become Quiescent Following Optic Nerve Damage.” Molecular Neurobiology, vol. 57, no. 2, Springer Nature, 2020, pp. 1070–1084, doi:10.1007/s12035-019-01783-7."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"page":"1049-1052","date_published":"2020-02-01T00:00:00Z","doi":"10.1111/nph.16203","date_created":"2019-11-12T11:41:32Z","isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"New Phytologist","quality_controlled":"1","publisher":"Wiley","oa":1,"author":[{"last_name":"Zhang","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["31603260"],"isi":["000489638800001"]},"article_processing_charge":"Yes (via OA deal)","title":"Auxin guides roots to avoid obstacles during gravitropic growth","citation":{"mla":"Zhang, Yuzhou, and Jiří Friml. “Auxin Guides Roots to Avoid Obstacles during Gravitropic Growth.” New Phytologist, vol. 225, no. 3, Wiley, 2020, pp. 1049–52, doi:10.1111/nph.16203.","apa":"Zhang, Y., & Friml, J. (2020). Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. Wiley. https://doi.org/10.1111/nph.16203","ama":"Zhang Y, Friml J. Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. 2020;225(3):1049-1052. doi:10.1111/nph.16203","ieee":"Y. Zhang and J. Friml, “Auxin guides roots to avoid obstacles during gravitropic growth,” New Phytologist, vol. 225, no. 3. Wiley, pp. 1049–1052, 2020.","short":"Y. Zhang, J. Friml, New Phytologist 225 (2020) 1049–1052.","chicago":"Zhang, Yuzhou, and Jiří Friml. “Auxin Guides Roots to Avoid Obstacles during Gravitropic Growth.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16203.","ista":"Zhang Y, Friml J. 2020. Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. 225(3), 1049–1052."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"volume":225,"issue":"3","ec_funded":1,"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"publication_status":"published","file":[{"date_created":"2020-11-18T16:42:48Z","file_name":"2020_NewPhytologist_Zhang.pdf","date_updated":"2020-11-18T16:42:48Z","file_size":717345,"creator":"dernst","file_id":"8772","checksum":"cd42ffdb381fd52812b9583d4d407139","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"02","intvolume":" 225","pmid":1,"oa_version":"Published Version","department":[{"_id":"JiFr"}],"file_date_updated":"2020-11-18T16:42:48Z","date_updated":"2023-08-17T14:01:49Z","ddc":["580"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6997"},{"date_created":"2019-11-12T14:01:27Z","doi":"10.1007/s00220-019-03575-5","date_published":"2020-06-01T00:00:00Z","page":"1803-1873","publication":"Communications in Mathematical Physics","day":"01","year":"2020","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","title":"Cohomological Hall algebras, vertex algebras and instantons","article_processing_charge":"No","external_id":{"arxiv":["1810.10402"],"isi":["000536255500004"]},"author":[{"first_name":"Miroslav","full_name":"Rapcak, Miroslav","last_name":"Rapcak"},{"first_name":"Yan","full_name":"Soibelman, Yan","last_name":"Soibelman"},{"last_name":"Yang","full_name":"Yang, Yaping","first_name":"Yaping"},{"last_name":"Zhao","full_name":"Zhao, Gufang","first_name":"Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Rapcak, Miroslav, Yan Soibelman, Yaping Yang, and Gufang Zhao. “Cohomological Hall Algebras, Vertex Algebras and Instantons.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03575-5.","ista":"Rapcak M, Soibelman Y, Yang Y, Zhao G. 2020. Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. 376, 1803–1873.","mla":"Rapcak, Miroslav, et al. “Cohomological Hall Algebras, Vertex Algebras and Instantons.” Communications in Mathematical Physics, vol. 376, Springer Nature, 2020, pp. 1803–73, doi:10.1007/s00220-019-03575-5.","apa":"Rapcak, M., Soibelman, Y., Yang, Y., & Zhao, G. (2020). Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03575-5","ama":"Rapcak M, Soibelman Y, Yang Y, Zhao G. Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. 2020;376:1803-1873. doi:10.1007/s00220-019-03575-5","short":"M. Rapcak, Y. Soibelman, Y. Yang, G. Zhao, Communications in Mathematical Physics 376 (2020) 1803–1873.","ieee":"M. Rapcak, Y. Soibelman, Y. Yang, and G. Zhao, “Cohomological Hall algebras, vertex algebras and instantons,” Communications in Mathematical Physics, vol. 376. Springer Nature, pp. 1803–1873, 2020."},"project":[{"call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces"}],"ec_funded":1,"volume":376,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"intvolume":" 376","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1810.10402","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds.","lang":"eng"}],"department":[{"_id":"TaHa"}],"date_updated":"2023-08-17T14:02:59Z","status":"public","article_type":"original","type":"journal_article","_id":"7004"},{"publication":"Advanced Science","day":"05","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2019-12-22T23:00:43Z","doi":"10.1002/advs.201901455","date_published":"2020-02-05T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Li, Yang, et al. “Root Growth Adaptation Is Mediated by PYLs ABA Receptor-PP2A Protein Phosphatase Complex.” Advanced Science, vol. 7, no. 3, 1901455, Wiley, 2020, doi:10.1002/advs.201901455.","short":"Y. Li, Y. Wang, S. Tan, Z. Li, Z. Yuan, M. Glanc, D. Domjan, K. Wang, W. Xuan, Y. Guo, Z. Gong, J. Friml, J. Zhang, Advanced Science 7 (2020).","ieee":"Y. Li et al., “Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex,” Advanced Science, vol. 7, no. 3. Wiley, 2020.","ama":"Li Y, Wang Y, Tan S, et al. Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex. Advanced Science. 2020;7(3). doi:10.1002/advs.201901455","apa":"Li, Y., Wang, Y., Tan, S., Li, Z., Yuan, Z., Glanc, M., … Zhang, J. (2020). Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex. Advanced Science. Wiley. https://doi.org/10.1002/advs.201901455","chicago":"Li, Yang, Yaping Wang, Shutang Tan, Zhen Li, Zhi Yuan, Matous Glanc, David Domjan, et al. “Root Growth Adaptation Is Mediated by PYLs ABA Receptor-PP2A Protein Phosphatase Complex.” Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.201901455.","ista":"Li Y, Wang Y, Tan S, Li Z, Yuan Z, Glanc M, Domjan D, Wang K, Xuan W, Guo Y, Gong Z, Friml J, Zhang J. 2020. Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex. Advanced Science. 7(3), 1901455."},"title":"Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex","article_processing_charge":"No","external_id":{"pmid":["32042554"],"isi":["000501912800001"]},"author":[{"first_name":"Yang","last_name":"Li","full_name":"Li, Yang"},{"last_name":"Wang","full_name":"Wang, Yaping","first_name":"Yaping"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zhen","last_name":"Li","full_name":"Li, Zhen"},{"full_name":"Yuan, Zhi","last_name":"Yuan","first_name":"Zhi"},{"last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous"},{"first_name":"David","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","last_name":"Domjan","full_name":"Domjan, David","orcid":"0000-0003-2267-106X"},{"last_name":"Wang","full_name":"Wang, Kai","first_name":"Kai"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"full_name":"Guo, Yan","last_name":"Guo","first_name":"Yan"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Jing","last_name":"Zhang","full_name":"Zhang, Jing"}],"article_number":"1901455","language":[{"iso":"eng"}],"file":[{"file_name":"2020_AdvScience_Li.pdf","date_created":"2020-02-24T14:29:54Z","file_size":3586924,"date_updated":"2020-07-14T12:47:53Z","creator":"dernst","file_id":"7519","checksum":"016eeab5860860af038e2da95ffe75c3","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["2198-3844"]},"volume":7,"issue":"3","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Plant root architecture dynamically adapts to various environmental conditions, such as salt‐containing soil. The phytohormone abscisic acid (ABA) is involved among others also in these developmental adaptations, but the underlying molecular mechanism remains elusive. Here, a novel branch of the ABA signaling pathway in Arabidopsis involving PYR/PYL/RCAR (abbreviated as PYLs) receptor‐protein phosphatase 2A (PP2A) complex that acts in parallel to the canonical PYLs‐protein phosphatase 2C (PP2C) mechanism is identified. The PYLs‐PP2A signaling modulates root gravitropism and lateral root formation through regulating phytohormone auxin transport. In optimal conditions, PYLs ABA receptor interacts with the catalytic subunits of PP2A, increasing their phosphatase activity and thus counteracting PINOID (PID) kinase‐mediated phosphorylation of PIN‐FORMED (PIN) auxin transporters. By contrast, in salt and osmotic stress conditions, ABA binds to PYLs, inhibiting the PP2A activity, which leads to increased PIN phosphorylation and consequently modulated directional auxin transport leading to adapted root architecture. This work reveals an adaptive mechanism that may flexibly adjust plant root growth to withstand saline and osmotic stresses. It occurs via the cross‐talk between the stress hormone ABA and the versatile developmental regulator auxin.","lang":"eng"}],"intvolume":" 7","month":"02","scopus_import":"1","ddc":["580"],"date_updated":"2023-08-17T14:13:17Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:53Z","_id":"7204","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original"},{"publisher":"American Chemical Society","quality_controlled":"1","oa":1,"doi":"10.1021/acs.nanolett.9b04445","date_published":"2020-01-08T00:00:00Z","date_created":"2019-12-10T15:36:05Z","page":"669-676","day":"08","publication":"Nano Letters","isi":1,"year":"2020","title":"Collective force generation by molecular motors is determined by strain-induced unbinding","author":[{"last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"first_name":"Reinhard","last_name":"Lipowsky","full_name":"Lipowsky, Reinhard"}],"external_id":{"isi":["000507151600087"],"pmid":["31797672"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.9b04445.","ista":"Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 20(1), 669–676.","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters, vol. 20, no. 1, American Chemical Society, 2020, pp. 669–76, doi:10.1021/acs.nanolett.9b04445.","apa":"Ucar, M. C., & Lipowsky, R. (2020). Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b04445","ama":"Ucar MC, Lipowsky R. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 2020;20(1):669-676. doi:10.1021/acs.nanolett.9b04445","short":"M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676.","ieee":"M. C. Ucar and R. Lipowsky, “Collective force generation by molecular motors is determined by strain-induced unbinding,” Nano Letters, vol. 20, no. 1. American Chemical Society, pp. 669–676, 2020."},"month":"01","intvolume":" 20","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.9b04445","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors."}],"issue":"1","volume":20,"related_material":{"record":[{"id":"9726","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9885"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"letter_note","_id":"7166","department":[{"_id":"EdHa"}],"date_updated":"2023-08-17T14:07:52Z"},{"_id":"7234","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-17T14:21:12Z","ddc":["570"],"file_date_updated":"2020-11-19T11:22:33Z","department":[{"_id":"MiSi"}],"abstract":[{"text":"T lymphocytes utilize amoeboid migration to navigate effectively within complex microenvironments. The precise rearrangement of the actin cytoskeleton required for cellular forward propulsion is mediated by actin regulators, including the actin‐related protein 2/3 (Arp2/3) complex, a macromolecular machine that nucleates branched actin filaments at the leading edge. The consequences of modulating Arp2/3 activity on the biophysical properties of the actomyosin cortex and downstream T cell function are incompletely understood. We report that even a moderate decrease of Arp3 levels in T cells profoundly affects actin cortex integrity. Reduction in total F‐actin content leads to reduced cortical tension and disrupted lamellipodia formation. Instead, in Arp3‐knockdown cells, the motility mode is dominated by blebbing migration characterized by transient, balloon‐like protrusions at the leading edge. Although this migration mode seems to be compatible with interstitial migration in three‐dimensional environments, diminished locomotion kinetics and impaired cytotoxicity interfere with optimal T cell function. These findings define the importance of finely tuned, Arp2/3‐dependent mechanophysical membrane integrity in cytotoxic effector T lymphocyte activities.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 98","month":"02","publication_status":"published","publication_identifier":{"eissn":["14401711"],"issn":["08189641"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c389477b4b52172ef76afff8a06c6775","file_id":"8775","success":1,"creator":"dernst","date_updated":"2020-11-19T11:22:33Z","file_size":8569945,"date_created":"2020-11-19T11:22:33Z","file_name":"2020_ImmunologyCellBio_Obeidy.pdf"}],"issue":"2","volume":98,"citation":{"ista":"Obeidy P, Ju LA, Oehlers SH, Zulkhernain NS, Lee Q, Galeano Niño JL, Kwan RYQ, Tikoo S, Cavanagh LL, Mrass P, Cook AJL, Jackson SP, Biro M, Roediger B, Sixt MK, Weninger W. 2020. Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes. Immunology and Cell Biology. 98(2), 93–113.","chicago":"Obeidy, Peyman, Lining A. Ju, Stefan H. Oehlers, Nursafwana S. Zulkhernain, Quintin Lee, Jorge L. Galeano Niño, Rain Y.Q. Kwan, et al. “Partial Loss of Actin Nucleator Actin-Related Protein 2/3 Activity Triggers Blebbing in Primary T Lymphocytes.” Immunology and Cell Biology. Wiley, 2020. https://doi.org/10.1111/imcb.12304.","ieee":"P. Obeidy et al., “Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes,” Immunology and Cell Biology, vol. 98, no. 2. Wiley, pp. 93–113, 2020.","short":"P. Obeidy, L.A. Ju, S.H. Oehlers, N.S. Zulkhernain, Q. Lee, J.L. Galeano Niño, R.Y.Q. Kwan, S. Tikoo, L.L. Cavanagh, P. Mrass, A.J.L. Cook, S.P. Jackson, M. Biro, B. Roediger, M.K. Sixt, W. Weninger, Immunology and Cell Biology 98 (2020) 93–113.","apa":"Obeidy, P., Ju, L. A., Oehlers, S. H., Zulkhernain, N. S., Lee, Q., Galeano Niño, J. L., … Weninger, W. (2020). Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes. Immunology and Cell Biology. Wiley. https://doi.org/10.1111/imcb.12304","ama":"Obeidy P, Ju LA, Oehlers SH, et al. Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes. Immunology and Cell Biology. 2020;98(2):93-113. doi:10.1111/imcb.12304","mla":"Obeidy, Peyman, et al. “Partial Loss of Actin Nucleator Actin-Related Protein 2/3 Activity Triggers Blebbing in Primary T Lymphocytes.” Immunology and Cell Biology, vol. 98, no. 2, Wiley, 2020, pp. 93–113, doi:10.1111/imcb.12304."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000503885600001"],"pmid":["31698518"]},"article_processing_charge":"No","author":[{"first_name":"Peyman","full_name":"Obeidy, Peyman","last_name":"Obeidy"},{"last_name":"Ju","full_name":"Ju, Lining A.","first_name":"Lining A."},{"first_name":"Stefan H.","last_name":"Oehlers","full_name":"Oehlers, Stefan H."},{"first_name":"Nursafwana S.","last_name":"Zulkhernain","full_name":"Zulkhernain, Nursafwana S."},{"first_name":"Quintin","last_name":"Lee","full_name":"Lee, Quintin"},{"first_name":"Jorge L.","last_name":"Galeano Niño","full_name":"Galeano Niño, Jorge L."},{"full_name":"Kwan, Rain Y.Q.","last_name":"Kwan","first_name":"Rain Y.Q."},{"full_name":"Tikoo, Shweta","last_name":"Tikoo","first_name":"Shweta"},{"first_name":"Lois L.","last_name":"Cavanagh","full_name":"Cavanagh, Lois L."},{"full_name":"Mrass, Paulus","last_name":"Mrass","first_name":"Paulus"},{"first_name":"Adam J.L.","last_name":"Cook","full_name":"Cook, Adam J.L."},{"full_name":"Jackson, Shaun P.","last_name":"Jackson","first_name":"Shaun P."},{"last_name":"Biro","full_name":"Biro, Maté","first_name":"Maté"},{"first_name":"Ben","last_name":"Roediger","full_name":"Roediger, Ben"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"first_name":"Wolfgang","full_name":"Weninger, Wolfgang","last_name":"Weninger"}],"title":"Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes","oa":1,"publisher":"Wiley","quality_controlled":"1","year":"2020","has_accepted_license":"1","isi":1,"publication":"Immunology and Cell Biology","day":"01","page":"93-113","date_created":"2020-01-05T23:00:48Z","doi":"10.1111/imcb.12304","date_published":"2020-02-01T00:00:00Z"},{"acknowledged_ssus":[{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"The cyclin-dependent kinase inhibitor p57KIP2 is encoded by the imprinted Cdkn1c locus, exhibits maternal expression, and is essential for cerebral cortex development. How Cdkn1c regulates corticogenesis is however not clear. To this end we employ Mosaic Analysis with Double Markers (MADM) technology to genetically dissect Cdkn1c gene function in corticogenesis at single cell resolution. We find that the previously described growth-inhibitory Cdkn1c function is a non-cell-autonomous one, acting on the whole organism. In contrast we reveal a growth-promoting cell-autonomous Cdkn1c function which at the mechanistic level mediates radial glial progenitor cell and nascent projection neuron survival. Strikingly, the growth-promoting function of Cdkn1c is highly dosage sensitive but not subject to genomic imprinting. Collectively, our results suggest that the Cdkn1c locus regulates cortical development through distinct cell-autonomous and non-cell-autonomous mechanisms. More generally, our study highlights the importance to probe the relative contributions of cell intrinsic gene function and tissue-wide mechanisms to the overall phenotype."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 11","month":"01","publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7261","checksum":"ebf1ed522f4e0be8d94c939c1806a709","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-01-13T07:42:31Z","file_name":"2020_NatureComm_Laukoter.pdf","date_updated":"2020-07-14T12:47:54Z","file_size":8063333,"creator":"dernst"}],"ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-function-for-potential-tumour-suppressor-in-brain-development/"}]},"volume":11,"_id":"7253","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-17T14:23:41Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"SiHi"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2020","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"10","date_created":"2020-01-11T10:42:48Z","date_published":"2020-01-10T00:00:00Z","doi":"10.1038/s41467-019-14077-2","article_number":"195","project":[{"grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"S. Laukoter, R.J. Beattie, F. Pauler, N. Amberg, K.I. Nakayama, S. Hippenmeyer, Nature Communications 11 (2020).","ieee":"S. Laukoter, R. J. Beattie, F. Pauler, N. Amberg, K. I. Nakayama, and S. Hippenmeyer, “Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Laukoter, S., Beattie, R. J., Pauler, F., Amberg, N., Nakayama, K. I., & Hippenmeyer, S. (2020). Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-14077-2","ama":"Laukoter S, Beattie RJ, Pauler F, Amberg N, Nakayama KI, Hippenmeyer S. Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development. Nature Communications. 2020;11. doi:10.1038/s41467-019-14077-2","mla":"Laukoter, Susanne, et al. “Imprinted Cdkn1c Genomic Locus Cell-Autonomously Promotes Cell Survival in Cerebral Cortex Development.” Nature Communications, vol. 11, 195, Springer Nature, 2020, doi:10.1038/s41467-019-14077-2.","ista":"Laukoter S, Beattie RJ, Pauler F, Amberg N, Nakayama KI, Hippenmeyer S. 2020. Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development. Nature Communications. 11, 195.","chicago":"Laukoter, Susanne, Robert J Beattie, Florian Pauler, Nicole Amberg, Keiichi I. Nakayama, and Simon Hippenmeyer. “Imprinted Cdkn1c Genomic Locus Cell-Autonomously Promotes Cell Survival in Cerebral Cortex Development.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-019-14077-2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000551459000005"]},"author":[{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne","last_name":"Laukoter","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","last_name":"Beattie","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"last_name":"Amberg","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"full_name":"Nakayama, Keiichi I.","last_name":"Nakayama","first_name":"Keiichi I."},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"title":"Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development"},{"article_processing_charge":"No","external_id":{"isi":["000505167600013"],"pmid":["31767677"]},"author":[{"last_name":"Piriya Ananda Babu","full_name":"Piriya Ananda Babu, Lashmi","first_name":"Lashmi"},{"full_name":"Wang, Han Ying","last_name":"Wang","first_name":"Han Ying"},{"full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku"},{"full_name":"Guillaud, Laurent","last_name":"Guillaud","first_name":"Laurent"},{"first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki","last_name":"Takahashi"}],"title":"Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission","citation":{"mla":"Piriya Ananda Babu, Lashmi, et al. “Microtubule and Actin Differentially Regulate Synaptic Vesicle Cycling to Maintain High-Frequency Neurotransmission.” Journal of Neuroscience, vol. 40, no. 1, Society for Neuroscience, 2020, pp. 131–42, doi:10.1523/JNEUROSCI.1571-19.2019.","short":"L. Piriya Ananda Babu, H.Y. Wang, K. Eguchi, L. Guillaud, T. Takahashi, Journal of Neuroscience 40 (2020) 131–142.","ieee":"L. Piriya Ananda Babu, H. Y. Wang, K. Eguchi, L. Guillaud, and T. Takahashi, “Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission,” Journal of neuroscience, vol. 40, no. 1. Society for Neuroscience, pp. 131–142, 2020.","ama":"Piriya Ananda Babu L, Wang HY, Eguchi K, Guillaud L, Takahashi T. Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. Journal of neuroscience. 2020;40(1):131-142. doi:10.1523/JNEUROSCI.1571-19.2019","apa":"Piriya Ananda Babu, L., Wang, H. Y., Eguchi, K., Guillaud, L., & Takahashi, T. (2020). Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1571-19.2019","chicago":"Piriya Ananda Babu, Lashmi, Han Ying Wang, Kohgaku Eguchi, Laurent Guillaud, and Tomoyuki Takahashi. “Microtubule and Actin Differentially Regulate Synaptic Vesicle Cycling to Maintain High-Frequency Neurotransmission.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.1571-19.2019.","ista":"Piriya Ananda Babu L, Wang HY, Eguchi K, Guillaud L, Takahashi T. 2020. Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. Journal of neuroscience. 40(1), 131–142."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Society for Neuroscience","page":"131-142","date_created":"2020-01-19T23:00:38Z","date_published":"2020-01-02T00:00:00Z","doi":"10.1523/JNEUROSCI.1571-19.2019","year":"2020","has_accepted_license":"1","isi":1,"publication":"Journal of neuroscience","day":"02","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"7339","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:56Z","date_updated":"2023-08-17T14:25:23Z","ddc":["570"],"scopus_import":"1","intvolume":" 40","month":"01","abstract":[{"lang":"eng","text":"Cytoskeletal filaments such as microtubules (MTs) and filamentous actin (F-actin) dynamically support cell structure and functions. In central presynaptic terminals, F-actin is expressed along the release edge and reportedly plays diverse functional roles, but whether axonal MTs extend deep into terminals and play any physiological role remains controversial. At the calyx of Held in rats of either sex, confocal and high-resolution microscopy revealed that MTs enter deep into presynaptic terminal swellings and partially colocalize with a subset of synaptic vesicles (SVs). Electrophysiological analysis demonstrated that depolymerization of MTs specifically prolonged the slow-recovery time component of EPSCs from short-term depression induced by a train of high-frequency stimulation, whereas depolymerization of F-actin specifically prolonged the fast-recovery component. In simultaneous presynaptic and postsynaptic action potential recordings, depolymerization of MTs or F-actin significantly impaired the fidelity of high-frequency neurotransmission. We conclude that MTs and F-actin differentially contribute to slow and fast SV replenishment, thereby maintaining high-frequency neurotransmission."}],"oa_version":"Published Version","pmid":1,"issue":"1","volume":40,"publication_status":"published","publication_identifier":{"eissn":["15292401"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7345","checksum":"92f5e8a47f454fc131fb94cd7f106e60","creator":"dernst","file_size":4460781,"date_updated":"2020-07-14T12:47:56Z","file_name":"2020_JourNeuroscience_Piriya.pdf","date_created":"2020-01-20T14:44:10Z"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Nibau C, Gallemi M, Dadarou D, Doonan JH, Cavallari N. 2020. Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. Frontiers in Plant Science. 10, 1680.","chicago":"Nibau, Candida, Marçal Gallemi, Despoina Dadarou, John H. Doonan, and Nicola Cavallari. “Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2.” Frontiers in Plant Science. Frontiers Media, 2020. https://doi.org/10.3389/fpls.2019.01680.","ieee":"C. Nibau, M. Gallemi, D. Dadarou, J. H. Doonan, and N. Cavallari, “Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2,” Frontiers in Plant Science, vol. 10. Frontiers Media, 2020.","short":"C. Nibau, M. Gallemi, D. Dadarou, J.H. Doonan, N. Cavallari, Frontiers in Plant Science 10 (2020).","ama":"Nibau C, Gallemi M, Dadarou D, Doonan JH, Cavallari N. Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. Frontiers in Plant Science. 2020;10. doi:10.3389/fpls.2019.01680","apa":"Nibau, C., Gallemi, M., Dadarou, D., Doonan, J. H., & Cavallari, N. (2020). Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. Frontiers in Plant Science. Frontiers Media. https://doi.org/10.3389/fpls.2019.01680","mla":"Nibau, Candida, et al. “Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2.” Frontiers in Plant Science, vol. 10, 1680, Frontiers Media, 2020, doi:10.3389/fpls.2019.01680."},"title":"Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2","author":[{"last_name":"Nibau","full_name":"Nibau, Candida","first_name":"Candida"},{"orcid":"0000-0003-4675-6893","full_name":"Gallemi, Marçal","last_name":"Gallemi","first_name":"Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dadarou, Despoina","last_name":"Dadarou","first_name":"Despoina"},{"first_name":"John H.","full_name":"Doonan, John H.","last_name":"Doonan"},{"full_name":"Cavallari, Nicola","last_name":"Cavallari","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000511376000001"]},"article_number":"1680","day":"22","publication":"Frontiers in Plant Science","isi":1,"has_accepted_license":"1","year":"2020","date_published":"2020-01-22T00:00:00Z","doi":"10.3389/fpls.2019.01680","date_created":"2020-01-22T15:23:57Z","quality_controlled":"1","publisher":"Frontiers Media","oa":1,"ddc":["580"],"date_updated":"2023-08-17T14:21:45Z","file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"EvBe"}],"_id":"7350","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"2020_FrontiersPlantScience_Nibau.pdf","date_created":"2020-01-27T09:07:02Z","file_size":1951438,"date_updated":"2020-07-14T12:47:56Z","creator":"dernst","checksum":"d1f92e60a713fbd15097ce895e5c7ccb","file_id":"7366","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1664-462X"]},"publication_status":"published","volume":10,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The ability to sense environmental temperature and to coordinate growth and development accordingly, is critical to the reproductive success of plants. Flowering time is regulated at the level of gene expression by a complex network of factors that integrate environmental and developmental cues. One of the main players, involved in modulating flowering time in response to changes in ambient temperature is FLOWERING LOCUS M (FLM). FLM transcripts can undergo extensive alternative splicing producing multiple variants, of which FLM-β and FLM-δ are the most representative. While FLM-β codes for the flowering repressor FLM protein, translation of FLM-δ has the opposite effect on flowering. Here we show that the cyclin-dependent kinase G2 (CDKG2), together with its cognate cyclin, CYCLYN L1 (CYCL1) affects the alternative splicing of FLM, balancing the levels of FLM-β and FLM-δ across the ambient temperature range. In the absence of the CDKG2/CYCL1 complex, FLM-β expression is reduced while FLM-δ is increased in a temperature dependent manner and these changes are associated with an early flowering phenotype in the cdkg2 mutant lines. In addition, we found that transcript variants retaining the full FLM intron 1 are sequestered in the cell nucleus. Strikingly, FLM intron 1 splicing is also regulated by CDKG2/CYCL1. Our results provide evidence that temperature and CDKs regulate the alternative splicing of FLM, contributing to flowering time definition."}],"month":"01","intvolume":" 10","scopus_import":"1"},{"ddc":["004","519","570"],"date_updated":"2023-08-17T14:35:22Z","file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"SaSi"}],"_id":"7369","status":"public","keyword":["Time series analysis","Multiple time scale analysis","Spike train data","Information theory","Bayesian decoding"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2020-01-28T09:31:09Z","file_name":"10827_2020_740_MOESM1_ESM.pdf","date_updated":"2020-07-14T12:47:56Z","file_size":1941355,"creator":"rcubero","checksum":"036e9451d6cd0c190ad25791bf82393b","file_id":"7380","content_type":"application/pdf","access_level":"open_access","relation":"supplementary_material"},{"creator":"rcubero","date_updated":"2020-07-14T12:47:56Z","file_size":3257880,"date_created":"2020-01-28T09:31:09Z","file_name":"Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7381","checksum":"4dd8b1fd4b54486f79d82ac7b2a412b2"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1573-6873"],"issn":["0929-5313"]},"publication_status":"published","volume":48,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Neuronal responses to complex stimuli and tasks can encompass a wide range of time scales. Understanding these responses requires measures that characterize how the information on these response patterns are represented across multiple temporal resolutions. In this paper we propose a metric – which we call multiscale relevance (MSR) – to capture the dynamical variability of the activity of single neurons across different time scales. The MSR is a non-parametric, fully featureless indicator in that it uses only the time stamps of the firing activity without resorting to any a priori covariate or invoking any specific structure in the tuning curve for neural activity. When applied to neural data from the mEC and from the ADn and PoS regions of freely-behaving rodents, we found that neurons having low MSR tend to have low mutual information and low firing sparsity across the correlates that are believed to be encoded by the region of the brain where the recordings were made. In addition, neurons with high MSR contain significant information on spatial navigation and allow to decode spatial position or head direction as efficiently as those neurons whose firing activity has high mutual information with the covariate to be decoded and significantly better than the set of neurons with high local variations in their interspike intervals. Given these results, we propose that the MSR can be used as a measure to rank and select neurons for their information content without the need to appeal to any a priori covariate."}],"month":"02","intvolume":" 48","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Cubero, R. J., Marsili, M., & Roudi, Y. (2020). Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. Springer Nature. https://doi.org/10.1007/s10827-020-00740-x","ama":"Cubero RJ, Marsili M, Roudi Y. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 2020;48:85-102. doi:10.1007/s10827-020-00740-x","ieee":"R. J. Cubero, M. Marsili, and Y. Roudi, “Multiscale relevance and informative encoding in neuronal spike trains,” Journal of Computational Neuroscience, vol. 48. Springer Nature, pp. 85–102, 2020.","short":"R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience 48 (2020) 85–102.","mla":"Cubero, Ryan J., et al. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” Journal of Computational Neuroscience, vol. 48, Springer Nature, 2020, pp. 85–102, doi:10.1007/s10827-020-00740-x.","ista":"Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 48, 85–102.","chicago":"Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” Journal of Computational Neuroscience. Springer Nature, 2020. https://doi.org/10.1007/s10827-020-00740-x."},"title":"Multiscale relevance and informative encoding in neuronal spike trains","author":[{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","last_name":"Cubero"},{"first_name":"Matteo","last_name":"Marsili","full_name":"Marsili, Matteo"},{"first_name":"Yasser","last_name":"Roudi","full_name":"Roudi, Yasser"}],"external_id":{"isi":["000515321800006"]},"article_processing_charge":"Yes (via OA deal)","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"day":"01","publication":"Journal of Computational Neuroscience","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-02-01T00:00:00Z","doi":"10.1007/s10827-020-00740-x","date_created":"2020-01-28T10:34:00Z","page":"85-102","acknowledgement":"This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation). RJC is currently receiving funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","_id":"7364","file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"BjHo"}],"ddc":["000"],"date_updated":"2023-08-17T14:29:59Z","intvolume":" 11","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We present nsCouette, a highly scalable software tool to solve the Navier–Stokes equations for incompressible fluid flow between differentially heated and independently rotating, concentric cylinders. It is based on a pseudospectral spatial discretization and dynamic time-stepping. It is implemented in modern Fortran with a hybrid MPI-OpenMP parallelization scheme and thus designed to compute turbulent flows at high Reynolds and Rayleigh numbers. An additional GPU implementation (C-CUDA) for intermediate problem sizes and a version for pipe flow (nsPipe) are also provided."}],"volume":11,"language":[{"iso":"eng"}],"file":[{"file_name":"2020_SoftwareX_Lopez.pdf","date_created":"2020-01-27T07:32:46Z","file_size":679707,"date_updated":"2020-07-14T12:47:56Z","creator":"dernst","checksum":"2af1a1a3cc33557b345145276f221668","file_id":"7365","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["23527110"]},"article_number":"100395","title":"nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow","external_id":{"isi":["000552271200011"],"arxiv":["1908.00587"]},"article_processing_charge":"No","author":[{"first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso"},{"last_name":"Feldmann","full_name":"Feldmann, Daniel","first_name":"Daniel"},{"full_name":"Rampp, Markus","last_name":"Rampp","first_name":"Markus"},{"first_name":"Alberto","last_name":"Vela-Martín","full_name":"Vela-Martín, Alberto"},{"first_name":"Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","last_name":"Shi","full_name":"Shi, Liang"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Lopez Alonso, Jose M., et al. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” SoftwareX, vol. 11, 100395, Elsevier, 2020, doi:10.1016/j.softx.2019.100395.","apa":"Lopez Alonso, J. M., Feldmann, D., Rampp, M., Vela-Martín, A., Shi, L., & Avila, M. (2020). nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. SoftwareX. Elsevier. https://doi.org/10.1016/j.softx.2019.100395","ama":"Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. SoftwareX. 2020;11. doi:10.1016/j.softx.2019.100395","short":"J.M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, M. Avila, SoftwareX 11 (2020).","ieee":"J. M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, and M. Avila, “nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow,” SoftwareX, vol. 11. Elsevier, 2020.","chicago":"Lopez Alonso, Jose M, Daniel Feldmann, Markus Rampp, Alberto Vela-Martín, Liang Shi, and Marc Avila. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” SoftwareX. Elsevier, 2020. https://doi.org/10.1016/j.softx.2019.100395.","ista":"Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. 2020. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. SoftwareX. 11, 100395."},"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2020-01-26T23:00:35Z","date_published":"2020-01-17T00:00:00Z","doi":"10.1016/j.softx.2019.100395","publication":"SoftwareX","day":"17","year":"2020","has_accepted_license":"1","isi":1},{"article_number":"0623","citation":{"chicago":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” Journal of the Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0623.","ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623.","mla":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” Journal of the Royal Society Interface, vol. 17, no. 162, 0623, The Royal Society, 2020, doi:10.1098/rsif.2019.0623.","ieee":"A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation,” Journal of the Royal Society Interface, vol. 17, no. 162. The Royal Society, 2020.","short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","ama":"Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 2020;17(162). doi:10.1098/rsif.2019.0623","apa":"Kolchinsky, A., & Corominas-Murtra, B. (2020). Decomposing information into copying versus transformation. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0623"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Artemy","last_name":"Kolchinsky","full_name":"Kolchinsky, Artemy"},{"first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra"}],"external_id":{"pmid":["31964273"],"isi":["000538369800002"],"arxiv":["1903.10693"]},"article_processing_charge":"No","title":"Decomposing information into copying versus transformation","acknowledgement":"AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation, and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions, as well as the anonymous\r\nreviewers for their insightful suggestions. ","publisher":"The Royal Society","quality_controlled":"1","oa":1,"isi":1,"year":"2020","day":"29","publication":"Journal of the Royal Society Interface","doi":"10.1098/rsif.2019.0623","date_published":"2020-01-29T00:00:00Z","date_created":"2020-02-02T23:01:03Z","_id":"7431","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-17T14:31:28Z","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance."}],"oa_version":"Preprint","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1903.10693","open_access":"1"}],"month":"01","intvolume":" 17","publication_identifier":{"eissn":["17425662"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":17,"issue":"162"},{"project":[{"_id":"26A455A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"846294","name":"Geometric study of Wasserstein spaces and free probability"}],"title":"Isometric study of Wasserstein spaces - the real line","external_id":{"arxiv":["2002.00859"],"isi":["000551418100018"]},"article_processing_charge":"No","author":[{"full_name":"Geher, Gyorgy Pal","last_name":"Geher","first_name":"Gyorgy Pal"},{"first_name":"Tamas","full_name":"Titkos, Tamas","last_name":"Titkos"},{"last_name":"Virosztek","orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Geher, Gyorgy Pal, et al. “Isometric Study of Wasserstein Spaces - the Real Line.” Transactions of the American Mathematical Society, vol. 373, no. 8, American Mathematical Society, 2020, pp. 5855–83, doi:10.1090/tran/8113.","ama":"Geher GP, Titkos T, Virosztek D. Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. 2020;373(8):5855-5883. doi:10.1090/tran/8113","apa":"Geher, G. P., Titkos, T., & Virosztek, D. (2020). Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/8113","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Isometric study of Wasserstein spaces - the real line,” Transactions of the American Mathematical Society, vol. 373, no. 8. American Mathematical Society, pp. 5855–5883, 2020.","short":"G.P. Geher, T. Titkos, D. Virosztek, Transactions of the American Mathematical Society 373 (2020) 5855–5883.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Isometric Study of Wasserstein Spaces - the Real Line.” Transactions of the American Mathematical Society. American Mathematical Society, 2020. https://doi.org/10.1090/tran/8113.","ista":"Geher GP, Titkos T, Virosztek D. 2020. Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. 373(8), 5855–5883."},"oa":1,"publisher":"American Mathematical Society","quality_controlled":"1","date_created":"2020-01-29T10:20:46Z","date_published":"2020-08-01T00:00:00Z","doi":"10.1090/tran/8113","page":"5855-5883","publication":"Transactions of the American Mathematical Society","day":"01","year":"2020","isi":1,"keyword":["Wasserstein space","isometric embeddings","isometric rigidity","exotic isometry flow"],"status":"public","type":"journal_article","article_type":"original","_id":"7389","department":[{"_id":"LaEr"}],"ddc":["515"],"date_updated":"2023-08-17T14:31:03Z","intvolume":" 373","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/2002.00859","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Recently Kloeckner described the structure of the isometry group of the quadratic Wasserstein space W_2(R^n). It turned out that the case of the real line is exceptional in the sense that there exists an exotic isometry flow. Following this line of investigation, we compute Isom(W_p(R)), the isometry group of the Wasserstein space\r\nW_p(R) for all p \\in [1,\\infty) \\setminus {2}. We show that W_2(R) is also exceptional regarding the\r\nparameter p: W_p(R) is isometrically rigid if and only if p is not equal to 2. Regarding the underlying\r\nspace, we prove that the exceptionality of p = 2 disappears if we replace R by the compact\r\ninterval [0,1]. Surprisingly, in that case, W_p([0,1]) is isometrically rigid if and only if\r\np is not equal to 1. Moreover, W_1([0,1]) admits isometries that split mass, and Isom(W_1([0,1]))\r\ncannot be embedded into Isom(W_1(R))."}],"ec_funded":1,"issue":"8","volume":373,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10886850"],"issn":["00029947"]}},{"author":[{"last_name":"Cadavid","full_name":"Cadavid, Doris","first_name":"Doris"},{"first_name":"Silvia","last_name":"Ortega","full_name":"Ortega, Silvia"},{"full_name":"Illera, Sergio","last_name":"Illera","first_name":"Sergio"},{"first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","last_name":"Liu"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"first_name":"Yu","full_name":"Zhang, Yu","last_name":"Zhang"},{"first_name":"Mengyao","full_name":"Li, Mengyao","last_name":"Li"},{"last_name":"López","full_name":"López, Antonio M.","first_name":"Antonio M."},{"first_name":"Germán","last_name":"Noriega","full_name":"Noriega, Germán"},{"full_name":"Durá, Oscar Juan","last_name":"Durá","first_name":"Oscar Juan"},{"full_name":"López De La Torre, M. A.","last_name":"López De La Torre","first_name":"M. A."},{"last_name":"Prades","full_name":"Prades, Joan Daniel","first_name":"Joan Daniel"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"external_id":{"isi":["000526598300012"]},"article_processing_charge":"No","title":"Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials","citation":{"mla":"Cadavid, Doris, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” ACS Applied Energy Materials, vol. 3, no. 3, American Chemical Society, 2020, pp. 2120–29, doi:10.1021/acsaem.9b02137.","ieee":"D. Cadavid et al., “Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials,” ACS Applied Energy Materials, vol. 3, no. 3. American Chemical Society, pp. 2120–2129, 2020.","short":"D. Cadavid, S. Ortega, S. Illera, Y. Liu, M. Ibáñez, A. Shavel, Y. Zhang, M. Li, A.M. López, G. Noriega, O.J. Durá, M.A. López De La Torre, J.D. Prades, A. Cabot, ACS Applied Energy Materials 3 (2020) 2120–2129.","apa":"Cadavid, D., Ortega, S., Illera, S., Liu, Y., Ibáñez, M., Shavel, A., … Cabot, A. (2020). Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. American Chemical Society. https://doi.org/10.1021/acsaem.9b02137","ama":"Cadavid D, Ortega S, Illera S, et al. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. 2020;3(3):2120-2129. doi:10.1021/acsaem.9b02137","chicago":"Cadavid, Doris, Silvia Ortega, Sergio Illera, Yu Liu, Maria Ibáñez, Alexey Shavel, Yu Zhang, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” ACS Applied Energy Materials. American Chemical Society, 2020. https://doi.org/10.1021/acsaem.9b02137.","ista":"Cadavid D, Ortega S, Illera S, Liu Y, Ibáñez M, Shavel A, Zhang Y, Li M, López AM, Noriega G, Durá OJ, López De La Torre MA, Prades JD, Cabot A. 2020. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. 3(3), 2120–2129."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"page":"2120-2129","date_published":"2020-03-01T00:00:00Z","doi":"10.1021/acsaem.9b02137","date_created":"2020-02-09T23:00:52Z","has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"ACS Applied Energy Materials","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"acknowledgement":"This work was supported by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R) and the Generalitat de Catalunya through the project 2017SGR1246. D.C. acknowledges support from Universidad Nacional de Colombia. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 754411. M.I. acknowledges financial support from IST Austria.","department":[{"_id":"MaIb"}],"file_date_updated":"2022-08-23T08:34:17Z","date_updated":"2023-08-17T14:36:16Z","ddc":["540"],"article_type":"original","type":"journal_article","status":"public","_id":"7467","issue":"3","volume":3,"ec_funded":1,"publication_identifier":{"eissn":["2574-0962"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"11942","checksum":"f23be731a766a480c77c962c1380315c","file_size":6423548,"date_updated":"2022-08-23T08:34:17Z","creator":"dernst","file_name":"2020_ACSAppliedEnergyMat_Cadavid.pdf","date_created":"2022-08-23T08:34:17Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 3","abstract":[{"lang":"eng","text":"Nanomaterials produced from the bottom-up assembly of nanocrystals may incorporate ∼1020–1021 cm–3 not fully coordinated surface atoms, i.e., ∼1020–1021 cm–3 potential donor or acceptor states that can strongly affect transport properties. Therefore, to exploit the full potential of nanocrystal building blocks to produce functional nanomaterials and thin films, a proper control of their surface chemistry is required. Here, we analyze how the ligand stripping procedure influences the charge and heat transport properties of sintered PbSe nanomaterials produced from the bottom-up assembly of colloidal PbSe nanocrystals. First, we show that the removal of the native organic ligands by thermal decomposition in an inert atmosphere leaves relatively large amounts of carbon at the crystal interfaces. This carbon blocks crystal growth during consolidation and at the same time hampers charge and heat transport through the final nanomaterial. Second, we demonstrate that, by stripping ligands from the nanocrystal surface before consolidation, nanomaterials with larger crystal domains, lower porosity, and higher charge carrier concentrations are obtained, thus resulting in nanomaterials with higher electrical and thermal conductivities. In addition, the ligand displacement leaves the nanocrystal surface unprotected, facilitating oxidation and chalcogen evaporation. The influence of the ligand displacement on the nanomaterial charge transport properties is rationalized here using a two-band model based on the standard Boltzmann transport equation with the relaxation time approximation. Finally, we present an application of the produced functional nanomaterials by modeling, fabricating, and testing a simple PbSe-based thermoelectric device with a ring geometry."}],"oa_version":"Submitted Version"},{"publisher":"Elsevier","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Plant Science","doi":"10.1016/j.plantsci.2020.110414","date_published":"2020-04-01T00:00:00Z","date_created":"2020-02-09T23:00:50Z","article_number":"110414","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"citation":{"ieee":"E. Mazur, M. C. Gallei, M. Adamowski, H. Han, H. S. Robert, and J. Friml, “Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis,” Plant Science, vol. 293, no. 4. Elsevier, 2020.","short":"E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020).","ama":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 2020;293(4). doi:10.1016/j.plantsci.2020.110414","apa":"Mazur, E., Gallei, M. C., Adamowski, M., Han, H., Robert, H. S., & Friml, J. (2020). Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110414","mla":"Mazur, Ewa, et al. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” Plant Science, vol. 293, no. 4, 110414, Elsevier, 2020, doi:10.1016/j.plantsci.2020.110414.","ista":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. 2020. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 293(4), 110414.","chicago":"Mazur, Ewa, Michelle C Gallei, Maciek Adamowski, Huibin Han, Hélène S. Robert, and Jiří Friml. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” Plant Science. Elsevier, 2020. https://doi.org/10.1016/j.plantsci.2020.110414."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Ewa","full_name":"Mazur, Ewa","last_name":"Mazur"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin"},{"full_name":"Robert, Hélène S.","last_name":"Robert","first_name":"Hélène S."},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"No","external_id":{"isi":["000520609800009"]},"title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","abstract":[{"lang":"eng","text":"The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 293","publication_identifier":{"issn":["01689452"],"eissn":["18732259"]},"publication_status":"published","file":[{"file_id":"7471","checksum":"f7f27c6a8fea985ceb9279be2204461c","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PlantScience_Mazur.pdf","date_created":"2020-02-10T08:59:36Z","creator":"dernst","file_size":3499069,"date_updated":"2020-07-14T12:47:59Z"}],"language":[{"iso":"eng"}],"issue":"4","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"}]},"volume":293,"ec_funded":1,"_id":"7465","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-17T14:37:32Z","ddc":["580"],"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"JiFr"}]},{"year":"2020","has_accepted_license":"1","isi":1,"publication":"eLife","day":"20","date_created":"2020-02-09T23:00:51Z","doi":"10.7554/eLife.51595","date_published":"2020-01-20T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","citation":{"chicago":"Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent, Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.51595.","ista":"Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595.","mla":"Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” ELife, vol. 9, e51595, eLife Sciences Publications, 2020, doi:10.7554/eLife.51595.","ieee":"K. Kierdorf et al., “Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila,” eLife, vol. 9. eLife Sciences Publications, 2020.","short":"K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou, A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020).","ama":"Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 2020;9. doi:10.7554/eLife.51595","apa":"Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou, J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51595"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000512304800001"]},"article_processing_charge":"No","author":[{"last_name":"Kierdorf","full_name":"Kierdorf, Katrin","first_name":"Katrin"},{"full_name":"Hersperger, Fabian","last_name":"Hersperger","first_name":"Fabian"},{"first_name":"Jessica","last_name":"Sharrock","full_name":"Sharrock, Jessica"},{"last_name":"Vincent","full_name":"Vincent, Crystal M.","first_name":"Crystal M."},{"first_name":"Pinar","full_name":"Ustaoglu, Pinar","last_name":"Ustaoglu"},{"first_name":"Jiawen","last_name":"Dou","full_name":"Dou, Jiawen"},{"first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila","orcid":"0000-0002-1819-198X","last_name":"György"},{"full_name":"Groß, Olaf","last_name":"Groß","first_name":"Olaf"},{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dionne, Marc S.","last_name":"Dionne","first_name":"Marc S."}],"title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","article_number":"e51595","project":[{"grant_number":"P29638","name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3a072be843f416c7a7d532a51dc0addb","file_id":"7470","date_updated":"2020-07-14T12:47:59Z","file_size":4959933,"creator":"dernst","date_created":"2020-02-10T08:53:16Z","file_name":"2020_eLife_Kierdorf.pdf"}],"volume":9,"abstract":[{"text":"Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"01","date_updated":"2023-08-17T14:36:39Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"DaSi"}],"_id":"7466","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public"},{"doi":"10.1016/j.neuron.2020.01.015","date_published":"2020-04-08T00:00:00Z","date_created":"2020-02-10T15:45:48Z","page":"P154-165.e6","day":"08","publication":"Neuron","isi":1,"year":"2020","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"We thank Todor Asenov and Thomas Menner from the Machine Shop for the drive design and production, Hugo Malagon-Vina for assistance in maze automatization, Jago Wallenschus for taking the images of the histology, and Federico Stella and Juan Felipe Ramirez-Villegas for comments on an earlier version of the manuscript. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616 ).","title":"Replay of behavioral sequences in the medial prefrontal cortex during rule switching","author":[{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","last_name":"Käfer","full_name":"Käfer, Karola"},{"orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","last_name":"Nardin","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karel","id":"3EA859AE-F248-11E8-B48F-1D18A9856A87","last_name":"Blahna","full_name":"Blahna, Karel"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000525319300016"],"pmid":["32032512"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Käfer, Karola, et al. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” Neuron, vol. 106, no. 1, Elsevier, 2020, p. P154–165.e6, doi:10.1016/j.neuron.2020.01.015.","ieee":"K. Käfer, M. Nardin, K. Blahna, and J. L. Csicsvari, “Replay of behavioral sequences in the medial prefrontal cortex during rule switching,” Neuron, vol. 106, no. 1. Elsevier, p. P154–165.e6, 2020.","short":"K. Käfer, M. Nardin, K. Blahna, J.L. Csicsvari, Neuron 106 (2020) P154–165.e6.","apa":"Käfer, K., Nardin, M., Blahna, K., & Csicsvari, J. L. (2020). Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.01.015","ama":"Käfer K, Nardin M, Blahna K, Csicsvari JL. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. 2020;106(1):P154-165.e6. doi:10.1016/j.neuron.2020.01.015","chicago":"Käfer, Karola, Michele Nardin, Karel Blahna, and Jozsef L Csicsvari. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.01.015.","ista":"Käfer K, Nardin M, Blahna K, Csicsvari JL. 2020. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. 106(1), P154–165.e6."},"project":[{"_id":"257BBB4C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Inter-and intracellular signalling in schizophrenia","grant_number":"607616"}],"volume":106,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/this-brain-area-helps-us-decide/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"1","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","month":"04","intvolume":" 106","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2020.01.015","open_access":"1"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Temporally organized reactivation of experiences during awake immobility periods is thought to underlie cognitive processes like planning and evaluation. While replay of trajectories is well established for the hippocampus, it is unclear whether the medial prefrontal cortex (mPFC) can reactivate sequential behavioral experiences in the awake state to support task execution. We simultaneously recorded from hippocampal and mPFC principal neurons in rats performing a mPFC-dependent rule-switching task on a plus maze. We found that mPFC neuronal activity encoded relative positions between the start and goal. During awake immobility periods, the mPFC replayed temporally organized sequences of these generalized positions, resembling entire spatial trajectories. The occurrence of mPFC trajectory replay positively correlated with rule-switching performance. However, hippocampal and mPFC trajectory replay occurred independently, indicating different functions. These results demonstrate that the mPFC can replay ordered activity patterns representing generalized locations and suggest that mPFC replay might have a role in flexible behavior.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"department":[{"_id":"JoCs"}],"date_updated":"2023-08-17T14:38:02Z","status":"public","article_type":"original","type":"journal_article","_id":"7472"},{"volume":37,"issue":"3","publication_identifier":{"issn":["0294-1449"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1902.07635","open_access":"1"}],"month":"05","intvolume":" 37","abstract":[{"text":"We give a Wong-Zakai type characterisation of the solutions of quasilinear heat equations driven by space-time white noise in 1 + 1 dimensions. In order to show that the renormalisation counterterms are local in the solution, a careful arrangement of a few hundred terms is required. The main tool in this computation is a general ‘integration by parts’ formula that provides a number of linear identities for the renormalisation constants.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"JaMa"}],"date_updated":"2023-08-17T14:35:46Z","type":"journal_article","article_type":"original","status":"public","_id":"7388","page":"663-682","date_published":"2020-05-01T00:00:00Z","doi":"10.1016/j.anihpc.2020.01.003","date_created":"2020-01-29T09:39:41Z","isi":1,"year":"2020","day":"01","publication":"Annales de l'Institut Henri Poincaré C, Analyse non linéaire","quality_controlled":"1","publisher":"Elsevier","oa":1,"author":[{"last_name":"Gerencser","full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate"}],"article_processing_charge":"No","external_id":{"isi":["000531049800007"],"arxiv":["1902.07635"]},"title":"Nondivergence form quasilinear heat equations driven by space-time white noise","citation":{"mla":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire, vol. 37, no. 3, Elsevier, 2020, pp. 663–82, doi:10.1016/j.anihpc.2020.01.003.","short":"M. Gerencser, Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire 37 (2020) 663–682.","ieee":"M. Gerencser, “Nondivergence form quasilinear heat equations driven by space-time white noise,” Annales de l’Institut Henri Poincaré C, Analyse non linéaire, vol. 37, no. 3. Elsevier, pp. 663–682, 2020.","apa":"Gerencser, M. (2020). Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire. Elsevier. https://doi.org/10.1016/j.anihpc.2020.01.003","ama":"Gerencser M. Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse non linéaire. 2020;37(3):663-682. doi:10.1016/j.anihpc.2020.01.003","chicago":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire. Elsevier, 2020. https://doi.org/10.1016/j.anihpc.2020.01.003.","ista":"Gerencser M. 2020. Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse non linéaire. 37(3), 663–682."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"file":[{"date_created":"2020-02-18T07:43:21Z","file_name":"2020_ScientificReport_Lopez.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:59Z","file_size":4703751,"checksum":"c780bd87476a9c9e12668ff66de3dc96","file_id":"7495","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20452322"]},"publication_status":"published","issue":"1","volume":10,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-020-80651-0","relation":"erratum"}]},"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis playing a key role in cancer metabolic reprogramming. Humans express two types of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2 is repressed in many tumor cells and a better understanding of its function in tumorigenesis may further the development of new therapeutic approaches. We analyzed GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7 cells. We studied GLS2 expression after induction of differentiation with phorbol ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we investigated cell cycle progression and levels of p53, p21 and c-Myc proteins. Using the baculovirus system, human GLS2 protein was overexpressed, purified and analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform. We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry and subcellular fractionation gave consistent results demonstrating nuclear and mitochondrial locations, with the latter being predominant. Nuclear targeting was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins. We assessed the subnuclear location finding a widespread distribution of GLS2 in the nucleoplasm without clear overlapping with specific nuclear substructures. GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore, human GLS2 was identified as being hypusinated by MS analysis, a posttranslational modification which may be relevant for its nuclear targeting and/or function. Our studies provide evidence for a tumor suppressor role of GLS2 in certain types of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in cancer cells induced an antiproliferative response with cell cycle arrest at the G2/M phase.","lang":"eng"}],"month":"02","intvolume":" 10","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-18T06:35:13Z","department":[{"_id":"CaBe"}],"file_date_updated":"2020-07-14T12:47:59Z","_id":"7487","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"10","publication":"Scientific reports","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1038/s41598-020-58264-4","date_published":"2020-02-10T00:00:00Z","date_created":"2020-02-16T23:00:49Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona, M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M. García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J. Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020).","ieee":"A. R. López De La Oliva et al., “Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020.","ama":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-58264-4","apa":"López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona, C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-58264-4","mla":"López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:10.1038/s41598-020-58264-4.","ista":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D, Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 10(1), 2259.","chicago":"López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García, Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla, et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-58264-4."},"title":"Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation","author":[{"full_name":"López De La Oliva, Amada R.","last_name":"López De La Oliva","first_name":"Amada R."},{"full_name":"Campos-Sandoval, José A.","last_name":"Campos-Sandoval","first_name":"José A."},{"first_name":"María C.","last_name":"Gómez-García","full_name":"Gómez-García, María C."},{"first_name":"Carolina","full_name":"Cardona, Carolina","last_name":"Cardona"},{"first_name":"Mercedes","last_name":"Martín-Rufián","full_name":"Martín-Rufián, Mercedes"},{"first_name":"Fernando J.","last_name":"Sialana","full_name":"Sialana, Fernando J."},{"first_name":"Laura","full_name":"Castilla, Laura","last_name":"Castilla"},{"last_name":"Bae","full_name":"Bae, Narkhyun","first_name":"Narkhyun","id":"3A5F7CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lobo","full_name":"Lobo, Carolina","first_name":"Carolina"},{"first_name":"Ana","last_name":"Peñalver","full_name":"Peñalver, Ana"},{"full_name":"García-Frutos, Marina","last_name":"García-Frutos","first_name":"Marina"},{"last_name":"Carro","full_name":"Carro, David","first_name":"David"},{"last_name":"Enrique","full_name":"Enrique, Victoria","first_name":"Victoria"},{"last_name":"Paz","full_name":"Paz, José C.","first_name":"José C."},{"last_name":"Mirmira","full_name":"Mirmira, Raghavendra G.","first_name":"Raghavendra G."},{"last_name":"Gutiérrez","full_name":"Gutiérrez, Antonia","first_name":"Antonia"},{"full_name":"Alonso, Francisco J.","last_name":"Alonso","first_name":"Francisco J."},{"last_name":"Segura","full_name":"Segura, Juan A.","first_name":"Juan A."},{"first_name":"José M.","full_name":"Matés, José M.","last_name":"Matés"},{"last_name":"Lubec","full_name":"Lubec, Gert","first_name":"Gert"},{"last_name":"Márquez","full_name":"Márquez, Javier","first_name":"Javier"}],"external_id":{"pmid":["32042057"],"isi":["000560694800012"]},"article_processing_charge":"No","article_number":"2259"},{"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"day":"23","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-01-23T00:00:00Z","doi":"10.7554/eLife.52067","date_created":"2020-02-16T23:00:50Z","article_number":"e52067","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE, Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 9, e52067.","chicago":"Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann, Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.52067.","ama":"Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 2020;9. doi:10.7554/eLife.52067","apa":"Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas Perez, B. E., & Friml, J. (2020). Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.52067","ieee":"M. Narasimhan et al., “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences Publications, 2020.","short":"M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020).","mla":"Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife, vol. 9, e52067, eLife Sciences Publications, 2020, doi:10.7554/eLife.52067."},"title":"Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants","author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","full_name":"Prizak, Roshan"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["31971511"],"isi":["000514104100001"]},"article_processing_charge":"No","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"text":"In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.","lang":"eng"}],"month":"01","intvolume":" 9","scopus_import":"1","file":[{"file_id":"7494","checksum":"2052daa4be5019534f3a42f200a09f32","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-02-18T07:21:16Z","file_name":"2020_eLife_Narasimhan.pdf","date_updated":"2020-07-14T12:47:59Z","file_size":7247468,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","volume":9,"ec_funded":1,"_id":"7490","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570","580"],"date_updated":"2023-08-18T06:33:07Z","department":[{"_id":"JiFr"},{"_id":"GaTk"},{"_id":"EM-Fac"},{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:47:59Z"},{"author":[{"full_name":"Latorre-Pellicer, Ana","last_name":"Latorre-Pellicer","first_name":"Ana"},{"last_name":"Ascaso","full_name":"Ascaso, Ángela","first_name":"Ángela"},{"first_name":"Laura","last_name":"Trujillano","full_name":"Trujillano, Laura"},{"full_name":"Gil-Salvador, Marta","last_name":"Gil-Salvador","first_name":"Marta"},{"full_name":"Arnedo, Maria","last_name":"Arnedo","first_name":"Maria"},{"first_name":"Cristina","full_name":"Lucia-Campos, Cristina","last_name":"Lucia-Campos"},{"first_name":"Rebeca","last_name":"Antoñanzas-Pérez","full_name":"Antoñanzas-Pérez, Rebeca"},{"first_name":"Iñigo","last_name":"Marcos-Alcalde","full_name":"Marcos-Alcalde, Iñigo"},{"id":"D93538B0-5B71-11E9-AC62-02EBE5697425","first_name":"Ilaria","full_name":"Parenti, Ilaria","last_name":"Parenti"},{"last_name":"Bueno-Lozano","full_name":"Bueno-Lozano, Gloria","first_name":"Gloria"},{"first_name":"Antonio","last_name":"Musio","full_name":"Musio, Antonio"},{"first_name":"Beatriz","full_name":"Puisac, Beatriz","last_name":"Puisac"},{"full_name":"Kaiser, Frank J.","last_name":"Kaiser","first_name":"Frank J."},{"full_name":"Ramos, Feliciano J.","last_name":"Ramos","first_name":"Feliciano J."},{"last_name":"Gómez-Puertas","full_name":"Gómez-Puertas, Paulino","first_name":"Paulino"},{"full_name":"Pié, Juan","last_name":"Pié","first_name":"Juan"}],"external_id":{"isi":["000522551606028"]},"article_processing_charge":"No","title":"Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes","citation":{"ieee":"A. Latorre-Pellicer et al., “Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes,” International Journal of Molecular Sciences, vol. 21, no. 3. MDPI, 2020.","short":"A. Latorre-Pellicer, Á. Ascaso, L. Trujillano, M. Gil-Salvador, M. Arnedo, C. Lucia-Campos, R. Antoñanzas-Pérez, I. Marcos-Alcalde, I. Parenti, G. Bueno-Lozano, A. Musio, B. Puisac, F.J. Kaiser, F.J. Ramos, P. Gómez-Puertas, J. Pié, International Journal of Molecular Sciences 21 (2020).","apa":"Latorre-Pellicer, A., Ascaso, Á., Trujillano, L., Gil-Salvador, M., Arnedo, M., Lucia-Campos, C., … Pié, J. (2020). Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21031042","ama":"Latorre-Pellicer A, Ascaso Á, Trujillano L, et al. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. 2020;21(3). doi:10.3390/ijms21031042","mla":"Latorre-Pellicer, Ana, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” International Journal of Molecular Sciences, vol. 21, no. 3, 1042, MDPI, 2020, doi:10.3390/ijms21031042.","ista":"Latorre-Pellicer A, Ascaso Á, Trujillano L, Gil-Salvador M, Arnedo M, Lucia-Campos C, Antoñanzas-Pérez R, Marcos-Alcalde I, Parenti I, Bueno-Lozano G, Musio A, Puisac B, Kaiser FJ, Ramos FJ, Gómez-Puertas P, Pié J. 2020. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. 21(3), 1042.","chicago":"Latorre-Pellicer, Ana, Ángela Ascaso, Laura Trujillano, Marta Gil-Salvador, Maria Arnedo, Cristina Lucia-Campos, Rebeca Antoñanzas-Pérez, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21031042."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"1042","date_published":"2020-02-04T00:00:00Z","doi":"10.3390/ijms21031042","date_created":"2020-02-16T23:00:49Z","isi":1,"has_accepted_license":"1","year":"2020","day":"04","publication":"International Journal of Molecular Sciences","publisher":"MDPI","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"GaNo"}],"date_updated":"2023-08-18T06:35:41Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7488","issue":"3","volume":21,"publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"publication_status":"published","file":[{"file_name":"2020_IntMolecSciences_Latorre.pdf","date_created":"2020-02-18T07:49:22Z","file_size":4271234,"date_updated":"2020-07-14T12:47:59Z","creator":"dernst","checksum":"0e6658c4fe329d55d4d9bef01c5b15d0","file_id":"7496","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"02","intvolume":" 21","abstract":[{"lang":"eng","text":"Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS."}],"oa_version":"Published Version"},{"file_date_updated":"2020-09-21T07:12:32Z","department":[{"_id":"ToHe"}],"date_updated":"2023-08-18T06:38:16Z","ddc":["000"],"conference":{"name":"ECAI: European Conference on Artificial Intelligence","start_date":"2020-08-29","end_date":"2020-09-08","location":"Santiago de Compostela, Spain"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"conference","status":"public","_id":"7505","ec_funded":1,"volume":325,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"80642fa0b6cd7da95dcd87d63789ad5e","file_id":"8540","success":1,"date_updated":"2020-09-21T07:12:32Z","file_size":1692214,"creator":"dernst","date_created":"2020-09-21T07:12:32Z","file_name":"2020_ECAI_Henzinger.pdf"}],"alternative_title":["Frontiers in Artificial Intelligence and Applications"],"intvolume":" 325","month":"02","abstract":[{"lang":"eng","text":"Neural networks have demonstrated unmatched performance in a range of classification tasks. Despite numerous efforts of the research community, novelty detection remains one of the significant limitations of neural networks. The ability to identify previously unseen inputs as novel is crucial for our understanding of the decisions made by neural networks. At runtime, inputs not falling into any of the categories learned during training cannot be classified correctly by the neural network. Existing approaches treat the neural network as a black box and try to detect novel inputs based on the confidence of the output predictions. However, neural networks are not trained to reduce their confidence for novel inputs, which limits the effectiveness of these approaches. We propose a framework to monitor a neural network by observing the hidden layers. We employ a common abstraction from program analysis - boxes - to identify novel behaviors in the monitored layers, i.e., inputs that cause behaviors outside the box. For each neuron, the boxes range over the values seen in training. The framework is efficient and flexible to achieve a desired trade-off between raising false warnings and detecting novel inputs. We illustrate the performance and the robustness to variability in the unknown classes on popular image-classification benchmarks."}],"oa_version":"Published Version","article_processing_charge":"No","external_id":{"isi":["000650971303002"],"arxiv":["1911.09032"]},"author":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Lukina, Anna","last_name":"Lukina","first_name":"Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425"},{"last_name":"Schilling","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"}],"title":"Outside the box: Abstraction-based monitoring of neural networks","citation":{"mla":"Henzinger, Thomas A., et al. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” 24th European Conference on Artificial Intelligence, vol. 325, IOS Press, 2020, pp. 2433–40, doi:10.3233/FAIA200375.","ieee":"T. A. Henzinger, A. Lukina, and C. Schilling, “Outside the box: Abstraction-based monitoring of neural networks,” in 24th European Conference on Artificial Intelligence, Santiago de Compostela, Spain, 2020, vol. 325, pp. 2433–2440.","short":"T.A. Henzinger, A. Lukina, C. Schilling, in:, 24th European Conference on Artificial Intelligence, IOS Press, 2020, pp. 2433–2440.","ama":"Henzinger TA, Lukina A, Schilling C. Outside the box: Abstraction-based monitoring of neural networks. In: 24th European Conference on Artificial Intelligence. Vol 325. IOS Press; 2020:2433-2440. doi:10.3233/FAIA200375","apa":"Henzinger, T. A., Lukina, A., & Schilling, C. (2020). Outside the box: Abstraction-based monitoring of neural networks. In 24th European Conference on Artificial Intelligence (Vol. 325, pp. 2433–2440). Santiago de Compostela, Spain: IOS Press. https://doi.org/10.3233/FAIA200375","chicago":"Henzinger, Thomas A, Anna Lukina, and Christian Schilling. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” In 24th European Conference on Artificial Intelligence, 325:2433–40. IOS Press, 2020. https://doi.org/10.3233/FAIA200375.","ista":"Henzinger TA, Lukina A, Schilling C. 2020. Outside the box: Abstraction-based monitoring of neural networks. 24th European Conference on Artificial Intelligence. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 325, 2433–2440."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"page":"2433-2440","date_created":"2020-02-21T16:44:03Z","doi":"10.3233/FAIA200375","date_published":"2020-02-24T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"24th European Conference on Artificial Intelligence","day":"24","oa":1,"publisher":"IOS Press","quality_controlled":"1","acknowledgement":"We thank Christoph Lampert and Nikolaus Mayer for fruitful discussions. This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement No. 754411."},{"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nL.B. gratefully acknowledges the support by the German Research Foundation (DFG) within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and wishes to thank Stefan Teufel, Sören Petrat and Marcello Porta for helpful discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. N.P. gratefully acknowledges support from NSF grant DMS-1516228 and DMS-1840314. P.P.’s research was funded by DFG Grant no. PI 1114/3-1. Part of this work was done when N.P. and P.P. were visiting CCNU, Wuhan. N.P. and P.P. thank A.S. for his hospitality at CCNU.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Journal of Statistical Physics","day":"21","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-02-23T09:45:51Z","doi":"10.1007/s10955-020-02500-8","date_published":"2020-02-21T00:00:00Z","page":"1362-1396","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"L. Bossmann, N. Pavlović, P. Pickl, A. Soffer, Journal of Statistical Physics 178 (2020) 1362–1396.","ieee":"L. Bossmann, N. Pavlović, P. Pickl, and A. Soffer, “Higher order corrections to the mean-field description of the dynamics of interacting bosons,” Journal of Statistical Physics, vol. 178. Springer Nature, pp. 1362–1396, 2020.","ama":"Bossmann L, Pavlović N, Pickl P, Soffer A. Higher order corrections to the mean-field description of the dynamics of interacting bosons. Journal of Statistical Physics. 2020;178:1362-1396. doi:10.1007/s10955-020-02500-8","apa":"Bossmann, L., Pavlović, N., Pickl, P., & Soffer, A. (2020). Higher order corrections to the mean-field description of the dynamics of interacting bosons. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-020-02500-8","mla":"Bossmann, Lea, et al. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” Journal of Statistical Physics, vol. 178, Springer Nature, 2020, pp. 1362–96, doi:10.1007/s10955-020-02500-8.","ista":"Bossmann L, Pavlović N, Pickl P, Soffer A. 2020. Higher order corrections to the mean-field description of the dynamics of interacting bosons. Journal of Statistical Physics. 178, 1362–1396.","chicago":"Bossmann, Lea, Nataša Pavlović, Peter Pickl, and Avy Soffer. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-020-02500-8."},"title":"Higher order corrections to the mean-field description of the dynamics of interacting bosons","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000516342200001"],"arxiv":["1905.06164"]},"author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343","last_name":"Bossmann"},{"first_name":"Nataša","full_name":"Pavlović, Nataša","last_name":"Pavlović"},{"first_name":"Peter","full_name":"Pickl, Peter","last_name":"Pickl"},{"full_name":"Soffer, Avy","last_name":"Soffer","first_name":"Avy"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this paper, we introduce a novel method for deriving higher order corrections to the mean-field description of the dynamics of interacting bosons. More precisely, we consider the dynamics of N d-dimensional bosons for large N. The bosons initially form a Bose–Einstein condensate and interact with each other via a pair potential of the form (N−1)−1Ndβv(Nβ·)forβ∈[0,14d). We derive a sequence of N-body functions which approximate the true many-body dynamics in L2(RdN)-norm to arbitrary precision in powers of N−1. The approximating functions are constructed as Duhamel expansions of finite order in terms of the first quantised analogue of a Bogoliubov time evolution."}],"intvolume":" 178","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"643e230bf147e64d9cdb3f6cc573679d","file_id":"8780","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_JournStatPhysics_Bossmann.pdf","date_created":"2020-11-20T09:26:46Z","file_size":576726,"date_updated":"2020-11-20T09:26:46Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"ec_funded":1,"volume":178,"_id":"7508","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["510"],"date_updated":"2023-08-18T06:37:46Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-11-20T09:26:46Z"},{"scopus_import":"1","month":"02","intvolume":" 11","abstract":[{"text":"Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.","lang":"eng"}],"oa_version":"Published Version","volume":11,"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:59Z","file_size":2027529,"date_created":"2020-02-24T14:00:54Z","file_name":"2020_NatureComm_Turonova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7517","checksum":"2c8d10475e1b0d397500760e28bdf561"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7511","department":[{"_id":"FlSc"}],"file_date_updated":"2020-07-14T12:47:59Z","date_updated":"2023-08-18T06:36:41Z","ddc":["570"],"quality_controlled":"1","publisher":"Springer Nature","oa":1,"doi":"10.1038/s41467-020-14535-2","date_published":"2020-02-13T00:00:00Z","date_created":"2020-02-23T23:00:35Z","has_accepted_license":"1","isi":1,"year":"2020","day":"13","publication":"Nature Communications","article_number":"876","author":[{"last_name":"Turoňová","full_name":"Turoňová, Beata","first_name":"Beata"},{"first_name":"Wim J.H.","full_name":"Hagen, Wim J.H.","last_name":"Hagen"},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Obr","full_name":"Obr, Martin","orcid":"0000-0003-1756-6564"},{"first_name":"Shyamal","full_name":"Mosalaganti, Shyamal","last_name":"Mosalaganti"},{"first_name":"J. Wouter","last_name":"Beugelink","full_name":"Beugelink, J. Wouter"},{"first_name":"Christian E.","full_name":"Zimmerli, Christian E.","last_name":"Zimmerli"},{"last_name":"Kräusslich","full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg"},{"full_name":"Beck, Martin","last_name":"Beck","first_name":"Martin"}],"external_id":{"isi":["000514928000017"]},"article_processing_charge":"No","title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","citation":{"short":"B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020).","ieee":"B. Turoňová et al., “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” Nature Communications, vol. 11. Springer Nature, 2020.","ama":"Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 2020;11. doi:10.1038/s41467-020-14535-2","apa":"Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W., Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-14535-2","mla":"Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature Communications, vol. 11, 876, Springer Nature, 2020, doi:10.1038/s41467-020-14535-2.","ista":"Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 11, 876.","chicago":"Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-14535-2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"_id":"7497","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-18T06:44:16Z","department":[{"_id":"JiFr"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover, the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross‐talk between JA signalling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants."}],"month":"09","intvolume":" 62","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1111/jipb.12905","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"publication_status":"published","issue":"9","volume":62,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Han, L, X Zhou, Y Zhao, S Zhu, L Wu, Y He, X Ping, et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” Journal of Integrative Plant Biology. Wiley, 2020. https://doi.org/10.1111/jipb.12905.","ista":"Han L, Zhou X, Zhao Y, Zhu S, Wu L, He Y, Ping X, Lu X, Huang W, Qian J, Zhang L, Jiang X, Zhu D, Luo C, Li S, Dong Q, Fu Q, Deng K, Wang X, Wang L, Peng S, Wu J, Li W, Friml J, Zhu Y, He X, Du Y. 2020. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. 62(9), 1433–1451.","mla":"Han, L., et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” Journal of Integrative Plant Biology, vol. 62, no. 9, Wiley, 2020, pp. 1433–51, doi:10.1111/jipb.12905.","short":"L. Han, X. Zhou, Y. Zhao, S. Zhu, L. Wu, Y. He, X. Ping, X. Lu, W. Huang, J. Qian, L. Zhang, X. Jiang, D. Zhu, C. Luo, S. Li, Q. Dong, Q. Fu, K. Deng, X. Wang, L. Wang, S. Peng, J. Wu, W. Li, J. Friml, Y. Zhu, X. He, Y. Du, Journal of Integrative Plant Biology 62 (2020) 1433–1451.","ieee":"L. Han et al., “Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid,” Journal of Integrative Plant Biology, vol. 62, no. 9. Wiley, pp. 1433–1451, 2020.","ama":"Han L, Zhou X, Zhao Y, et al. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. 2020;62(9):1433-1451. doi:10.1111/jipb.12905","apa":"Han, L., Zhou, X., Zhao, Y., Zhu, S., Wu, L., He, Y., … Du, Y. (2020). Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.12905"},"title":"Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid","author":[{"full_name":"Han, L","last_name":"Han","first_name":"L"},{"first_name":"X","full_name":"Zhou, X","last_name":"Zhou"},{"last_name":"Zhao","full_name":"Zhao, Y","first_name":"Y"},{"first_name":"S","last_name":"Zhu","full_name":"Zhu, S"},{"full_name":"Wu, L","last_name":"Wu","first_name":"L"},{"full_name":"He, Y","last_name":"He","first_name":"Y"},{"last_name":"Ping","full_name":"Ping, X","first_name":"X"},{"first_name":"X","full_name":"Lu, X","last_name":"Lu"},{"full_name":"Huang, W","last_name":"Huang","first_name":"W"},{"last_name":"Qian","full_name":"Qian, J","first_name":"J"},{"last_name":"Zhang","full_name":"Zhang, L","first_name":"L"},{"first_name":"X","full_name":"Jiang, X","last_name":"Jiang"},{"full_name":"Zhu, D","last_name":"Zhu","first_name":"D"},{"first_name":"C","last_name":"Luo","full_name":"Luo, C"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"full_name":"Dong, Q","last_name":"Dong","first_name":"Q"},{"first_name":"Q","last_name":"Fu","full_name":"Fu, Q"},{"first_name":"K","full_name":"Deng, K","last_name":"Deng"},{"first_name":"X","last_name":"Wang","full_name":"Wang, X"},{"first_name":"L","last_name":"Wang","full_name":"Wang, L"},{"first_name":"S","full_name":"Peng, S","last_name":"Peng"},{"full_name":"Wu, J","last_name":"Wu","first_name":"J"},{"last_name":"Li","full_name":"Li, W","first_name":"W"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Y","full_name":"Zhu, Y","last_name":"Zhu"},{"first_name":"X","last_name":"He","full_name":"He, X"},{"full_name":"Du, Y","last_name":"Du","first_name":"Y"}],"external_id":{"isi":["000515803000001"],"pmid":["31912615"]},"article_processing_charge":"No","acknowledgement":"We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for providing generous support with the IAA and JA measurements. We thank Professor Guohua Xu (Nanjing Agricultural University) for generously providing the Nipponbare rice expressing DR5::GUS. We thank Professor Muyuan Zhu (Zhejiang University) for generously providing a rice line expressing 35S::miR393b. We thank Professor Yinong Yang (Pennsylvania State University) for generously providing the rice line coi1-18. This work was supported by grants from the National Natural Science Foundation of China (31660501, 31460453, 31860064 and 31470382), the Major Special Program for Scientific Research, Education Department of Yunnan Province (ZD2015005), the Project sponsored by SRF for ROCS, SEM ([2013] 1792), the Major Science and Technique Programs in Yunnan Province (2016ZF001), the Key Projects of the Applied Basic Research Plan of Yunnan Province (2017FA018), the National Key R&D Program of China (2018YFD0201100) and the China Agriculture Research System (CARS-21).","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"01","publication":"Journal of Integrative Plant Biology","isi":1,"year":"2020","date_published":"2020-09-01T00:00:00Z","doi":"10.1111/jipb.12905","date_created":"2020-02-18T10:02:25Z","page":"1433-1451"},{"date_updated":"2023-08-18T06:44:46Z","department":[{"_id":"BjHo"}],"_id":"7534","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2469-990X"]},"volume":5,"issue":"2","oa_version":"Preprint","abstract":[{"text":"In the past two decades, our understanding of the transition to turbulence in shear flows with linearly stable laminar solutions has greatly improved. Regarding the susceptibility of the laminar flow, two concepts have been particularly useful: the edge states and the minimal seeds. In this nonlinear picture of the transition, the basin boundary of turbulence is set by the edge state's stable manifold and this manifold comes closest in energy to the laminar equilibrium at the minimal seed. We begin this paper by presenting numerical experiments in which three-dimensional perturbations are too energetic to trigger turbulence in pipe flow but they do lead to turbulence when their amplitude is reduced. We show that this seemingly counterintuitive observation is in fact consistent with the fully nonlinear description of the transition mediated by the edge state. In order to understand the physical mechanisms behind this process, we measure the turbulent kinetic energy production and dissipation rates as a function of the radial coordinate. Our main observation is that the transition to turbulence relies on the energy amplification away from the wall, as opposed to the turbulence itself, whose energy is predominantly produced near the wall. This observation is further supported by the similar analyses on the minimal seeds and the edge states. Furthermore, we show that the time evolution of production-over-dissipation curves provides a clear distinction between the different initial amplification stages of the transition to turbulence from the minimal seed.","lang":"eng"}],"intvolume":" 5","month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1912.09270","open_access":"1"}],"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Budanur NB, Marensi E, Willis AP, Hof B. 2020. Upper edge of chaos and the energetics of transition in pipe flow. Physical Review Fluids. 5(2), 023903.","chicago":"Budanur, Nazmi B, Elena Marensi, Ashley P. Willis, and Björn Hof. “Upper Edge of Chaos and the Energetics of Transition in Pipe Flow.” Physical Review Fluids. American Physical Society, 2020. https://doi.org/10.1103/physrevfluids.5.023903.","ieee":"N. B. Budanur, E. Marensi, A. P. Willis, and B. Hof, “Upper edge of chaos and the energetics of transition in pipe flow,” Physical Review Fluids, vol. 5, no. 2. American Physical Society, 2020.","short":"N.B. Budanur, E. Marensi, A.P. Willis, B. Hof, Physical Review Fluids 5 (2020).","ama":"Budanur NB, Marensi E, Willis AP, Hof B. Upper edge of chaos and the energetics of transition in pipe flow. Physical Review Fluids. 2020;5(2). doi:10.1103/physrevfluids.5.023903","apa":"Budanur, N. B., Marensi, E., Willis, A. P., & Hof, B. (2020). Upper edge of chaos and the energetics of transition in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/physrevfluids.5.023903","mla":"Budanur, Nazmi B., et al. “Upper Edge of Chaos and the Energetics of Transition in Pipe Flow.” Physical Review Fluids, vol. 5, no. 2, 023903, American Physical Society, 2020, doi:10.1103/physrevfluids.5.023903."},"title":"Upper edge of chaos and the energetics of transition in pipe flow","external_id":{"isi":["000515065100001"],"arxiv":["1912.09270"]},"article_processing_charge":"No","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"},{"first_name":"Elena","last_name":"Marensi","full_name":"Marensi, Elena"},{"last_name":"Willis","full_name":"Willis, Ashley P.","first_name":"Ashley P."},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"article_number":"023903","publication":"Physical Review Fluids","day":"21","year":"2020","isi":1,"date_created":"2020-02-27T10:26:57Z","date_published":"2020-02-21T00:00:00Z","doi":"10.1103/physrevfluids.5.023903","oa":1,"quality_controlled":"1","publisher":"American Physical Society"},{"_id":"7512","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-18T06:36:10Z","department":[{"_id":"LaEr"}],"abstract":[{"text":"We consider general self-adjoint polynomials in several independent random matrices whose entries are centered and have the same variance. We show that under certain conditions the local law holds up to the optimal scale, i.e., the eigenvalue density on scales just above the eigenvalue spacing follows the global density of states which is determined by free probability theory. We prove that these conditions hold for general homogeneous polynomials of degree two and for symmetrized products of independent matrices with i.i.d. entries, thus establishing the optimal bulk local law for these classes of ensembles. In particular, we generalize a similar result of Anderson for anticommutator. For more general polynomials our conditions are effectively checkable numerically.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1804.11340","open_access":"1"}],"month":"07","intvolume":" 278","publication_identifier":{"issn":["00221236"],"eissn":["10960783"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"12","volume":278,"ec_funded":1,"article_number":"108507","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"citation":{"ista":"Erdös L, Krüger TH, Nemish Y. 2020. Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. 278(12), 108507.","chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Local Laws for Polynomials of Wigner Matrices.” Journal of Functional Analysis. Elsevier, 2020. https://doi.org/10.1016/j.jfa.2020.108507.","apa":"Erdös, L., Krüger, T. H., & Nemish, Y. (2020). Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2020.108507","ama":"Erdös L, Krüger TH, Nemish Y. Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. 2020;278(12). doi:10.1016/j.jfa.2020.108507","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Local laws for polynomials of Wigner matrices,” Journal of Functional Analysis, vol. 278, no. 12. Elsevier, 2020.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Journal of Functional Analysis 278 (2020).","mla":"Erdös, László, et al. “Local Laws for Polynomials of Wigner Matrices.” Journal of Functional Analysis, vol. 278, no. 12, 108507, Elsevier, 2020, doi:10.1016/j.jfa.2020.108507."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger"},{"last_name":"Nemish","full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","first_name":"Yuriy"}],"external_id":{"arxiv":["1804.11340"],"isi":["000522798900001"]},"article_processing_charge":"No","title":"Local laws for polynomials of Wigner matrices","acknowledgement":"The authors are grateful to Oskari Ajanki for his invaluable help at the initial stage of this project, to Serban Belinschi for useful discussions, to Alexander Tikhomirov for calling our attention to the model example in Section 6.2 and to the anonymous referee for suggesting to simplify certain proofs. Erdös: Partially funded by ERC Advanced Grant RANMAT No. 338804\r\n","quality_controlled":"1","publisher":"Elsevier","oa":1,"isi":1,"year":"2020","day":"01","publication":"Journal of Functional Analysis","doi":"10.1016/j.jfa.2020.108507","date_published":"2020-07-01T00:00:00Z","date_created":"2020-02-23T23:00:36Z"},{"title":"From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture","author":[{"id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan","full_name":"Zhang, Haonan","last_name":"Zhang"}],"article_processing_charge":"No","external_id":{"arxiv":["1811.01205"],"isi":["000522798000001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Zhang H. 2020. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. 365, 107053.","chicago":"Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” Advances in Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.aim.2020.107053.","ama":"Zhang H. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. 2020;365. doi:10.1016/j.aim.2020.107053","apa":"Zhang, H. (2020). From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2020.107053","ieee":"H. Zhang, “From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture,” Advances in Mathematics, vol. 365. Elsevier, 2020.","short":"H. Zhang, Advances in Mathematics 365 (2020).","mla":"Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” Advances in Mathematics, vol. 365, 107053, Elsevier, 2020, doi:10.1016/j.aim.2020.107053."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_number":"107053","doi":"10.1016/j.aim.2020.107053","date_published":"2020-05-13T00:00:00Z","date_created":"2020-02-23T21:43:50Z","day":"13","publication":"Advances in Mathematics","isi":1,"year":"2020","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"The author would like to thank Quanhua Xu, Adam Skalski, Ke Li and Zhi Yin for their valuable comments. He also would like to thank the anonymous referees for pointing out some errors in an earlier version of this paper and for helpful comments and suggestions that make this paper better. The research was partially supported by the NCN (National Centre of Science) grant 2014/14/E/ST1/00525, the French project ISITE-BFC (contract ANR-15-IDEX-03), NSFC No. 11826012, and the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","department":[{"_id":"JaMa"}],"ddc":["515"],"date_updated":"2023-08-18T06:37:09Z","status":"public","article_type":"original","type":"journal_article","_id":"7509","volume":365,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"05","intvolume":" 365","main_file_link":[{"url":"https://arxiv.org/abs/1811.01205","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"In this paper we study the joint convexity/concavity of the trace functions Ψp,q,s(A,B)=Tr(Bq2K∗ApKBq2)s, p,q,s∈R,\r\nwhere A and B are positive definite matrices and K is any fixed invertible matrix. We will give full range of (p,q,s)∈R3 for Ψp,q,s to be jointly convex/concave for all K. As a consequence, we confirm a conjecture of Carlen, Frank and Lieb. In particular, we confirm a weaker conjecture of Audenaert and Datta and obtain the full range of (α,z) for α-z Rényi relative entropies to be monotone under completely positive trace preserving maps. We also give simpler proofs of many known results, including the concavity of Ψp,0,1/p for 0
Neuron. Cell Press, 2020. https://doi.org/10.1016/j.neuron.2019.10.001.","ista":"Beets I, Zhang G, Fenk LA, Chen C, Nelson GM, Félix M-A, de Bono M. 2020. Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. Neuron. 105(1), 106–121.e10.","mla":"Beets, Isabel, et al. “Natural Variation in a Dendritic Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide Expression.” Neuron, vol. 105, no. 1, Cell Press, 2020, p. 106–121.e10, doi:10.1016/j.neuron.2019.10.001.","ieee":"I. Beets et al., “Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression,” Neuron, vol. 105, no. 1. Cell Press, p. 106–121.e10, 2020.","short":"I. Beets, G. Zhang, L.A. Fenk, C. Chen, G.M. Nelson, M.-A. Félix, M. de Bono, Neuron 105 (2020) 106–121.e10.","ama":"Beets I, Zhang G, Fenk LA, et al. Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. Neuron. 2020;105(1):106-121.e10. doi:10.1016/j.neuron.2019.10.001","apa":"Beets, I., Zhang, G., Fenk, L. A., Chen, C., Nelson, G. M., Félix, M.-A., & de Bono, M. (2020). Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2019.10.001"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["31757604"],"isi":["000507341300012"]},"article_processing_charge":"No","author":[{"full_name":"Beets, Isabel","last_name":"Beets","first_name":"Isabel"},{"first_name":"Gaotian","full_name":"Zhang, Gaotian","last_name":"Zhang"},{"full_name":"Fenk, Lorenz A.","last_name":"Fenk","first_name":"Lorenz A."},{"first_name":"Changchun","full_name":"Chen, Changchun","last_name":"Chen"},{"last_name":"Nelson","full_name":"Nelson, Geoffrey M.","first_name":"Geoffrey M."},{"full_name":"Félix, Marie-Anne","last_name":"Félix","first_name":"Marie-Anne"},{"orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"}],"title":"Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression","publication_status":"published","publication_identifier":{"issn":["0896-6273"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"799bfd297a008753a688b30d3958fa48","file_id":"7558","file_size":3294066,"date_updated":"2020-07-14T12:48:00Z","creator":"dernst","file_name":"2020_Neuron_Beets.pdf","date_created":"2020-03-02T15:43:57Z"}],"issue":"1","volume":105,"abstract":[{"lang":"eng","text":"The extent to which behavior is shaped by experience varies between individuals. Genetic differences contribute to this variation, but the neural mechanisms are not understood. Here, we dissect natural variation in the behavioral flexibility of two Caenorhabditis elegans wild strains. In one strain, a memory of exposure to 21% O2 suppresses CO2-evoked locomotory arousal; in the other, CO2 evokes arousal regardless of previous O2 experience. We map that variation to a polymorphic dendritic scaffold protein, ARCP-1, expressed in sensory neurons. ARCP-1 binds the Ca2+-dependent phosphodiesterase PDE-1 and co-localizes PDE-1 with molecular sensors for CO2 at dendritic ends. Reducing ARCP-1 or PDE-1 activity promotes CO2 escape by altering neuropeptide expression in the BAG CO2 sensors. Variation in ARCP-1 alters behavioral plasticity in multiple paradigms. Our findings are reminiscent of genetic accommodation, an evolutionary process by which phenotypic flexibility in response to environmental variation is reset by genetic change."}],"pmid":1,"oa_version":"Published Version","intvolume":" 105","month":"01","date_updated":"2023-08-18T06:46:23Z","ddc":["570"],"department":[{"_id":"MaDe"}],"file_date_updated":"2020-07-14T12:48:00Z","_id":"7546","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan","last_name":"Yalniz"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur"}],"external_id":{"isi":["000519254800002"],"arxiv":["1910.04584"]},"article_processing_charge":"No","title":"Inferring symbolic dynamics of chaotic flows from persistence","citation":{"mla":"Yalniz, Gökhan, and Nazmi B. Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” Chaos, vol. 30, no. 3, 033109, AIP Publishing, 2020, doi:10.1063/1.5122969.","ieee":"G. Yalniz and N. B. Budanur, “Inferring symbolic dynamics of chaotic flows from persistence,” Chaos, vol. 30, no. 3. AIP Publishing, 2020.","short":"G. Yalniz, N.B. Budanur, Chaos 30 (2020).","ama":"Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 2020;30(3). doi:10.1063/1.5122969","apa":"Yalniz, G., & Budanur, N. B. (2020). Inferring symbolic dynamics of chaotic flows from persistence. Chaos. AIP Publishing. https://doi.org/10.1063/1.5122969","chicago":"Yalniz, Gökhan, and Nazmi B Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” Chaos. AIP Publishing, 2020. https://doi.org/10.1063/1.5122969.","ista":"Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 30(3), 033109."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"033109","date_published":"2020-03-03T00:00:00Z","doi":"10.1063/1.5122969","date_created":"2020-03-04T08:06:25Z","isi":1,"year":"2020","day":"03","publication":"Chaos","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"department":[{"_id":"BjHo"}],"date_updated":"2023-08-18T06:47:16Z","type":"journal_article","article_type":"original","status":"public","_id":"7563","volume":30,"issue":"3","publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1063/1.5122969","open_access":"1"}],"month":"03","intvolume":" 30","abstract":[{"text":"We introduce “state space persistence analysis” for deducing the symbolic dynamics of time series data obtained from high-dimensional chaotic attractors. To this end, we adapt a topological data analysis technique known as persistent homology for the characterization of state space projections of chaotic trajectories and periodic orbits. By comparing the shapes along a chaotic trajectory to those of the periodic orbits, state space persistence analysis quantifies the shape similarity of chaotic trajectory segments and periodic orbits. We demonstrate the method by applying it to the three-dimensional Rössler system and a 30-dimensional discretization of the Kuramoto–Sivashinsky partial differential equation in (1+1) dimensions.\r\nOne way of studying chaotic attractors systematically is through their symbolic dynamics, in which one partitions the state space into qualitatively different regions and assigns a symbol to each such region.1–3 This yields a “coarse-grained” state space of the system, which can then be reduced to a Markov chain encoding all possible transitions between the states of the system. While it is possible to obtain the symbolic dynamics of low-dimensional chaotic systems with standard tools such as Poincaré maps, when applied to high-dimensional systems such as turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5 In this paper, we develop “state space persistence analysis” and demonstrate that it can be utilized to infer the symbolic dynamics in very high-dimensional settings.","lang":"eng"}],"oa_version":"Published Version"},{"_id":"7554","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-18T06:45:48Z","department":[{"_id":"HeEd"}],"abstract":[{"lang":"eng","text":"Slicing a Voronoi tessellation in ${R}^n$ with a $k$-plane gives a $k$-dimensional weighted Voronoi tessellation, also known as a power diagram or Laguerre tessellation. Mapping every simplex of the dual weighted Delaunay mosaic to the radius of the smallest empty circumscribed sphere whose center lies in the $k$-plane gives a generalized discrete Morse function. Assuming the Voronoi tessellation is generated by a Poisson point process in ${R}^n$, we study the expected number of simplices in the $k$-dimensional weighted Delaunay mosaic as well as the expected number of intervals of the Morse function, both as functions of a radius threshold. As a by-product, we obtain a new proof for the expected number of connected components (clumps) in a line section of a circular Boolean model in ${R}^n$."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.08735"}],"month":"02","intvolume":" 64","publication_identifier":{"eissn":["10957219"],"issn":["0040585X"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":64,"issue":"4","ec_funded":1,"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.” Theory of Probability and Its Applications, vol. 64, no. 4, SIAM, 2020, pp. 595–614, doi:10.1137/S0040585X97T989726.","ieee":"H. Edelsbrunner and A. Nikitenko, “Weighted Poisson–Delaunay mosaics,” Theory of Probability and its Applications, vol. 64, no. 4. SIAM, pp. 595–614, 2020.","short":"H. Edelsbrunner, A. Nikitenko, Theory of Probability and Its Applications 64 (2020) 595–614.","apa":"Edelsbrunner, H., & Nikitenko, A. (2020). Weighted Poisson–Delaunay mosaics. Theory of Probability and Its Applications. SIAM. https://doi.org/10.1137/S0040585X97T989726","ama":"Edelsbrunner H, Nikitenko A. Weighted Poisson–Delaunay mosaics. Theory of Probability and its Applications. 2020;64(4):595-614. doi:10.1137/S0040585X97T989726","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.” Theory of Probability and Its Applications. SIAM, 2020. https://doi.org/10.1137/S0040585X97T989726.","ista":"Edelsbrunner H, Nikitenko A. 2020. Weighted Poisson–Delaunay mosaics. Theory of Probability and its Applications. 64(4), 595–614."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton"}],"external_id":{"arxiv":["1705.08735"],"isi":["000551393100007"]},"article_processing_charge":"No","title":"Weighted Poisson–Delaunay mosaics","quality_controlled":"1","publisher":"SIAM","oa":1,"isi":1,"year":"2020","day":"13","publication":"Theory of Probability and its Applications","page":"595-614","date_published":"2020-02-13T00:00:00Z","doi":"10.1137/S0040585X97T989726","date_created":"2020-03-01T23:00:39Z"},{"article_number":"011055","author":[{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","last_name":"Michailidis","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064"},{"first_name":"C. J.","full_name":"Turner, C. J.","last_name":"Turner"},{"last_name":"Papić","full_name":"Papić, Z.","first_name":"Z."},{"first_name":"D. A.","last_name":"Abanin","full_name":"Abanin, D. A."},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000517969300001"],"arxiv":["1905.08564"]},"article_processing_charge":"No","title":"Slow quantum thermalization and many-body revivals from mixed phase space","citation":{"mla":"Michailidis, Alexios, et al. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” Physical Review X, vol. 10, no. 1, 011055, American Physical Society, 2020, doi:10.1103/physrevx.10.011055.","ama":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. Slow quantum thermalization and many-body revivals from mixed phase space. Physical Review X. 2020;10(1). doi:10.1103/physrevx.10.011055","apa":"Michailidis, A., Turner, C. J., Papić, Z., Abanin, D. A., & Serbyn, M. (2020). Slow quantum thermalization and many-body revivals from mixed phase space. Physical Review X. American Physical Society. https://doi.org/10.1103/physrevx.10.011055","ieee":"A. Michailidis, C. J. Turner, Z. Papić, D. A. Abanin, and M. Serbyn, “Slow quantum thermalization and many-body revivals from mixed phase space,” Physical Review X, vol. 10, no. 1. American Physical Society, 2020.","short":"A. Michailidis, C.J. Turner, Z. Papić, D.A. Abanin, M. Serbyn, Physical Review X 10 (2020).","chicago":"Michailidis, Alexios, C. J. Turner, Z. Papić, D. A. Abanin, and Maksym Serbyn. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” Physical Review X. American Physical Society, 2020. https://doi.org/10.1103/physrevx.10.011055.","ista":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. 2020. Slow quantum thermalization and many-body revivals from mixed phase space. Physical Review X. 10(1), 011055."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"American Physical Society","oa":1,"date_published":"2020-03-04T00:00:00Z","doi":"10.1103/physrevx.10.011055","date_created":"2020-03-08T18:02:01Z","has_accepted_license":"1","isi":1,"year":"2020","day":"04","publication":"Physical Review X","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7570","department":[{"_id":"MaSe"}],"file_date_updated":"2020-07-14T12:48:00Z","date_updated":"2023-08-18T07:01:07Z","ddc":["530"],"scopus_import":"1","month":"03","intvolume":" 10","abstract":[{"lang":"eng","text":"The relaxation of few-body quantum systems can strongly depend on the initial state when the system’s semiclassical phase space is mixed; i.e., regions of chaotic motion coexist with regular islands. In recent years, there has been much effort to understand the process of thermalization in strongly interacting quantum systems that often lack an obvious semiclassical limit. The time-dependent variational principle (TDVP) allows one to systematically derive an effective classical (nonlinear) dynamical system by projecting unitary many-body dynamics onto a manifold of weakly entangled variational states. We demonstrate that such dynamical systems generally possess mixed phase space. When TDVP errors are small, the mixed phase space leaves a footprint on the exact dynamics of the quantum model. For example, when the system is initialized in a state belonging to a stable periodic orbit or the surrounding regular region, it exhibits persistent many-body quantum revivals. As a proof of principle, we identify new types of “quantum many-body scars,” i.e., initial states that lead to long-time oscillations in a model of interacting Rydberg atoms in one and two dimensions. Intriguingly, the initial states that give rise to most robust revivals are typically entangled states. On the other hand, even when TDVP errors are large, as in the thermalizing tilted-field Ising model, initializing the system in a regular region of phase space leads to a surprising slowdown of thermalization. Our work establishes TDVP as a method for identifying interacting quantum systems with anomalous dynamics in arbitrary dimensions. Moreover, the mixed phase space classical variational equations allow one to find slowly thermalizing initial conditions in interacting models. Our results shed light on a link between classical and quantum chaos, pointing toward possible extensions of the classical Kolmogorov-Arnold-Moser theorem to quantum systems."}],"oa_version":"Published Version","volume":10,"issue":"1","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/classical-physics-helps-predict-fate-of-interacting-quantum-systems/","description":"News on IST Homepage"}]},"publication_identifier":{"issn":["2160-3308"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"4b3f2c13873d35230173c73d0e11c408","file_id":"7581","creator":"dernst","date_updated":"2020-07-14T12:48:00Z","file_size":17828638,"date_created":"2020-03-12T12:13:07Z","file_name":"2020_PhysicalReviewX_Michailidis.pdf"}],"language":[{"iso":"eng"}]},{"date_updated":"2023-08-18T07:07:08Z","ddc":["580"],"file_date_updated":"2020-07-14T12:48:00Z","department":[{"_id":"JiFr"}],"_id":"7582","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["22237747"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-03-23T13:37:00Z","file_name":"2020_Plants_Moturu.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:00Z","file_size":2373484,"file_id":"7614","checksum":"6d5af3e17266a48996b4af4e67e88a85","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":9,"issue":"3","abstract":[{"lang":"eng","text":"Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"03","citation":{"ista":"Moturu TR, Sinha S, Salava H, Thula S, Nodzyński T, Vařeková RS, Friml J, Simon S. 2020. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. Plants. 9(3), 299.","chicago":"Moturu, Taraka Ramji, Sansrity Sinha, Hymavathi Salava, Sravankumar Thula, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” Plants. MDPI, 2020. https://doi.org/10.3390/plants9030299.","ama":"Moturu TR, Sinha S, Salava H, et al. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. Plants. 2020;9(3). doi:10.3390/plants9030299","apa":"Moturu, T. R., Sinha, S., Salava, H., Thula, S., Nodzyński, T., Vařeková, R. S., … Simon, S. (2020). Molecular evolution and diversification of proteins involved in miRNA maturation pathway. Plants. MDPI. https://doi.org/10.3390/plants9030299","ieee":"T. R. Moturu et al., “Molecular evolution and diversification of proteins involved in miRNA maturation pathway,” Plants, vol. 9, no. 3. MDPI, 2020.","short":"T.R. Moturu, S. Sinha, H. Salava, S. Thula, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Plants 9 (2020).","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” Plants, vol. 9, no. 3, 299, MDPI, 2020, doi:10.3390/plants9030299."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000525315000035"],"pmid":["32121542"]},"author":[{"first_name":"Taraka Ramji","last_name":"Moturu","full_name":"Moturu, Taraka Ramji"},{"full_name":"Sinha, Sansrity","last_name":"Sinha","first_name":"Sansrity"},{"first_name":"Hymavathi","last_name":"Salava","full_name":"Salava, Hymavathi"},{"first_name":"Sravankumar","full_name":"Thula, Sravankumar","last_name":"Thula"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Radka Svobodová","last_name":"Vařeková","full_name":"Vařeková, Radka Svobodová"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon"}],"title":"Molecular evolution and diversification of proteins involved in miRNA maturation pathway","article_number":"299","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"year":"2020","has_accepted_license":"1","isi":1,"publication":"Plants","day":"01","date_created":"2020-03-15T23:00:52Z","date_published":"2020-03-01T00:00:00Z","doi":"10.3390/plants9030299","oa":1,"publisher":"MDPI","quality_controlled":"1"},{"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Heterozygous loss of human PAFAH1B1 (coding for LIS1) results in the disruption of neurogenesis and neuronal migration via dysregulation of microtubule (MT) stability and dynein motor function/localization that alters mitotic spindle orientation, chromosomal segregation, and nuclear migration. Recently, human induced pluripotent stem cell (iPSC) models revealed an important role for LIS1 in controlling the length of terminal cell divisions of outer radial glial (oRG) progenitors, suggesting cellular functions of LIS1 in regulating neural progenitor cell (NPC) daughter cell separation. Here we examined the late mitotic stages NPCs in vivo and mouse embryonic fibroblasts (MEFs) in vitro from Pafah1b1-deficient mutants. Pafah1b1-deficient neocortical NPCs and MEFs similarly exhibited cleavage plane displacement with mislocalization of furrow-associated markers, associated with actomyosin dysfunction and cell membrane hyper-contractility. Thus, it suggests LIS1 acts as a key molecular link connecting MTs/dynein and actomyosin, ensuring that cell membrane contractility is tightly controlled to execute proper daughter cell separation."}],"month":"03","intvolume":" 9","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/751958","open_access":"1"}],"file":[{"success":1,"file_id":"8567","checksum":"396ceb2dd10b102ef4e699666b9342c3","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_elife_Moon.pdf","date_created":"2020-09-24T07:03:20Z","file_size":15089438,"date_updated":"2020-09-24T07:03:20Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","volume":9,"_id":"7593","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-18T07:06:31Z","file_date_updated":"2020-09-24T07:03:20Z","department":[{"_id":"SiHi"}],"publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"day":"11","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.7554/elife.51512","date_published":"2020-03-11T00:00:00Z","date_created":"2020-03-20T13:16:41Z","article_number":"51512","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Moon, Hyang Mi, Simon Hippenmeyer, Liqun Luo, and Anthony Wynshaw-Boris. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.51512.","ista":"Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. 2020. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. eLife. 9, 51512.","mla":"Moon, Hyang Mi, et al. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” ELife, vol. 9, 51512, eLife Sciences Publications, 2020, doi:10.7554/elife.51512.","ieee":"H. M. Moon, S. Hippenmeyer, L. Luo, and A. Wynshaw-Boris, “LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility,” eLife, vol. 9. eLife Sciences Publications, 2020.","short":"H.M. Moon, S. Hippenmeyer, L. Luo, A. Wynshaw-Boris, ELife 9 (2020).","apa":"Moon, H. M., Hippenmeyer, S., Luo, L., & Wynshaw-Boris, A. (2020). LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.51512","ama":"Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. eLife. 2020;9. doi:10.7554/elife.51512"},"title":"LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility","author":[{"full_name":"Moon, Hyang Mi","last_name":"Moon","first_name":"Hyang Mi"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"},{"first_name":"Anthony","full_name":"Wynshaw-Boris, Anthony","last_name":"Wynshaw-Boris"}],"article_processing_charge":"No","external_id":{"isi":["000522835800001"],"pmid":["32159512"]}},{"page":"556-569","date_created":"2020-03-21T16:34:16Z","date_published":"2020-05-01T00:00:00Z","doi":"10.1038/s41477-020-0648-9","year":"2020","isi":1,"publication":"Nature Plants","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer Nature","external_id":{"pmid":["32393881"],"isi":["000531787500006"]},"article_processing_charge":"No","author":[{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","last_name":"Zhang"},{"full_name":"Kong, Wei","last_name":"Kong","first_name":"Wei"},{"full_name":"Yang, Xiao-Li","last_name":"Yang","first_name":"Xiao-Li"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely"},{"first_name":"Zuzana","last_name":"Vondráková","full_name":"Vondráková, Zuzana"},{"first_name":"Roberta","last_name":"Filepová","full_name":"Filepová, Roberta"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Hong-Wei","full_name":"Xue, Hong-Wei","last_name":"Xue"}],"title":"The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis","citation":{"ieee":"S. Tan et al., “The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis,” Nature Plants, vol. 6. Springer Nature, pp. 556–569, 2020.","short":"S. Tan, X. Zhang, W. Kong, X.-L. Yang, G. Molnar, Z. Vondráková, R. Filepová, J. Petrášek, J. Friml, H.-W. Xue, Nature Plants 6 (2020) 556–569.","ama":"Tan S, Zhang X, Kong W, et al. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. 2020;6:556-569. doi:10.1038/s41477-020-0648-9","apa":"Tan, S., Zhang, X., Kong, W., Yang, X.-L., Molnar, G., Vondráková, Z., … Xue, H.-W. (2020). The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-020-0648-9","mla":"Tan, Shutang, et al. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” Nature Plants, vol. 6, Springer Nature, 2020, pp. 556–69, doi:10.1038/s41477-020-0648-9.","ista":"Tan S, Zhang X, Kong W, Yang X-L, Molnar G, Vondráková Z, Filepová R, Petrášek J, Friml J, Xue H-W. 2020. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. 6, 556–569.","chicago":"Tan, Shutang, Xixi Zhang, Wei Kong, Xiao-Li Yang, Gergely Molnar, Zuzana Vondráková, Roberta Filepová, Jan Petrášek, Jiří Friml, and Hong-Wei Xue. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” Nature Plants. Springer Nature, 2020. https://doi.org/10.1038/s41477-020-0648-9."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship","grant_number":"723-2015"}],"ec_funded":1,"volume":6,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41477-020-0719-y"}]},"publication_status":"published","publication_identifier":{"eissn":["20550278"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/755504","open_access":"1"}],"scopus_import":"1","intvolume":" 6","month":"05","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Directional intercellular transport of the phytohormone auxin mediated by PIN FORMED (PIN) efflux carriers plays essential roles in both coordinating patterning processes and integrating multiple external cues by rapidly redirecting auxin fluxes. Multilevel regulations of PIN activity under internal and external cues are complicated; however, the underlying molecular mechanism remains elusive. Here we demonstrate that 3’-Phosphoinositide-Dependent Protein Kinase1 (PDK1), which is conserved in plants and mammals, functions as a molecular hub integrating the upstream lipid signalling and the downstream substrate activity through phosphorylation. Genetic analysis uncovers that loss-of-function Arabidopsis mutant pdk1.1 pdk1.2 exhibits a plethora of abnormalities in organogenesis and growth, due to the defective PIN-dependent auxin transport. Further cellular and biochemical analyses reveal that PDK1 phosphorylates D6 Protein Kinase to facilitate its activity towards PIN proteins. Our studies establish a lipid-dependent phosphorylation cascade connecting membrane composition-based cellular signalling with plant growth and patterning by regulating morphogenetic auxin fluxes.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"department":[{"_id":"JiFr"}],"date_updated":"2023-08-18T07:05:57Z","type":"journal_article","article_type":"original","status":"public","_id":"7600"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants."}],"month":"02","intvolume":" 11","scopus_import":"1","file":[{"file_size":507414,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_name":"2020_FrontiersPlants_Nimeth.pdf","date_created":"2020-03-23T09:03:40Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7607","checksum":"57c37209f7b6712ced86c0f11b2be74e"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664462X"]},"publication_status":"published","volume":11,"_id":"7603","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"date_updated":"2023-08-18T07:05:18Z","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:48:01Z","publisher":"Frontiers","quality_controlled":"1","oa":1,"day":"19","publication":"Frontiers in Plant Science","isi":1,"has_accepted_license":"1","year":"2020","date_published":"2020-02-19T00:00:00Z","doi":"10.3389/fpls.2020.00091","date_created":"2020-03-22T23:00:46Z","article_number":"91","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing and DNA Damage Response in Plants.” Frontiers in Plant Science. Frontiers, 2020. https://doi.org/10.3389/fpls.2020.00091.","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91.","mla":"Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response in Plants.” Frontiers in Plant Science, vol. 11, 91, Frontiers, 2020, doi:10.3389/fpls.2020.00091.","apa":"Nimeth, B. A., Riegler, S., & Kalyna, M. (2020). Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.00091","ama":"Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.00091","ieee":"B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage response in plants,” Frontiers in Plant Science, vol. 11. Frontiers, 2020.","short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020)."},"title":"Alternative splicing and DNA damage response in plants","author":[{"last_name":"Nimeth","full_name":"Nimeth, Barbara Anna","first_name":"Barbara Anna"},{"first_name":"Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","orcid":"0000-0003-3413-1343","full_name":"Riegler, Stefan","last_name":"Riegler"},{"last_name":"Kalyna","full_name":"Kalyna, Maria","first_name":"Maria"}],"external_id":{"isi":["000518903600001"]},"article_processing_charge":"No"},{"oa":1,"quality_controlled":"1","publisher":"EMBO Press","acknowledgement":"We thank T. Stauber and T. Breiderhoff for cloning expression constructs; K. Räbel, S. Hohensee, and C. Backhaus for technical assistance; R. Jahn (MPIbpc, Göttingen) for providing the equipment required for SV purification; and A\r\nWoehler (MDC, Berlin) for assistance with SV imaging. Supported, in part, by grants from the Deutsche Forschungsgemeinschaft (JE164/9-2, SFB740 TP C5, FOR 2625 (JE164/14-1), NeuroCure Cluster of Excellence), the European Research Council Advanced Grant CYTOVOLION (ERC 294435) and the Prix Louis-Jeantet de Médecine to TJJ, and Peter and Traudl Engelhorn fellowship to ZF.","date_created":"2020-03-15T23:00:55Z","date_published":"2020-03-02T00:00:00Z","doi":"10.15252/embj.2019103358","year":"2020","isi":1,"has_accepted_license":"1","publication":"EMBO Journal","day":"02","article_number":"e103358","external_id":{"isi":["000517335000001"],"pmid":["32118314"]},"article_processing_charge":"No","author":[{"first_name":"Stefanie","last_name":"Weinert","full_name":"Weinert, Stefanie"},{"full_name":"Gimber, Niclas","last_name":"Gimber","first_name":"Niclas"},{"full_name":"Deuschel, Dorothea","last_name":"Deuschel","first_name":"Dorothea"},{"last_name":"Stuhlmann","full_name":"Stuhlmann, Till","first_name":"Till"},{"first_name":"Dmytro","last_name":"Puchkov","full_name":"Puchkov, Dmytro"},{"full_name":"Farsi, Zohreh","last_name":"Farsi","first_name":"Zohreh"},{"full_name":"Ludwig, Carmen F.","last_name":"Ludwig","first_name":"Carmen F."},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"last_name":"López-Cayuqueo","full_name":"López-Cayuqueo, Karen I.","first_name":"Karen I."},{"first_name":"Rosa","full_name":"Planells-Cases, Rosa","last_name":"Planells-Cases"},{"last_name":"Jentsch","full_name":"Jentsch, Thomas J.","first_name":"Thomas J."}],"title":"Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration","citation":{"mla":"Weinert, Stefanie, et al. “Uncoupling Endosomal CLC Chloride/Proton Exchange Causes Severe Neurodegeneration.” EMBO Journal, vol. 39, e103358, EMBO Press, 2020, doi:10.15252/embj.2019103358.","apa":"Weinert, S., Gimber, N., Deuschel, D., Stuhlmann, T., Puchkov, D., Farsi, Z., … Jentsch, T. J. (2020). Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. EMBO Journal. EMBO Press. https://doi.org/10.15252/embj.2019103358","ama":"Weinert S, Gimber N, Deuschel D, et al. Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. EMBO Journal. 2020;39. doi:10.15252/embj.2019103358","short":"S. Weinert, N. Gimber, D. Deuschel, T. Stuhlmann, D. Puchkov, Z. Farsi, C.F. Ludwig, G. Novarino, K.I. López-Cayuqueo, R. Planells-Cases, T.J. Jentsch, EMBO Journal 39 (2020).","ieee":"S. Weinert et al., “Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration,” EMBO Journal, vol. 39. EMBO Press, 2020.","chicago":"Weinert, Stefanie, Niclas Gimber, Dorothea Deuschel, Till Stuhlmann, Dmytro Puchkov, Zohreh Farsi, Carmen F. Ludwig, et al. “Uncoupling Endosomal CLC Chloride/Proton Exchange Causes Severe Neurodegeneration.” EMBO Journal. EMBO Press, 2020. https://doi.org/10.15252/embj.2019103358.","ista":"Weinert S, Gimber N, Deuschel D, Stuhlmann T, Puchkov D, Farsi Z, Ludwig CF, Novarino G, López-Cayuqueo KI, Planells-Cases R, Jentsch TJ. 2020. Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. EMBO Journal. 39, e103358."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 39","month":"03","abstract":[{"text":"CLC chloride/proton exchangers may support acidification of endolysosomes and raise their luminal Cl− concentration. Disruption of endosomal ClC‐3 causes severe neurodegeneration. To assess the importance of ClC‐3 Cl−/H+ exchange, we now generate Clcn3unc/unc mice in which ClC‐3 is converted into a Cl− channel. Unlike Clcn3−/− mice, Clcn3unc/unc mice appear normal owing to compensation by ClC‐4 with which ClC‐3 forms heteromers. ClC‐4 protein levels are strongly reduced in Clcn3−/−, but not in Clcn3unc/unc mice because ClC‐3unc binds and stabilizes ClC‐4 like wild‐type ClC‐3. Although mice lacking ClC‐4 appear healthy, its absence in Clcn3unc/unc/Clcn4−/− mice entails even stronger neurodegeneration than observed in Clcn3−/− mice. A fraction of ClC‐3 is found on synaptic vesicles, but miniature postsynaptic currents and synaptic vesicle acidification are not affected in Clcn3unc/unc or Clcn3−/− mice before neurodegeneration sets in. Both, Cl−/H+‐exchange activity and the stabilizing effect on ClC‐4, are central to the biological function of ClC‐3.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":39,"publication_status":"published","publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"language":[{"iso":"eng"}],"file":[{"file_size":12243278,"date_updated":"2020-07-14T12:48:00Z","creator":"dernst","file_name":"2020_EMBO_Weinert.pdf","date_created":"2020-03-23T13:51:11Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7615","checksum":"82750a7a93e3740decbce8474004111a"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","_id":"7586","department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:48:00Z","date_updated":"2023-08-18T07:07:36Z","ddc":["570"]},{"day":"01","publication":"Letters in Mathematical Physics","isi":1,"year":"2020","date_published":"2020-08-01T00:00:00Z","doi":"10.1007/s11005-020-01282-0","date_created":"2020-03-25T15:57:48Z","page":"2039-2052","acknowledgement":"J. Pitrik was supported by the Hungarian Academy of Sciences Lendület-Momentum Grant for Quantum\r\nInformation Theory, No. 96 141, and by the Hungarian National Research, Development and Innovation\r\nOffice (NKFIH) via Grants Nos. K119442, K124152 and KH129601. D. Virosztek was supported by the\r\nISTFELLOW program of the Institute of Science and Technology Austria (Project Code IC1027FELL01),\r\nby the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSklodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National\r\nResearch, Development and Innovation Office (NKFIH) via Grants Nos. K124152 and KH129601.\r\nWe are grateful to Milán Mosonyi for drawing our attention to Ref.’s [6,14,15,17,\r\n20,21], for comments on earlier versions of this paper, and for several discussions on the topic. We are\r\nalso grateful to Miklós Pálfia for several discussions; to László Erdös for his essential suggestions on the\r\nstructure and highlights of this paper, and for his comments on earlier versions; and to the anonymous\r\nreferee for his/her valuable comments and suggestions.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Pitrik, Jozsef, and Daniel Virosztek. “Quantum Hellinger Distances Revisited.” Letters in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s11005-020-01282-0.","ista":"Pitrik J, Virosztek D. 2020. Quantum Hellinger distances revisited. Letters in Mathematical Physics. 110(8), 2039–2052.","mla":"Pitrik, Jozsef, and Daniel Virosztek. “Quantum Hellinger Distances Revisited.” Letters in Mathematical Physics, vol. 110, no. 8, Springer Nature, 2020, pp. 2039–52, doi:10.1007/s11005-020-01282-0.","apa":"Pitrik, J., & Virosztek, D. (2020). Quantum Hellinger distances revisited. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-020-01282-0","ama":"Pitrik J, Virosztek D. Quantum Hellinger distances revisited. Letters in Mathematical Physics. 2020;110(8):2039-2052. doi:10.1007/s11005-020-01282-0","ieee":"J. Pitrik and D. Virosztek, “Quantum Hellinger distances revisited,” Letters in Mathematical Physics, vol. 110, no. 8. Springer Nature, pp. 2039–2052, 2020.","short":"J. Pitrik, D. Virosztek, Letters in Mathematical Physics 110 (2020) 2039–2052."},"title":"Quantum Hellinger distances revisited","author":[{"first_name":"Jozsef","full_name":"Pitrik, Jozsef","last_name":"Pitrik"},{"orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel","last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"}],"article_processing_charge":"No","external_id":{"isi":["000551556000002"],"arxiv":["1903.10455"]},"project":[{"grant_number":"846294","name":"Geometric study of Wasserstein spaces and free probability","_id":"26A455A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"publication_status":"published","issue":"8","volume":110,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"This short note aims to study quantum Hellinger distances investigated recently by Bhatia et al. (Lett Math Phys 109:1777–1804, 2019) with a particular emphasis on barycenters. We introduce the family of generalized quantum Hellinger divergences that are of the form ϕ(A,B)=Tr((1−c)A+cB−AσB), where σ is an arbitrary Kubo–Ando mean, and c∈(0,1) is the weight of σ. We note that these divergences belong to the family of maximal quantum f-divergences, and hence are jointly convex, and satisfy the data processing inequality. We derive a characterization of the barycenter of finitely many positive definite operators for these generalized quantum Hellinger divergences. We note that the characterization of the barycenter as the weighted multivariate 1/2-power mean, that was claimed in Bhatia et al. (2019), is true in the case of commuting operators, but it is not correct in the general case. "}],"month":"08","intvolume":" 110","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.10455"}],"date_updated":"2023-08-18T10:17:26Z","department":[{"_id":"LaEr"}],"_id":"7618","status":"public","article_type":"original","type":"journal_article"},{"date_updated":"2023-08-18T10:25:13Z","ddc":["570"],"file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"SaSi"}],"_id":"7632","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["20452322"]},"publication_status":"published","file":[{"file_id":"7644","checksum":"e6cfaaaf7986532132934400038b824a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_ScientificReports_Tombaz.pdf","date_created":"2020-04-06T10:44:23Z","creator":"dernst","file_size":2621249,"date_updated":"2020-07-14T12:48:01Z"}],"language":[{"iso":"eng"}],"issue":"1","volume":10,"abstract":[{"text":"The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical network supporting goal-directed behaviour, with functions including sensorimotor transformations and decision making. In primates, this network links performed and observed actions via mirror neurons, which fire both when individuals perform an action and when they observe the same action performed by a conspecific. Mirror neurons are believed to be important for social learning, but it is not known whether mirror-like neurons occur in similar networks in other social species, such as rodents, or if they can be measured in such models using paradigms where observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching and wheel-running tasks, and found that cell populations in both areas robustly encoded several naturalistic behaviours. However, neural responses to the same set of observed actions were absent, although we verified that observer mice were attentive to performers and that PPC neurons responded reliably to visual cues. Statistical modelling also indicated that executed actions outperformed observed actions in predicting neural responses. These results raise the possibility that sensorimotor action recognition in rodents could take place outside of the parieto-frontal circuit, and underscore that detecting socially-driven neural coding depends critically on the species and behavioural paradigm used.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 10","citation":{"ista":"Tombaz T, Dunn BA, Hovde K, Cubero RJ, Mimica B, Mamidanna P, Roudi Y, Whitlock JR. 2020. Action representation in the mouse parieto-frontal network. Scientific reports. 10(1), 5559.","chicago":"Tombaz, Tuce, Benjamin A. Dunn, Karoline Hovde, Ryan J Cubero, Bartul Mimica, Pranav Mamidanna, Yasser Roudi, and Jonathan R. Whitlock. “Action Representation in the Mouse Parieto-Frontal Network.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-62089-6.","apa":"Tombaz, T., Dunn, B. A., Hovde, K., Cubero, R. J., Mimica, B., Mamidanna, P., … Whitlock, J. R. (2020). Action representation in the mouse parieto-frontal network. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-62089-6","ama":"Tombaz T, Dunn BA, Hovde K, et al. Action representation in the mouse parieto-frontal network. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-62089-6","ieee":"T. Tombaz et al., “Action representation in the mouse parieto-frontal network,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020.","short":"T. Tombaz, B.A. Dunn, K. Hovde, R.J. Cubero, B. Mimica, P. Mamidanna, Y. Roudi, J.R. Whitlock, Scientific Reports 10 (2020).","mla":"Tombaz, Tuce, et al. “Action Representation in the Mouse Parieto-Frontal Network.” Scientific Reports, vol. 10, no. 1, 5559, Springer Nature, 2020, doi:10.1038/s41598-020-62089-6."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Tuce","full_name":"Tombaz, Tuce","last_name":"Tombaz"},{"last_name":"Dunn","full_name":"Dunn, Benjamin A.","first_name":"Benjamin A."},{"last_name":"Hovde","full_name":"Hovde, Karoline","first_name":"Karoline"},{"last_name":"Cubero","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J"},{"last_name":"Mimica","full_name":"Mimica, Bartul","first_name":"Bartul"},{"first_name":"Pranav","last_name":"Mamidanna","full_name":"Mamidanna, Pranav"},{"first_name":"Yasser","last_name":"Roudi","full_name":"Roudi, Yasser"},{"first_name":"Jonathan R.","last_name":"Whitlock","full_name":"Whitlock, Jonathan R."}],"external_id":{"isi":["000560406800007"]},"article_processing_charge":"No","title":"Action representation in the mouse parieto-frontal network","article_number":"5559","has_accepted_license":"1","isi":1,"year":"2020","day":"27","publication":"Scientific reports","doi":"10.1038/s41598-020-62089-6","date_published":"2020-03-27T00:00:00Z","date_created":"2020-04-05T22:00:47Z","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"title":"The IYPT and the 'Ring Oiler' problem","article_processing_charge":"No","external_id":{"arxiv":["1910.03290"],"isi":["000537425400001"]},"author":[{"full_name":"Plesch, Martin","last_name":"Plesch","first_name":"Martin"},{"first_name":"Samuel","full_name":"Plesník, Samuel","last_name":"Plesník"},{"last_name":"Ruzickova","full_name":"Ruzickova, Natalia","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001.","chicago":"Plesch, Martin, Samuel Plesník, and Natalia Ruzickova. “The IYPT and the ‘Ring Oiler’ Problem.” European Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1361-6404/ab6414.","ieee":"M. Plesch, S. Plesník, and N. Ruzickova, “The IYPT and the ‘Ring Oiler’ problem,” European Journal of Physics, vol. 41, no. 3. IOP Publishing, 2020.","short":"M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (2020).","apa":"Plesch, M., Plesník, S., & Ruzickova, N. (2020). The IYPT and the “Ring Oiler” problem. European Journal of Physics. IOP Publishing. https://doi.org/10.1088/1361-6404/ab6414","ama":"Plesch M, Plesník S, Ruzickova N. The IYPT and the “Ring Oiler” problem. European Journal of Physics. 2020;41(3). doi:10.1088/1361-6404/ab6414","mla":"Plesch, Martin, et al. “The IYPT and the ‘Ring Oiler’ Problem.” European Journal of Physics, vol. 41, no. 3, 034001, IOP Publishing, 2020, doi:10.1088/1361-6404/ab6414."},"article_number":"034001","date_created":"2020-03-31T11:25:04Z","doi":"10.1088/1361-6404/ab6414","date_published":"2020-02-24T00:00:00Z","publication":"European Journal of Physics","day":"24","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"publisher":"IOP Publishing","quality_controlled":"1","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:48:01Z","ddc":["530"],"date_updated":"2023-08-18T10:18:29Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"7622","issue":"3","volume":41,"language":[{"iso":"eng"}],"file":[{"checksum":"47dda164e33b6c0c6c3ed14aad298376","file_id":"7641","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_EuropJourPhysics_Plesch.pdf","date_created":"2020-04-06T08:53:53Z","creator":"dernst","file_size":1533672,"date_updated":"2020-07-14T12:48:01Z"}],"publication_status":"published","publication_identifier":{"issn":["01430807"],"eissn":["13616404"]},"intvolume":" 41","month":"02","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The International Young Physicists' Tournament (IYPT) continued in 2018 in Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The IYPT is a modern scientific competition for teams of high school students, also known as the Physics World Cup. It involves long-term theoretical and experimental work focused on solving 17 publicly announced open-ended problems in teams of five. On top of that, teams have to present their solutions in front of other teams and a scientific jury, and get opposed and reviewed by their peers. Here we present a brief information about the competition with a specific focus on one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical problem appeared to be of such a complexity that even the dozens of participating teams and jurying scientists were not able to solve all of its subtleties."}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Jankowiak, Gaspard, Diane Peurichard, Anne Reversat, Christian Schmeiser, and Michael K Sixt. “Modeling Adhesion-Independent Cell Migration.” Mathematical Models and Methods in Applied Sciences. World Scientific, 2020. https://doi.org/10.1142/S021820252050013X.","ista":"Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. 2020. Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. 30(3), 513–537.","mla":"Jankowiak, Gaspard, et al. “Modeling Adhesion-Independent Cell Migration.” Mathematical Models and Methods in Applied Sciences, vol. 30, no. 3, World Scientific, 2020, pp. 513–37, doi:10.1142/S021820252050013X.","ama":"Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. 2020;30(3):513-537. doi:10.1142/S021820252050013X","apa":"Jankowiak, G., Peurichard, D., Reversat, A., Schmeiser, C., & Sixt, M. K. (2020). Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. World Scientific. https://doi.org/10.1142/S021820252050013X","short":"G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, M.K. Sixt, Mathematical Models and Methods in Applied Sciences 30 (2020) 513–537.","ieee":"G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, and M. K. Sixt, “Modeling adhesion-independent cell migration,” Mathematical Models and Methods in Applied Sciences, vol. 30, no. 3. World Scientific, pp. 513–537, 2020."},"title":"Modeling adhesion-independent cell migration","author":[{"first_name":"Gaspard","full_name":"Jankowiak, Gaspard","last_name":"Jankowiak"},{"first_name":"Diane","full_name":"Peurichard, Diane","last_name":"Peurichard"},{"full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne"},{"first_name":"Christian","last_name":"Schmeiser","full_name":"Schmeiser, Christian"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000525349900003"],"arxiv":["1903.09426"]},"article_processing_charge":"No","project":[{"grant_number":"LS13-029","name":"Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments","_id":"25AD6156-B435-11E9-9278-68D0E5697425"}],"day":"18","publication":"Mathematical Models and Methods in Applied Sciences","isi":1,"year":"2020","doi":"10.1142/S021820252050013X","date_published":"2020-03-18T00:00:00Z","date_created":"2020-03-31T11:25:05Z","page":"513-537","acknowledgement":"This work has been supported by the Vienna Science and Technology Fund, Grant no. LS13-029. G.J. and C.S. also acknowledge support by the Austrian Science Fund, Grants no. W1245, F 65, and W1261, as well as by the Fondation Sciences Mathématiques de Paris, and by Paris-Sciences-et-Lettres.","quality_controlled":"1","publisher":"World Scientific","oa":1,"date_updated":"2023-08-18T10:18:56Z","department":[{"_id":"MiSi"}],"_id":"7623","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["02182025"]},"publication_status":"published","volume":30,"issue":"3","oa_version":"Preprint","abstract":[{"text":"A two-dimensional mathematical model for cells migrating without adhesion capabilities is presented and analyzed. Cells are represented by their cortex, which is modeled as an elastic curve, subject to an internal pressure force. Net polymerization or depolymerization in the cortex is modeled via local addition or removal of material, driving a cortical flow. The model takes the form of a fully nonlinear degenerate parabolic system. An existence analysis is carried out by adapting ideas from the theory of gradient flows. Numerical simulations show that these simple rules can account for the behavior observed in experiments, suggesting a possible mechanical mechanism for adhesion-independent motility.","lang":"eng"}],"month":"03","intvolume":" 30","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1903.09426","open_access":"1"}]},{"file_date_updated":"2020-10-06T07:41:35Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-08-18T10:27:52Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"7646","issue":"14","volume":71,"language":[{"iso":"eng"}],"file":[{"file_id":"8613","checksum":"b06aaaa93dc41896da805fe4b75cf3a1","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-06T07:41:35Z","file_name":"2020_JourExperimBotany_Lee.pdf","date_updated":"2020-10-06T07:41:35Z","file_size":1916031,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"intvolume":" 71","month":"07","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"In plant cells, environmental stressors promote changes in connectivity between the cortical ER and the PM. Although this process is tightly regulated in space and time, the molecular signals and structural components mediating these changes in inter-organelle communication are only starting to be characterized. In this report, we confirm the presence of a putative tethering complex containing the synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+ and lipid binding protein 1 (CLB1/SYT7). This complex is enriched at ER-PM contact sites (EPCS), have slow responses to changes in extracellular Ca2+, and display severe cytoskeleton-dependent rearrangements in response to the trivalent lanthanum (La3+) and gadolinium (Gd3+) rare earth elements (REEs). Although REEs are generally used as non-selective cation channel blockers at the PM, here we show that the slow internalization of REEs into the cytosol underlies the activation of the Ca2+/Calmodulin intracellular signaling, the accumulation of phosphatidylinositol-4-phosphate (PI4P) at the PM, and the cytoskeleton-dependent rearrangement of the SYT1/SYT5 EPCS complexes. We propose that the observed EPCS rearrangements act as a slow adaptive response to sustained stress conditions, and that this process involves the accumulation of stress-specific phosphoinositides species at the PM."}],"title":"Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis","external_id":{"pmid":["32179893"],"isi":["000553125400007"]},"article_processing_charge":"No","author":[{"last_name":"Lee","full_name":"Lee, E","first_name":"E"},{"last_name":"Vila Nova Santana","full_name":"Vila Nova Santana, B","first_name":"B"},{"first_name":"E","last_name":"Samuels","full_name":"Samuels, E"},{"first_name":"F","last_name":"Benitez-Fuente","full_name":"Benitez-Fuente, F"},{"first_name":"E","full_name":"Corsi, E","last_name":"Corsi"},{"full_name":"Botella, MA","last_name":"Botella","first_name":"MA"},{"full_name":"Perez-Sancho, J","last_name":"Perez-Sancho","first_name":"J"},{"first_name":"S","last_name":"Vanneste","full_name":"Vanneste, S"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Macho","full_name":"Macho, A","first_name":"A"},{"first_name":"A","last_name":"Alves Azevedo","full_name":"Alves Azevedo, A"},{"first_name":"A","full_name":"Rosado, A","last_name":"Rosado"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"E. Lee et al., “Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis,” Journal of Experimental Botany, vol. 71, no. 14. Oxford University Press, pp. 3986–3998, 2020.","short":"E. Lee, B. Vila Nova Santana, E. Samuels, F. Benitez-Fuente, E. Corsi, M. Botella, J. Perez-Sancho, S. Vanneste, J. Friml, A. Macho, A. Alves Azevedo, A. Rosado, Journal of Experimental Botany 71 (2020) 3986–3998.","ama":"Lee E, Vila Nova Santana B, Samuels E, et al. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. 2020;71(14):3986–3998. doi:10.1093/jxb/eraa138","apa":"Lee, E., Vila Nova Santana, B., Samuels, E., Benitez-Fuente, F., Corsi, E., Botella, M., … Rosado, A. (2020). Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa138","mla":"Lee, E., et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” Journal of Experimental Botany, vol. 71, no. 14, Oxford University Press, 2020, pp. 3986–3998, doi:10.1093/jxb/eraa138.","ista":"Lee E, Vila Nova Santana B, Samuels E, Benitez-Fuente F, Corsi E, Botella M, Perez-Sancho J, Vanneste S, Friml J, Macho A, Alves Azevedo A, Rosado A. 2020. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. 71(14), 3986–3998.","chicago":"Lee, E, B Vila Nova Santana, E Samuels, F Benitez-Fuente, E Corsi, MA Botella, J Perez-Sancho, et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2020. https://doi.org/10.1093/jxb/eraa138."},"date_created":"2020-04-06T10:57:08Z","doi":"10.1093/jxb/eraa138","date_published":"2020-07-06T00:00:00Z","page":"3986–3998","publication":"Journal of Experimental Botany","day":"06","year":"2020","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Oxford University Press"},{"oa":1,"quality_controlled":"1","publisher":"Frontiers","publication":"Frontiers in Computational Neuroscience","day":"13","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-04-12T22:00:40Z","doi":"10.3389/fncom.2020.00020","date_published":"2020-03-13T00:00:00Z","article_number":"20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Berry MJ, Tkačik G. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020","apa":"Berry, M. J., & Tkačik, G. (2020). Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. Frontiers. https://doi.org/10.3389/fncom.2020.00020","ieee":"M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle for population codes,” Frontiers in Computational Neuroscience, vol. 14. Frontiers, 2020.","short":"M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).","mla":"Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience, vol. 14, 20, Frontiers, 2020, doi:10.3389/fncom.2020.00020.","ista":"Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 14, 20.","chicago":"Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience. Frontiers, 2020. https://doi.org/10.3389/fncom.2020.00020."},"title":"Clustering of neural activity: A design principle for population codes","article_processing_charge":"No","external_id":{"pmid":["32231528"],"isi":["000525543200001"]},"author":[{"first_name":"Michael J.","full_name":"Berry, Michael J.","last_name":"Berry"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement."}],"intvolume":" 14","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"2b1da23823eae9cedbb42d701945b61e","file_id":"7659","file_size":4082937,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_name":"2020_Frontiers_Berry.pdf","date_created":"2020-04-14T12:20:39Z"}],"publication_status":"published","publication_identifier":{"eissn":["16625188"]},"volume":14,"_id":"7656","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-08-18T10:30:11Z","file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"GaTk"}]},{"ec_funded":1,"issue":"1","volume":2020,"publication_status":"published","publication_identifier":{"eissn":["17425468"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":3159026,"date_updated":"2020-07-14T12:48:01Z","file_name":"2020_JournStatisticalMech_DeNicola.pdf","date_created":"2020-04-06T13:15:49Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7648","checksum":"4030e683c15d30b7b4794ec7dc1b6537"}],"scopus_import":"1","intvolume":" 2020","month":"01","abstract":[{"lang":"eng","text":"Following on from our recent work, we investigate a stochastic approach to non-equilibrium quantum spin systems. We show how the method can be applied to a variety of physical observables and for different initial conditions. We provide exact formulae of broad applicability for the time-dependence of expectation values and correlation functions following a quantum quench in terms of averages over classical stochastic processes. We further explore the behavior of the classical stochastic variables in the presence of dynamical quantum phase transitions, including results for their distributions and correlation functions. We provide details on the numerical solution of the associated stochastic differential equations, and examine the growth of fluctuations in the classical description. We discuss the strengths and limitations of the current implementation of the stochastic approach and the potential for further development."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"MaSe"}],"date_updated":"2023-08-18T10:27:15Z","ddc":["530"],"type":"journal_article","article_type":"original","status":"public","_id":"7638","date_created":"2020-04-05T22:00:50Z","date_published":"2020-01-22T00:00:00Z","doi":"10.1088/1742-5468/ab6093","year":"2020","has_accepted_license":"1","isi":1,"publication":"Journal of Statistical Mechanics: Theory and Experiment","day":"22","oa":1,"publisher":"IOP Publishing","quality_controlled":"1","external_id":{"arxiv":["1909.13142"],"isi":["000520187500001"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano","last_name":"De Nicola","first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87"},{"first_name":"B.","last_name":"Doyon","full_name":"Doyon, B."},{"full_name":"Bhaseen, M. J.","last_name":"Bhaseen","first_name":"M. J."}],"title":"Non-equilibrium quantum spin dynamics from classical stochastic processes","citation":{"chicago":"De Nicola, Stefano, B. Doyon, and M. J. Bhaseen. “Non-Equilibrium Quantum Spin Dynamics from Classical Stochastic Processes.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2020. https://doi.org/10.1088/1742-5468/ab6093.","ista":"De Nicola S, Doyon B, Bhaseen MJ. 2020. Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. 2020(1), 013106.","mla":"De Nicola, Stefano, et al. “Non-Equilibrium Quantum Spin Dynamics from Classical Stochastic Processes.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2020, no. 1, 013106, IOP Publishing, 2020, doi:10.1088/1742-5468/ab6093.","ama":"De Nicola S, Doyon B, Bhaseen MJ. Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. 2020;2020(1). doi:10.1088/1742-5468/ab6093","apa":"De Nicola, S., Doyon, B., & Bhaseen, M. J. (2020). Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab6093","short":"S. De Nicola, B. Doyon, M.J. Bhaseen, Journal of Statistical Mechanics: Theory and Experiment 2020 (2020).","ieee":"S. De Nicola, B. Doyon, and M. J. Bhaseen, “Non-equilibrium quantum spin dynamics from classical stochastic processes,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2020, no. 1. IOP Publishing, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"article_number":"013106"},{"_id":"7637","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-18T10:26:07Z","department":[{"_id":"JuFi"}],"oa_version":"Preprint","abstract":[{"text":"The evolution of finitely many particles obeying Langevin dynamics is described by Dean–Kawasaki equations, a class of stochastic equations featuring a non-Lipschitz multiplicative noise in divergence form. We derive a regularised Dean–Kawasaki model based on second order Langevin dynamics by analysing a system of particles interacting via a pairwise potential. Key tools of our analysis are the propagation of chaos and Simon's compactness criterion. The model we obtain is a small-noise stochastic perturbation of the undamped McKean–Vlasov equation. We also provide a high-probability result for existence and uniqueness for our model.","lang":"eng"}],"intvolume":" 33","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.06448"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"issue":"2","volume":33,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Cornalba F, Shardlow T, Zimmer J. 2020. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 33(2), 864–891.","chicago":"Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab5174.","ama":"Cornalba F, Shardlow T, Zimmer J. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 2020;33(2):864-891. doi:10.1088/1361-6544/ab5174","apa":"Cornalba, F., Shardlow, T., & Zimmer, J. (2020). From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab5174","short":"F. Cornalba, T. Shardlow, J. Zimmer, Nonlinearity 33 (2020) 864–891.","ieee":"F. Cornalba, T. Shardlow, and J. Zimmer, “From weakly interacting particles to a regularised Dean-Kawasaki model,” Nonlinearity, vol. 33, no. 2. IOP Publishing, pp. 864–891, 2020.","mla":"Cornalba, Federico, et al. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” Nonlinearity, vol. 33, no. 2, IOP Publishing, 2020, pp. 864–91, doi:10.1088/1361-6544/ab5174."},"title":"From weakly interacting particles to a regularised Dean-Kawasaki model","article_processing_charge":"No","external_id":{"isi":["000508175400001"],"arxiv":["1811.06448"]},"author":[{"orcid":"0000-0002-6269-5149","full_name":"Cornalba, Federico","last_name":"Cornalba","id":"2CEB641C-A400-11E9-A717-D712E6697425","first_name":"Federico"},{"full_name":"Shardlow, Tony","last_name":"Shardlow","first_name":"Tony"},{"first_name":"Johannes","full_name":"Zimmer, Johannes","last_name":"Zimmer"}],"oa":1,"publisher":"IOP Publishing","quality_controlled":"1","publication":"Nonlinearity","day":"10","year":"2020","isi":1,"date_created":"2020-04-05T22:00:49Z","doi":"10.1088/1361-6544/ab5174","date_published":"2020-01-10T00:00:00Z","page":"864-891"},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7664","file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"RySh"}],"date_updated":"2023-08-21T06:13:19Z","ddc":["570"],"scopus_import":"1","month":"04","intvolume":" 21","abstract":[{"lang":"eng","text":"Metabotropic γ-aminobutyric acid (GABAB) receptors contribute to the control of network activity and information processing in hippocampal circuits by regulating neuronal excitability and synaptic transmission. The dysfunction in the dentate gyrus (DG) has been implicated in Alzheimer´s disease (AD). Given the involvement of GABAB receptors in AD, to determine their subcellular localisation and possible alteration in granule cells of the DG in a mouse model of AD at 12 months of age, we used high-resolution immunoelectron microscopic analysis. Immunohistochemistry at the light microscopic level showed that the regional and cellular expression pattern of GABAB1 was similar in an AD model mouse expressing mutated human amyloid precursor protein and presenilin1 (APP/PS1) and in age-matched wild type mice. High-resolution immunoelectron microscopy revealed a distance-dependent gradient of immunolabelling for GABAB receptors, increasing from proximal to distal dendrites in both wild type and APP/PS1 mice. However, the overall density of GABAB receptors at the neuronal surface of these postsynaptic compartments of granule cells was significantly reduced in APP/PS1 mice. Parallel to this reduction in surface receptors, we found a significant increase in GABAB1 at cytoplasmic sites. GABAB receptors were also detected at presynaptic sites in the molecular layer of the DG. We also found a decrease in plasma membrane GABAB receptors in axon terminals contacting dendritic spines of granule cells, which was more pronounced in the outer than in the inner molecular layer. Altogether, our data showing post- and presynaptic reduction in surface GABAB receptors in the DG suggest the alteration of the GABAB-mediated modulation of excitability and synaptic transmission in granule cells, which may contribute to the cognitive dysfunctions in the APP/PS1 model of AD"}],"oa_version":"Published Version","pmid":1,"issue":"7","volume":21,"publication_identifier":{"eissn":["14220067"]},"publication_status":"published","file":[{"date_created":"2020-04-20T11:43:18Z","file_name":"2020_JournMolecSciences_Martin_Belmonte.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:01Z","file_size":2941197,"file_id":"7669","checksum":"b9d2f1657d8c4a74b01a62b474d009b0","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"article_number":"2459","author":[{"full_name":"Martín-Belmonte, Alejandro","last_name":"Martín-Belmonte","first_name":"Alejandro"},{"first_name":"Carolina","full_name":"Aguado, Carolina","last_name":"Aguado"},{"first_name":"Rocío","last_name":"Alfaro-Ruíz","full_name":"Alfaro-Ruíz, Rocío"},{"last_name":"Moreno-Martínez","full_name":"Moreno-Martínez, Ana Esther","first_name":"Ana Esther"},{"first_name":"Luis","full_name":"De La Ossa, Luis","last_name":"De La Ossa"},{"first_name":"José","last_name":"Martínez-Hernández","full_name":"Martínez-Hernández, José"},{"first_name":"Alain","last_name":"Buisson","full_name":"Buisson, Alain"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"first_name":"Rafael","last_name":"Luján","full_name":"Luján, Rafael"}],"article_processing_charge":"No","external_id":{"isi":["000535574200201"],"pmid":["32252271"]},"title":"Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease","citation":{"chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, Ryuichi Shigemoto, Yugo Fukazawa, and Rafael Luján. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21072459.","ista":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Shigemoto R, Fukazawa Y, Luján R. 2020. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International journal of molecular sciences. 21(7), 2459.","mla":"Martín-Belmonte, Alejandro, et al. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International Journal of Molecular Sciences, vol. 21, no. 7, 2459, MDPI, 2020, doi:10.3390/ijms21072459.","ieee":"A. Martín-Belmonte et al., “Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease,” International journal of molecular sciences, vol. 21, no. 7. MDPI, 2020.","short":"A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, R. Shigemoto, Y. Fukazawa, R. Luján, International Journal of Molecular Sciences 21 (2020).","ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International journal of molecular sciences. 2020;21(7). doi:10.3390/ijms21072459","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21072459"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"MDPI","quality_controlled":"1","oa":1,"doi":"10.3390/ijms21072459","date_published":"2020-04-02T00:00:00Z","date_created":"2020-04-19T22:00:55Z","isi":1,"has_accepted_license":"1","year":"2020","day":"02","publication":"International journal of molecular sciences"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"7665","file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"JoDa"},{"_id":"RySh"}],"ddc":["570"],"date_updated":"2023-08-21T06:12:48Z","intvolume":" 14","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability. Furthermore, preparation at PT allows electrophysiological recording immediately after slicing resulting in higher detectability of long-term depression (LTD) after motor learning compared with that at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions.","lang":"eng"}],"ec_funded":1,"volume":14,"language":[{"iso":"eng"}],"file":[{"file_id":"7668","checksum":"1c145123c6f8dc3e2e4bd5a66a1ad60e","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-04-20T10:59:49Z","file_name":"2020_FrontiersCellularNeurosc_Eguchi.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:01Z","file_size":9227283}],"publication_status":"published","publication_identifier":{"issn":["16625102"]},"project":[{"call_identifier":"H2020","_id":"2659CC84-B435-11E9-9278-68D0E5697425","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","grant_number":"793482"},{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_number":"63","title":"Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000525582200001"]},"author":[{"last_name":"Eguchi","orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky"},{"id":"3C054040-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","full_name":"Hollergschwandtner, Elena","last_name":"Hollergschwandtner"},{"full_name":"Itakura, Makoto","last_name":"Itakura","first_name":"Makoto"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Eguchi, Kohgaku, Philipp Velicky, Elena Saeckl, Makoto Itakura, Yugo Fukazawa, Johann G Danzl, and Ryuichi Shigemoto. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” Frontiers in Cellular Neuroscience. Frontiers Media, 2020. https://doi.org/10.3389/fncel.2020.00063.","ista":"Eguchi K, Velicky P, Saeckl E, Itakura M, Fukazawa Y, Danzl JG, Shigemoto R. 2020. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 14, 63.","mla":"Eguchi, Kohgaku, et al. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” Frontiers in Cellular Neuroscience, vol. 14, 63, Frontiers Media, 2020, doi:10.3389/fncel.2020.00063.","ieee":"K. Eguchi et al., “Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions,” Frontiers in Cellular Neuroscience, vol. 14. Frontiers Media, 2020.","short":"K. Eguchi, P. Velicky, E. Saeckl, M. Itakura, Y. Fukazawa, J.G. Danzl, R. Shigemoto, Frontiers in Cellular Neuroscience 14 (2020).","apa":"Eguchi, K., Velicky, P., Saeckl, E., Itakura, M., Fukazawa, Y., Danzl, J. G., & Shigemoto, R. (2020). Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2020.00063","ama":"Eguchi K, Velicky P, Saeckl E, et al. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 2020;14. doi:10.3389/fncel.2020.00063"},"oa":1,"quality_controlled":"1","publisher":"Frontiers Media","date_created":"2020-04-19T22:00:55Z","doi":"10.3389/fncel.2020.00063","date_published":"2020-03-19T00:00:00Z","publication":"Frontiers in Cellular Neuroscience","day":"19","year":"2020","has_accepted_license":"1","isi":1},{"article_processing_charge":"No","external_id":{"isi":["000526413400055"],"pmid":["32196350"]},"author":[{"first_name":"Martin","full_name":"Felhofer, Martin","last_name":"Felhofer"},{"first_name":"Peter","last_name":"Bock","full_name":"Bock, Peter"},{"full_name":"Singh, Adya","last_name":"Singh","first_name":"Adya"},{"id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze","full_name":"Prats Mateu, Batirtze","last_name":"Prats Mateu"},{"first_name":"Ronald","full_name":"Zirbs, Ronald","last_name":"Zirbs"},{"first_name":"Notburga","last_name":"Gierlinger","full_name":"Gierlinger, Notburga"}],"title":"Wood deformation leads to rearrangement of molecules at the nanoscale","citation":{"chicago":"Felhofer, Martin, Peter Bock, Adya Singh, Batirtze Prats Mateu, Ronald Zirbs, and Notburga Gierlinger. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c00205.","ista":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. 2020. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 20(4), 2647–2653.","mla":"Felhofer, Martin, et al. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” Nano Letters, vol. 20, no. 4, American Chemical Society, 2020, pp. 2647–53, doi:10.1021/acs.nanolett.0c00205.","ama":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 2020;20(4):2647-2653. doi:10.1021/acs.nanolett.0c00205","apa":"Felhofer, M., Bock, P., Singh, A., Prats Mateu, B., Zirbs, R., & Gierlinger, N. (2020). Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c00205","short":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger, Nano Letters 20 (2020) 2647–2653.","ieee":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, and N. Gierlinger, “Wood deformation leads to rearrangement of molecules at the nanoscale,” Nano Letters, vol. 20, no. 4. American Chemical Society, pp. 2647–2653, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"2647-2653","date_created":"2020-04-19T22:00:54Z","date_published":"2020-04-08T00:00:00Z","doi":"10.1021/acs.nanolett.0c00205","year":"2020","isi":1,"has_accepted_license":"1","publication":"Nano Letters","day":"08","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","department":[{"_id":"MaLo"}],"file_date_updated":"2020-07-14T12:48:01Z","date_updated":"2023-08-21T06:12:09Z","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"7663","volume":20,"issue":"4","publication_status":"published","publication_identifier":{"eissn":["15306992"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"fe46146a9c4c620592a1932a8599069e","file_id":"7667","date_updated":"2020-07-14T12:48:01Z","file_size":7108014,"creator":"dernst","date_created":"2020-04-20T10:43:36Z","file_name":"2020_NanoLetters_Felhofer.pdf"}],"scopus_import":"1","intvolume":" 20","month":"04","abstract":[{"text":"Wood, as the most abundant carbon dioxide storing bioresource, is currently driven beyond its traditional use through creative innovations and nanotechnology. For many properties the micro- and nanostructure plays a crucial role and one key challenge is control and detection of chemical and physical processes in the confined microstructure and nanopores of the wooden cell wall. In this study, correlative Raman and atomic force microscopy show high potential for tracking in situ molecular rearrangement of wood polymers during compression. More water molecules (interpreted as wider cellulose microfibril distances) and disentangling of hemicellulose chains are detected in the opened cell wall regions, whereas an increase of lignin is revealed in the compressed areas. These results support a new more “loose” cell wall model based on flexible lignin nanodomains and advance our knowledge of the molecular reorganization during deformation of wood for optimized processing and utilization.","lang":"eng"}],"pmid":1,"oa_version":"Published Version"},{"file_date_updated":"2020-11-20T13:22:21Z","department":[{"_id":"HeEd"}],"date_updated":"2023-08-21T06:13:48Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"7666","ec_funded":1,"volume":64,"publication_status":"published","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8786","checksum":"f8cc96e497f00c38340b5dafe0cb91d7","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-11-20T13:22:21Z","file_name":"2020_DiscreteCompGeo_Edelsbrunner.pdf","date_updated":"2020-11-20T13:22:21Z","file_size":701673,"creator":"dernst"}],"scopus_import":"1","intvolume":" 64","month":"03","abstract":[{"text":"Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral complex, K, and every dimension, p, there is a partition of the set of p-cells into a maximal p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition is unique, and it can be computed by a matrix reduction algorithm that also constructs canonical bases of cycle and boundary groups.","lang":"eng"}],"oa_version":"Published Version","external_id":{"isi":["000520918800001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"last_name":"Ölsböck","full_name":"Ölsböck, Katharina","orcid":"0000-0002-4672-8297","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina"}],"title":"Tri-partitions and bases of an ordered complex","citation":{"ista":"Edelsbrunner H, Ölsböck K. 2020. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 64, 759–775.","chicago":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00188-x.","apa":"Edelsbrunner, H., & Ölsböck, K. (2020). Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00188-x","ama":"Edelsbrunner H, Ölsböck K. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 2020;64:759-775. doi:10.1007/s00454-020-00188-x","short":"H. Edelsbrunner, K. Ölsböck, Discrete and Computational Geometry 64 (2020) 759–775.","ieee":"H. Edelsbrunner and K. Ölsböck, “Tri-partitions and bases of an ordered complex,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 759–775, 2020.","mla":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 759–75, doi:10.1007/s00454-020-00188-x."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"page":"759-775","date_created":"2020-04-19T22:00:56Z","doi":"10.1007/s00454-020-00188-x","date_published":"2020-03-20T00:00:00Z","year":"2020","has_accepted_license":"1","isi":1,"publication":"Discrete and Computational Geometry","day":"20","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF)."},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2020-04-26T22:00:44Z","date_published":"2020-04-15T00:00:00Z","doi":"10.1007/s00029-020-00553-x","publication":"Selecta Mathematica, New Series","day":"15","year":"2020","has_accepted_license":"1","isi":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_number":"30","title":"Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces","external_id":{"arxiv":["1801.01429"],"isi":["000526036400001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"3E7C5304-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha","full_name":"Minets, Sasha","orcid":"0000-0003-3883-1806","last_name":"Minets"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” Selecta Mathematica, New Series. Springer Nature, 2020. https://doi.org/10.1007/s00029-020-00553-x.","ista":"Minets S. 2020. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 26(2), 30.","mla":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” Selecta Mathematica, New Series, vol. 26, no. 2, 30, Springer Nature, 2020, doi:10.1007/s00029-020-00553-x.","short":"S. Minets, Selecta Mathematica, New Series 26 (2020).","ieee":"S. Minets, “Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces,” Selecta Mathematica, New Series, vol. 26, no. 2. Springer Nature, 2020.","apa":"Minets, S. (2020). Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. Springer Nature. https://doi.org/10.1007/s00029-020-00553-x","ama":"Minets S. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 2020;26(2). doi:10.1007/s00029-020-00553-x"},"intvolume":" 26","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"For any free oriented Borel–Moore homology theory A, we construct an associative product on the A-theory of the stack of Higgs torsion sheaves over a projective curve C. We show that the resulting algebra AHa0C admits a natural shuffle presentation, and prove it is faithful when A is replaced with usual Borel–Moore homology groups. We also introduce moduli spaces of stable triples, heavily inspired by Nakajima quiver varieties, whose A-theory admits an AHa0C-action. These triples can be interpreted as certain sheaves on PC(ωC⊕OC). In particular, we obtain an action of AHa0C on the cohomology of Hilbert schemes of points on T∗C.","lang":"eng"}],"issue":"2","volume":26,"language":[{"iso":"eng"}],"file":[{"checksum":"2368c4662629b4759295eb365323b2ad","file_id":"7690","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-04-28T10:57:58Z","file_name":"2020_SelectaMathematica_Minets.pdf","date_updated":"2020-07-14T12:48:02Z","file_size":792469,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["14209020"],"issn":["10221824"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"7683","department":[{"_id":"TaHa"}],"file_date_updated":"2020-07-14T12:48:02Z","ddc":["510"],"date_updated":"2023-08-21T06:14:58Z"},{"author":[{"full_name":"Samojlov, Aleksej","last_name":"Samojlov","first_name":"Aleksej"},{"first_name":"David","last_name":"Schuster","full_name":"Schuster, David"},{"full_name":"Kahr, Jürgen","last_name":"Kahr","first_name":"Jürgen"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"}],"external_id":{"isi":["000582869700060"]},"article_processing_charge":"Yes (via OA deal)","title":"Surface and catalyst driven singlet oxygen formation in Li-O2 cells","citation":{"short":"A. Samojlov, D. Schuster, J. Kahr, S.A. Freunberger, Electrochimica Acta 362 (2020).","ieee":"A. Samojlov, D. Schuster, J. Kahr, and S. A. Freunberger, “Surface and catalyst driven singlet oxygen formation in Li-O2 cells,” Electrochimica Acta, vol. 362, no. 12. Elsevier, 2020.","ama":"Samojlov A, Schuster D, Kahr J, Freunberger SA. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 2020;362(12). doi:10.1016/j.electacta.2020.137175","apa":"Samojlov, A., Schuster, D., Kahr, J., & Freunberger, S. A. (2020). Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2020.137175","mla":"Samojlov, Aleksej, et al. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” Electrochimica Acta, vol. 362, no. 12, 137175, Elsevier, 2020, doi:10.1016/j.electacta.2020.137175.","ista":"Samojlov A, Schuster D, Kahr J, Freunberger SA. 2020. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 362(12), 137175.","chicago":"Samojlov, Aleksej, David Schuster, Jürgen Kahr, and Stefan Alexander Freunberger. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” Electrochimica Acta. Elsevier, 2020. https://doi.org/10.1016/j.electacta.2020.137175."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"137175","doi":"10.1016/j.electacta.2020.137175","date_published":"2020-12-01T00:00:00Z","date_created":"2020-04-20T19:29:31Z","isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Electrochimica Acta","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"S.A.F. thanks the International Society of Electrochemistry for awarding the Tajima Prize 2019 “in recognition of outstanding re- searches on Li-Air batteries by the use of a range of in-situ elec- trochemical methods to achieve comprehensive understanding of the reactions taking place at the oxygen electrode”. This article is dedicated to the special issue of Electrochmica Acta associated with the awarding conference. S.A.F. is indebted to and the Austrian Federal Ministry of Science, Research and Economy and the Austrian Research Promotion Agency (grant No. 845364 ) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 636069). The authors thank J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH and G. Strohmeier for help with HPLC measurements, S. Eder for cyclic voltammetry measurements, and C. Slugovc for discussions and continuous support. We thank S. Borisov for access and advice with fluorescence measurements. We thank EL-Cell GmbH, Hamburg, Germany for providing the PAT-Cell-Press electrochemical cell.","file_date_updated":"2020-10-01T13:20:45Z","department":[{"_id":"StFr"}],"date_updated":"2023-08-21T06:14:21Z","ddc":["540"],"type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"7672","volume":362,"issue":"12","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"1ab1aa2024d431e2a089ea336bc08298","file_id":"8593","creator":"dernst","file_size":1404030,"date_updated":"2020-10-01T13:20:45Z","file_name":"2020_ElectrochimicaActa_Samojlov.pdf","date_created":"2020-10-01T13:20:45Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 362","abstract":[{"text":"Large overpotentials upon discharge and charge of Li-O2 cells have motivated extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes with the aim to improve rate capability, round-trip efficiency and cycle life. These features are equally governed by parasitic reactions, which are now recognized to be caused by the highly reactive singlet oxygen (1O2). However, the link between the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown. Here, we show that, compared to pristine carbon black electrodes, a representative selection of electrocatalysts or non-carbon electrodes (noble metal, transition metal compounds) may both slightly reduce or severely increase the 1O2 formation. The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered, showing that 1O2 yield from superoxide disproportionation as well as the decomposition of trace H2O2 are sensitive to catalysts. Transition metal compounds in general are prone to increase 1O2.","lang":"eng"}],"oa_version":"Published Version"},{"citation":{"short":"I. Gridchyn, P. Schönenberger, J. O’Neill, J.L. Csicsvari, Neuron 106 (2020) 291–300.e6.","ieee":"I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Assembly-specific disruption of hippocampal replay leads to selective memory deficit,” Neuron, vol. 106, no. 2. Elsevier, p. 291–300.e6, 2020.","apa":"Gridchyn, I., Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2020). Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.01.021","ama":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. 2020;106(2):291-300.e6. doi:10.1016/j.neuron.2020.01.021","mla":"Gridchyn, Igor, et al. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” Neuron, vol. 106, no. 2, Elsevier, 2020, p. 291–300.e6, doi:10.1016/j.neuron.2020.01.021.","ista":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. 106(2), 291–300.e6.","chicago":"Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.01.021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000528268200013"],"pmid":["32070475"]},"author":[{"full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","first_name":"Igor"},{"full_name":"Schönenberger, Philipp","last_name":"Schönenberger","first_name":"Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"O'Neill","full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"}],"title":"Assembly-specific disruption of hippocampal replay leads to selective memory deficit","project":[{"call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"}],"year":"2020","isi":1,"publication":"Neuron","day":"22","page":"291-300.e6","date_created":"2020-04-26T22:00:45Z","date_published":"2020-04-22T00:00:00Z","doi":"10.1016/j.neuron.2020.01.021","oa":1,"publisher":"Elsevier","quality_controlled":"1","date_updated":"2023-08-21T06:15:31Z","department":[{"_id":"JoCs"}],"_id":"7684","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"2","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/librarian-of-memory/","relation":"press_release"}]},"volume":106,"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2020.01.021"}],"scopus_import":"1","intvolume":" 106","month":"04"},{"isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Biochimica et Biophysica Acta - Bioenergetics","date_published":"2020-08-01T00:00:00Z","doi":"10.1016/j.bbabio.2020.148213","date_created":"2020-05-03T22:00:47Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"citation":{"mla":"Adjobo-Hermans, Merel J. W., et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8, 148213, Elsevier, 2020, doi:10.1016/j.bbabio.2020.148213.","ama":"Adjobo-Hermans MJW, De Haas R, Willems PHGM, et al. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 2020;1861(8). doi:10.1016/j.bbabio.2020.148213","apa":"Adjobo-Hermans, M. J. W., De Haas, R., Willems, P. H. G. M., Wojtala, A., Van Emst-De Vries, S. E., Wagenaars, J. A., … Koopman, W. J. H. (2020). NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2020.148213","short":"M.J.W. Adjobo-Hermans, R. De Haas, P.H.G.M. Willems, A. Wojtala, S.E. Van Emst-De Vries, J.A. Wagenaars, M. Van Den Brand, R.J. Rodenburg, J.A.M. Smeitink, L.G. Nijtmans, L.A. Sazanov, M.R. Wieckowski, W.J.H. Koopman, Biochimica et Biophysica Acta - Bioenergetics 1861 (2020).","ieee":"M. J. W. Adjobo-Hermans et al., “NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8. Elsevier, 2020.","chicago":"Adjobo-Hermans, Merel J.W., Ria De Haas, Peter H.G.M. Willems, Aleksandra Wojtala, Sjenet E. Van Emst-De Vries, Jori A. Wagenaars, Mariel Van Den Brand, et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2020. https://doi.org/10.1016/j.bbabio.2020.148213.","ista":"Adjobo-Hermans MJW, De Haas R, Willems PHGM, Wojtala A, Van Emst-De Vries SE, Wagenaars JA, Van Den Brand M, Rodenburg RJ, Smeitink JAM, Nijtmans LG, Sazanov LA, Wieckowski MR, Koopman WJH. 2020. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 1861(8), 148213."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Merel J.W.","full_name":"Adjobo-Hermans, Merel J.W.","last_name":"Adjobo-Hermans"},{"last_name":"De Haas","full_name":"De Haas, Ria","first_name":"Ria"},{"first_name":"Peter H.G.M.","last_name":"Willems","full_name":"Willems, Peter H.G.M."},{"first_name":"Aleksandra","full_name":"Wojtala, Aleksandra","last_name":"Wojtala"},{"full_name":"Van Emst-De Vries, Sjenet E.","last_name":"Van Emst-De Vries","first_name":"Sjenet E."},{"first_name":"Jori A.","full_name":"Wagenaars, Jori A.","last_name":"Wagenaars"},{"last_name":"Van Den Brand","full_name":"Van Den Brand, Mariel","first_name":"Mariel"},{"first_name":"Richard J.","last_name":"Rodenburg","full_name":"Rodenburg, Richard J."},{"full_name":"Smeitink, Jan A.M.","last_name":"Smeitink","first_name":"Jan A.M."},{"first_name":"Leo G.","full_name":"Nijtmans, Leo G.","last_name":"Nijtmans"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov"},{"first_name":"Mariusz R.","last_name":"Wieckowski","full_name":"Wieckowski, Mariusz R."},{"last_name":"Koopman","full_name":"Koopman, Werner J.H.","first_name":"Werner J.H."}],"article_processing_charge":"No","external_id":{"pmid":["32335026"],"isi":["000540842000012"]},"title":"NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2","article_number":"148213","publication_identifier":{"eissn":["18792650"],"issn":["00052728"]},"publication_status":"published","file":[{"file_size":3826792,"date_updated":"2020-07-14T12:48:03Z","creator":"dernst","file_name":"2020_BBA_Adjobo_Hermans.pdf","date_created":"2020-05-04T12:25:19Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7798","checksum":"a9b152381307cf45fe266a8dc5640388"}],"language":[{"iso":"eng"}],"volume":1861,"issue":"8","abstract":[{"lang":"eng","text":"Mutations in NDUFS4, which encodes an accessory subunit of mitochondrial oxidative phosphorylation (OXPHOS) complex I (CI), induce Leigh syndrome (LS). LS is a poorly understood pediatric disorder featuring brain-specific anomalies and early death. To study the LS pathomechanism, we here compared OXPHOS proteomes between various Ndufs4−/− mouse tissues. Ndufs4−/− animals displayed significantly lower CI subunit levels in brain/diaphragm relative to other tissues (liver/heart/kidney/skeletal muscle), whereas other OXPHOS subunit levels were not reduced. Absence of NDUFS4 induced near complete absence of the NDUFA12 accessory subunit, a 50% reduction in other CI subunit levels, and an increase in specific CI assembly factors. Among the latter, NDUFAF2 was most highly increased. Regarding NDUFS4, NDUFA12 and NDUFAF2, identical results were obtained in Ndufs4−/− mouse embryonic fibroblasts (MEFs) and NDUFS4-mutated LS patient cells. Ndufs4−/− MEFs contained active CI in situ but blue-native-PAGE highlighted that NDUFAF2 attached to an inactive CI subcomplex (CI-830) and inactive assemblies of higher MW. In NDUFA12-mutated LS patient cells, NDUFA12 absence did not reduce NDUFS4 levels but triggered NDUFAF2 association to active CI. BN-PAGE revealed no such association in LS patient fibroblasts with mutations in other CI subunit-encoding genes where NDUFAF2 was attached to CI-830 (NDUFS1, NDUFV1 mutation) or not detected (NDUFS7 mutation). Supported by enzymological and CI in silico structural analysis, we conclude that absence of NDUFS4 induces near complete absence of NDUFA12 but not vice versa, and that NDUFAF2 stabilizes active CI in Ndufs4−/− mice and LS patient cells, perhaps in concert with mitochondrial inner membrane lipids."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"08","intvolume":" 1861","date_updated":"2023-08-21T06:19:18Z","ddc":["570"],"file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"LeSa"}],"_id":"7788","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"citation":{"ista":"Dekoninck S, Hannezo EB, Sifrim A, Miroshnikova YA, Aragona M, Malfait M, Gargouri S, De Neunheuser C, Dubois C, Voet T, Wickström SA, Simons BD, Blanpain C. 2020. Defining the design principles of skin epidermis postnatal growth. Cell. 181(3), 604–620.e22.","chicago":"Dekoninck, Sophie, Edouard B Hannezo, Alejandro Sifrim, Yekaterina A. Miroshnikova, Mariaceleste Aragona, Milan Malfait, Souhir Gargouri, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.03.015.","apa":"Dekoninck, S., Hannezo, E. B., Sifrim, A., Miroshnikova, Y. A., Aragona, M., Malfait, M., … Blanpain, C. (2020). Defining the design principles of skin epidermis postnatal growth. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.03.015","ama":"Dekoninck S, Hannezo EB, Sifrim A, et al. Defining the design principles of skin epidermis postnatal growth. Cell. 2020;181(3):604-620.e22. doi:10.1016/j.cell.2020.03.015","short":"S. Dekoninck, E.B. Hannezo, A. Sifrim, Y.A. Miroshnikova, M. Aragona, M. Malfait, S. Gargouri, C. De Neunheuser, C. Dubois, T. Voet, S.A. Wickström, B.D. Simons, C. Blanpain, Cell 181 (2020) 604–620.e22.","ieee":"S. Dekoninck et al., “Defining the design principles of skin epidermis postnatal growth,” Cell, vol. 181, no. 3. Elsevier, p. 604–620.e22, 2020.","mla":"Dekoninck, Sophie, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell, vol. 181, no. 3, Elsevier, 2020, p. 604–620.e22, doi:10.1016/j.cell.2020.03.015."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Dekoninck, Sophie","last_name":"Dekoninck","first_name":"Sophie"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Sifrim","full_name":"Sifrim, Alejandro","first_name":"Alejandro"},{"last_name":"Miroshnikova","full_name":"Miroshnikova, Yekaterina A.","first_name":"Yekaterina A."},{"first_name":"Mariaceleste","last_name":"Aragona","full_name":"Aragona, Mariaceleste"},{"last_name":"Malfait","full_name":"Malfait, Milan","first_name":"Milan"},{"first_name":"Souhir","last_name":"Gargouri","full_name":"Gargouri, Souhir"},{"first_name":"Charlotte","full_name":"De Neunheuser, Charlotte","last_name":"De Neunheuser"},{"full_name":"Dubois, Christine","last_name":"Dubois","first_name":"Christine"},{"full_name":"Voet, Thierry","last_name":"Voet","first_name":"Thierry"},{"full_name":"Wickström, Sara A.","last_name":"Wickström","first_name":"Sara A."},{"first_name":"Benjamin D.","full_name":"Simons, Benjamin D.","last_name":"Simons"},{"full_name":"Blanpain, Cédric","last_name":"Blanpain","first_name":"Cédric"}],"article_processing_charge":"No","external_id":{"pmid":["32259486"],"isi":["000530708400016"]},"title":"Defining the design principles of skin epidermis postnatal growth","has_accepted_license":"1","isi":1,"year":"2020","day":"30","publication":"Cell","page":"604-620.e22","date_published":"2020-04-30T00:00:00Z","doi":"10.1016/j.cell.2020.03.015","date_created":"2020-05-03T22:00:48Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2023-08-21T06:17:43Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:48:03Z","_id":"7789","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"publication_status":"published","file":[{"checksum":"e2114902f4e9d75a752e9efb5ae06011","file_id":"7795","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-04T10:20:55Z","file_name":"2020_Cell_Dekoninck.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:03Z","file_size":17992888}],"language":[{"iso":"eng"}],"issue":"3","volume":181,"abstract":[{"lang":"eng","text":"During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"04","intvolume":" 181"},{"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:48:03Z","date_updated":"2023-08-21T06:17:12Z","ddc":["580"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7793","volume":9,"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"15d740de1a741fdcc6ec128c48eed017","file_id":"7794","creator":"dernst","file_size":2893082,"date_updated":"2020-07-14T12:48:03Z","file_name":"2020_eLife_Kuhn.pdf","date_created":"2020-05-04T09:06:43Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 9","abstract":[{"text":"Hormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin whereby auxin directly affects the activity of the atypical auxin response factor (ARF), ETTIN towards target genes without the requirement for protein degradation. Here we show that ETTIN directly binds auxin, leading to dissociation from co-repressor proteins of the TOPLESS/TOPLESS-RELATED family followed by histone acetylation and induction of gene expression. This mechanism is reminiscent of animal hormone signalling as it affects the activity towards regulation of target genes and provides the first example of a DNA-bound hormone receptor in plants. Whilst auxin affects canonical ARFs indirectly by facilitating degradation of Aux/IAA repressors, direct ETTIN-auxin interactions allow switching between repressive and de-repressive chromatin states in an instantly-reversible manner.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","author":[{"full_name":"Kuhn, André","last_name":"Kuhn","first_name":"André"},{"last_name":"Ramans Harborough","full_name":"Ramans Harborough, Sigurd","first_name":"Sigurd"},{"last_name":"McLaughlin","full_name":"McLaughlin, Heather M","first_name":"Heather M"},{"last_name":"Natarajan","full_name":"Natarajan, Bhavani","first_name":"Bhavani"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan","full_name":"Kepinski, Stefan","last_name":"Kepinski"},{"last_name":"Østergaard","full_name":"Østergaard, Lars","first_name":"Lars"}],"external_id":{"pmid":["32267233"],"isi":["000527752200001"]},"article_processing_charge":"No","title":"Direct ETTIN-auxin interaction controls chromatin states in gynoecium development","citation":{"ama":"Kuhn A, Ramans Harborough S, McLaughlin HM, et al. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 2020;9. doi:10.7554/elife.51787","apa":"Kuhn, A., Ramans Harborough, S., McLaughlin, H. M., Natarajan, B., Verstraeten, I., Friml, J., … Østergaard, L. (2020). Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.51787","short":"A. Kuhn, S. Ramans Harborough, H.M. McLaughlin, B. Natarajan, I. Verstraeten, J. Friml, S. Kepinski, L. Østergaard, ELife 9 (2020).","ieee":"A. Kuhn et al., “Direct ETTIN-auxin interaction controls chromatin states in gynoecium development,” eLife, vol. 9. eLife Sciences Publications, 2020.","mla":"Kuhn, André, et al. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” ELife, vol. 9, e51787, eLife Sciences Publications, 2020, doi:10.7554/elife.51787.","ista":"Kuhn A, Ramans Harborough S, McLaughlin HM, Natarajan B, Verstraeten I, Friml J, Kepinski S, Østergaard L. 2020. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 9, e51787.","chicago":"Kuhn, André, Sigurd Ramans Harborough, Heather M McLaughlin, Bhavani Natarajan, Inge Verstraeten, Jiří Friml, Stefan Kepinski, and Lars Østergaard. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.51787."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e51787","date_published":"2020-04-08T00:00:00Z","doi":"10.7554/elife.51787","date_created":"2020-05-04T08:50:47Z","has_accepted_license":"1","isi":1,"year":"2020","day":"08","publication":"eLife","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1},{"_id":"7790","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-21T06:18:49Z","ddc":["510"],"file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"RoSe"}],"abstract":[{"text":"We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density 𝜌 and inverse temperature 𝛽 differs from the one of the noninteracting system by the correction term 𝜋𝜌𝜌𝛽𝛽 . Here, is the scattering length of the interaction potential, and 𝛽 is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. The result is valid in the dilute limit 𝜌 and if 𝛽𝜌 .","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 8","publication_identifier":{"eissn":["20505094"]},"publication_status":"published","file":[{"creator":"dernst","file_size":692530,"date_updated":"2020-07-14T12:48:03Z","file_name":"2020_ForumMath_Deuchert.pdf","date_created":"2020-05-04T12:02:41Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7797","checksum":"8a64da99d107686997876d7cad8cfe1e"}],"language":[{"iso":"eng"}],"volume":8,"related_material":{"record":[{"id":"7524","status":"public","relation":"earlier_version"}]},"ec_funded":1,"article_number":"e20","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” Forum of Mathematics, Sigma, vol. 8, e20, Cambridge University Press, 2020, doi:10.1017/fms.2020.17.","ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” Forum of Mathematics, Sigma, vol. 8. Cambridge University Press, 2020.","short":"A. Deuchert, S. Mayer, R. Seiringer, Forum of Mathematics, Sigma 8 (2020).","apa":"Deuchert, A., Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2020.17","ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 2020;8. doi:10.1017/fms.2020.17","chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” Forum of Mathematics, Sigma. Cambridge University Press, 2020. https://doi.org/10.1017/fms.2020.17.","ista":"Deuchert A, Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 8, e20."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","last_name":"Deuchert"},{"full_name":"Mayer, Simon","last_name":"Mayer","first_name":"Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1910.03372"],"isi":["000527342000001"]},"title":"The free energy of the two-dimensional dilute Bose gas. I. Lower bound","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"14","publication":"Forum of Mathematics, Sigma","doi":"10.1017/fms.2020.17","date_published":"2020-03-14T00:00:00Z","date_created":"2020-05-03T22:00:48Z"},{"has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Nature Communications","date_published":"2020-05-01T00:00:00Z","doi":"10.1038/s41467-020-15895-5","date_created":"2020-05-10T22:00:48Z","acknowledgement":"We thank Daria Siekhaus, Jiri Friml and Alexander Johnson for critical reading of the manuscript, Peter Pimpl, Christian Luschnig and Liwen Jiang for sharing published material, Lesia Rodriguez Solovey for technical assistance. This work was supported by the Austrian Science Fund (FWF01_I1774S) to A.H., K.Ö., and E.B., the German Research Foundation (DFG; He3424/6-1 to I.H.), by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] (to N.C.), by the EU in the framework of the Marie-Curie FP7 COFUND People Programme through the award of an AgreenSkills+ fellowship No. 609398 (to J.S.) and by the Scientific Service Units of IST-Austria through resources provided by the Bioimaging Facility, the Life Science Facility. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"mla":"Hurny, Andrej, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications, vol. 11, 2170, Springer Nature, 2020, doi:10.1038/s41467-020-15895-5.","ama":"Hurny A, Cuesta C, Cavallari N, et al. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 2020;11. doi:10.1038/s41467-020-15895-5","apa":"Hurny, A., Cuesta, C., Cavallari, N., Ötvös, K., Duclercq, J., Dokládal, L., … Benková, E. (2020). Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15895-5","ieee":"A. Hurny et al., “Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"A. Hurny, C. Cuesta, N. Cavallari, K. Ötvös, J. Duclercq, L. Dokládal, J.C. Montesinos López, M. Gallemi, H. Semerádová, T. Rauter, I. Stenzel, G. Persiau, F. Benade, R. Bhalearo, E. Sýkorová, A. Gorzsás, J. Sechet, G. Mouille, I. Heilmann, G. De Jaeger, J. Ludwig-Müller, E. Benková, Nature Communications 11 (2020).","chicago":"Hurny, Andrej, Candela Cuesta, Nicola Cavallari, Krisztina Ötvös, Jerome Duclercq, Ladislav Dokládal, Juan C Montesinos López, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15895-5.","ista":"Hurny A, Cuesta C, Cavallari N, Ötvös K, Duclercq J, Dokládal L, Montesinos López JC, Gallemi M, Semerádová H, Rauter T, Stenzel I, Persiau G, Benade F, Bhalearo R, Sýkorová E, Gorzsás A, Sechet J, Mouille G, Heilmann I, De Jaeger G, Ludwig-Müller J, Benková E. 2020. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 11, 2170."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426","last_name":"Hurny","first_name":"Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","last_name":"Cuesta","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela"},{"first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola","last_name":"Cavallari"},{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","last_name":"Ötvös","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983"},{"first_name":"Jerome","last_name":"Duclercq","full_name":"Duclercq, Jerome"},{"first_name":"Ladislav","full_name":"Dokládal, Ladislav","last_name":"Dokládal"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal","last_name":"Gallemi","full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893"},{"full_name":"Semeradova, Hana","last_name":"Semeradova","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","id":"A0385D1A-9376-11EA-A47D-9862C5E3AB22","last_name":"Rauter","full_name":"Rauter, Thomas"},{"full_name":"Stenzel, Irene","last_name":"Stenzel","first_name":"Irene"},{"first_name":"Geert","last_name":"Persiau","full_name":"Persiau, Geert"},{"first_name":"Freia","full_name":"Benade, Freia","last_name":"Benade"},{"first_name":"Rishikesh","last_name":"Bhalearo","full_name":"Bhalearo, Rishikesh"},{"first_name":"Eva","full_name":"Sýkorová, Eva","last_name":"Sýkorová"},{"full_name":"Gorzsás, András","last_name":"Gorzsás","first_name":"András"},{"last_name":"Sechet","full_name":"Sechet, Julien","first_name":"Julien"},{"full_name":"Mouille, Gregory","last_name":"Mouille","first_name":"Gregory"},{"full_name":"Heilmann, Ingo","last_name":"Heilmann","first_name":"Ingo"},{"full_name":"De Jaeger, Geert","last_name":"De Jaeger","first_name":"Geert"},{"first_name":"Jutta","full_name":"Ludwig-Müller, Jutta","last_name":"Ludwig-Müller"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["32358503"],"isi":["000531425900012"]},"title":"Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance","article_number":"2170","project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8614","checksum":"2cba327c9e9416d75cb96be54b0fb441","file_size":4743576,"date_updated":"2020-10-06T07:47:53Z","creator":"dernst","file_name":"2020_NatureComm_Hurny.pdf","date_created":"2020-10-06T07:47:53Z"}],"language":[{"iso":"eng"}],"volume":11,"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"05","intvolume":" 11","date_updated":"2023-08-21T06:21:56Z","ddc":["570"],"file_date_updated":"2020-10-06T07:47:53Z","department":[{"_id":"EvBe"}],"_id":"7805","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"7882","department":[{"_id":"MiLe"}],"file_date_updated":"2020-07-14T12:48:04Z","ddc":["510"],"date_updated":"2023-08-21T06:23:36Z","intvolume":" 8","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"A few-body cluster is a building block of a many-body system in a gas phase provided the temperature at most is of the order of the binding energy of this cluster. Here we illustrate this statement by considering a system of tubes filled with dipolar distinguishable particles. We calculate the partition function, which determines the probability to find a few-body cluster at a given temperature. The input for our calculations—the energies of few-body clusters—is estimated using the harmonic approximation. We first describe and demonstrate the validity of our numerical procedure. Then we discuss the results featuring melting of the zero-temperature many-body state into a gas of free particles and few-body clusters. For temperature higher than its binding energy threshold, the dimers overwhelmingly dominate the ensemble, where the remaining probability is in free particles. At very high temperatures free (harmonic oscillator trap-bound) particle dominance is eventually reached. This structure evolution appears both for one and two particles in each layer providing crucial information about the behavior of ultracold dipolar gases. The investigation addresses the transition region between few- and many-body physics as a function of temperature using a system of ten dipoles in five tubes.","lang":"eng"}],"ec_funded":1,"issue":"4","volume":8,"language":[{"iso":"eng"}],"file":[{"file_name":"2020_Mathematics_Armstrong.pdf","date_created":"2020-05-25T14:42:22Z","file_size":990540,"date_updated":"2020-07-14T12:48:04Z","creator":"dernst","checksum":"a05a7df724522203d079673a0d4de4bc","file_id":"7887","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["22277390"]},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"484","title":"Clusters in separated tubes of tilted dipoles","article_processing_charge":"No","external_id":{"isi":["000531824100024"]},"author":[{"full_name":"Armstrong, Jeremy R.","last_name":"Armstrong","first_name":"Jeremy R."},{"first_name":"Aksel S.","full_name":"Jensen, Aksel S.","last_name":"Jensen"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev"},{"full_name":"Zinner, Nikolaj T.","last_name":"Zinner","first_name":"Nikolaj T."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.” Mathematics, vol. 8, no. 4, 484, MDPI, 2020, doi:10.3390/math8040484.","apa":"Armstrong, J. R., Jensen, A. S., Volosniev, A., & Zinner, N. T. (2020). Clusters in separated tubes of tilted dipoles. Mathematics. MDPI. https://doi.org/10.3390/math8040484","ama":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes of tilted dipoles. Mathematics. 2020;8(4). doi:10.3390/math8040484","ieee":"J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in separated tubes of tilted dipoles,” Mathematics, vol. 8, no. 4. MDPI, 2020.","short":"J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).","chicago":"Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T. Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” Mathematics. MDPI, 2020. https://doi.org/10.3390/math8040484.","ista":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated tubes of tilted dipoles. Mathematics. 8(4), 484."},"oa":1,"quality_controlled":"1","publisher":"MDPI","date_created":"2020-05-24T22:01:00Z","doi":"10.3390/math8040484","date_published":"2020-04-01T00:00:00Z","publication":"Mathematics","day":"01","year":"2020","has_accepted_license":"1","isi":1},{"volume":11,"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7817","checksum":"dce367abf2c1a1d15f58fe6f7de82893","date_updated":"2020-07-14T12:48:03Z","file_size":4609120,"creator":"dernst","date_created":"2020-05-11T10:36:33Z","file_name":"2020_NatureComm_Flynn.pdf"}],"scopus_import":"1","intvolume":" 11","month":"04","abstract":[{"text":"Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate IL-17 signaling in neurons, and the extent it can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans neurons. We identify the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling from many immune receptors in mammals, but was not previously implicated in IL-17 signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1 is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1 signaling regulates multiple phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural circuit function downstream of IL-17 to remodel physiology and behavior.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"MaDe"}],"file_date_updated":"2020-07-14T12:48:03Z","date_updated":"2023-08-21T06:21:14Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"7804","date_created":"2020-05-10T22:00:47Z","doi":"10.1038/s41467-020-15872-y","date_published":"2020-04-29T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"29","oa":1,"quality_controlled":"1","publisher":"Springer Nature","external_id":{"isi":["000531855500029"]},"article_processing_charge":"No","author":[{"first_name":"Sean M.","full_name":"Flynn, Sean M.","last_name":"Flynn"},{"full_name":"Chen, Changchun","last_name":"Chen","first_name":"Changchun"},{"orcid":"0000-0001-8945-6992","full_name":"Artan, Murat","last_name":"Artan","first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425"},{"first_name":"Stephen","full_name":"Barratt, Stephen","last_name":"Barratt"},{"first_name":"Alastair","last_name":"Crisp","full_name":"Crisp, Alastair"},{"full_name":"Nelson, Geoffrey M.","last_name":"Nelson","first_name":"Geoffrey M."},{"first_name":"Sew Yeu","full_name":"Peak-Chew, Sew Yeu","last_name":"Peak-Chew"},{"first_name":"Farida","last_name":"Begum","full_name":"Begum, Farida"},{"last_name":"Skehel","full_name":"Skehel, Mark","first_name":"Mark"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono"}],"title":"MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity","citation":{"ista":"Flynn SM, Chen C, Artan M, Barratt S, Crisp A, Nelson GM, Peak-Chew SY, Begum F, Skehel M, de Bono M. 2020. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 11, 2099.","chicago":"Flynn, Sean M., Changchun Chen, Murat Artan, Stephen Barratt, Alastair Crisp, Geoffrey M. Nelson, Sew Yeu Peak-Chew, Farida Begum, Mark Skehel, and Mario de Bono. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15872-y.","ieee":"S. M. Flynn et al., “MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"S.M. Flynn, C. Chen, M. Artan, S. Barratt, A. Crisp, G.M. Nelson, S.Y. Peak-Chew, F. Begum, M. Skehel, M. de Bono, Nature Communications 11 (2020).","ama":"Flynn SM, Chen C, Artan M, et al. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 2020;11. doi:10.1038/s41467-020-15872-y","apa":"Flynn, S. M., Chen, C., Artan, M., Barratt, S., Crisp, A., Nelson, G. M., … de Bono, M. (2020). MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15872-y","mla":"Flynn, Sean M., et al. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications, vol. 11, 2099, Springer Nature, 2020, doi:10.1038/s41467-020-15872-y."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"2099"},{"citation":{"ista":"Kopf A, Renkawitz J, Hauschild R, Girkontaite I, Tedford K, Merrin J, Thorn-Seshold O, Trauner D, Häcker H, Fischer KD, Kiermaier E, Sixt MK. 2020. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 219(6), e201907154.","chicago":"Kopf, Aglaja, Jörg Renkawitz, Robert Hauschild, Irute Girkontaite, Kerry Tedford, Jack Merrin, Oliver Thorn-Seshold, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.201907154.","apa":"Kopf, A., Renkawitz, J., Hauschild, R., Girkontaite, I., Tedford, K., Merrin, J., … Sixt, M. K. (2020). Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201907154","ama":"Kopf A, Renkawitz J, Hauschild R, et al. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 2020;219(6). doi:10.1083/jcb.201907154","short":"A. Kopf, J. Renkawitz, R. Hauschild, I. Girkontaite, K. Tedford, J. Merrin, O. Thorn-Seshold, D. Trauner, H. Häcker, K.D. Fischer, E. Kiermaier, M.K. Sixt, The Journal of Cell Biology 219 (2020).","ieee":"A. Kopf et al., “Microtubules control cellular shape and coherence in amoeboid migrating cells,” The Journal of Cell Biology, vol. 219, no. 6. Rockefeller University Press, 2020.","mla":"Kopf, Aglaja, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology, vol. 219, no. 6, e201907154, Rockefeller University Press, 2020, doi:10.1083/jcb.201907154."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Kopf","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Irute","last_name":"Girkontaite","full_name":"Girkontaite, Irute"},{"full_name":"Tedford, Kerry","last_name":"Tedford","first_name":"Kerry"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oliver","full_name":"Thorn-Seshold, Oliver","last_name":"Thorn-Seshold"},{"first_name":"Dirk","id":"E8F27F48-3EBA-11E9-92A1-B709E6697425","full_name":"Trauner, Dirk","last_name":"Trauner"},{"full_name":"Häcker, Hans","last_name":"Häcker","first_name":"Hans"},{"full_name":"Fischer, Klaus Dieter","last_name":"Fischer","first_name":"Klaus Dieter"},{"first_name":"Eva","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","full_name":"Kiermaier, Eva","orcid":"0000-0001-6165-5738","last_name":"Kiermaier"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"article_processing_charge":"No","external_id":{"pmid":["32379884"],"isi":["000538141100020"]},"title":"Microtubules control cellular shape and coherence in amoeboid migrating cells","article_number":"e201907154","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373"},{"grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425"},{"_id":"252C3B08-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","grant_number":"W 1250-B20"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"The Journal of Cell Biology","doi":"10.1083/jcb.201907154","date_published":"2020-06-01T00:00:00Z","date_created":"2020-05-24T22:00:56Z","acknowledgement":"The authors thank the Scientific Service Units (Life Sciences, Bioimaging, Preclinical) of the Institute of Science and Technology Austria for excellent support. This work was funded by the European Research Council (ERC StG 281556 and CoG 724373), two grants from the Austrian\r\nScience Fund (FWF; P29911 and DK Nanocell W1250-B20 to M. Sixt) and by the German Research Foundation (DFG SFB1032 project B09) to O. Thorn-Seshold and D. Trauner. J. Renkawitz was supported by ISTFELLOW funding from the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under the Research Executive Agency grant agreement (291734) and a European Molecular Biology Organization long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409), E. Kiermaier by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC 2151—390873048, and H. Hacker by the American Lebanese Syrian Associated ¨Charities. K.-D. Fischer was supported by the Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes graduate school funded by the Ministry of Economics, Science, and Digitisation of the State Saxony-Anhalt and by the European Funds for Social and Regional Development.","quality_controlled":"1","publisher":"Rockefeller University Press","oa":1,"date_updated":"2023-08-21T06:28:17Z","ddc":["570"],"department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"file_date_updated":"2020-11-24T13:25:13Z","_id":"7875","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1540-8140"]},"publication_status":"published","file":[{"checksum":"cb0b9c77842ae1214caade7b77e4d82d","file_id":"8801","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-11-24T13:25:13Z","file_name":"2020_JCellBiol_Kopf.pdf","creator":"dernst","date_updated":"2020-11-24T13:25:13Z","file_size":7536712}],"language":[{"iso":"eng"}],"issue":"6","volume":219,"ec_funded":1,"abstract":[{"text":"Cells navigating through complex tissues face a fundamental challenge: while multiple protrusions explore different paths, the cell needs to avoid entanglement. How a cell surveys and then corrects its own shape is poorly understood. Here, we demonstrate that spatially distinct microtubule dynamics regulate amoeboid cell migration by locally promoting the retraction of protrusions. In migrating dendritic cells, local microtubule depolymerization within protrusions remote from the microtubule organizing center triggers actomyosin contractility controlled by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin localization, thereby causing two effects that rate-limit locomotion: (1) impaired cell edge coordination during path finding and (2) defective adhesion resolution. Compromised shape control is particularly hindering in geometrically complex microenvironments, where it leads to entanglement and ultimately fragmentation of the cell body. We thus demonstrate that microtubules can act as a proprioceptive device: they sense cell shape and control actomyosin retraction to sustain cellular coherence.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"06","intvolume":" 219"},{"_id":"7888","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-21T06:25:49Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:48:04Z","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order."}],"month":"04","intvolume":" 9","scopus_import":"1","file":[{"file_name":"2020_eLife_Schauer.pdf","date_created":"2020-05-25T15:15:43Z","file_size":7744848,"date_updated":"2020-07-14T12:48:04Z","creator":"dernst","checksum":"f6aad884cf706846ae9357fcd728f8b5","file_id":"7890","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","volume":9,"related_material":{"record":[{"relation":"dissertation_contains","id":"12891","status":"public"}]},"ec_funded":1,"article_number":"e55190","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190.","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications, 2020, doi:10.7554/elife.55190.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190"},"title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","author":[{"last_name":"Schauer","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","first_name":"Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"article_processing_charge":"No","external_id":{"pmid":["32250246"],"isi":["000531544400001"]},"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"day":"06","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.7554/elife.55190","date_published":"2020-04-06T00:00:00Z","date_created":"2020-05-25T15:01:40Z"},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2020-05-24T22:00:57Z","doi":"10.1016/j.celrep.2020.107647","date_published":"2020-05-19T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Cell Reports","day":"19","article_number":"107647","article_processing_charge":"No","external_id":{"isi":["000535655200005"]},"author":[{"last_name":"Parenti","full_name":"Parenti, Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","first_name":"Ilaria"},{"first_name":"Farah","last_name":"Diab","full_name":"Diab, Farah"},{"first_name":"Sara Ruiz","full_name":"Gil, Sara Ruiz","last_name":"Gil"},{"first_name":"Eskeatnaf","last_name":"Mulugeta","full_name":"Mulugeta, Eskeatnaf"},{"full_name":"Casa, Valentina","last_name":"Casa","first_name":"Valentina"},{"last_name":"Berutti","full_name":"Berutti, Riccardo","first_name":"Riccardo"},{"full_name":"Brouwer, Rutger W.W.","last_name":"Brouwer","first_name":"Rutger W.W."},{"last_name":"Dupé","full_name":"Dupé, Valerie","first_name":"Valerie"},{"first_name":"Juliane","last_name":"Eckhold","full_name":"Eckhold, Juliane"},{"first_name":"Elisabeth","full_name":"Graf, Elisabeth","last_name":"Graf"},{"first_name":"Beatriz","full_name":"Puisac, Beatriz","last_name":"Puisac"},{"first_name":"Feliciano","full_name":"Ramos, Feliciano","last_name":"Ramos"},{"first_name":"Thomas","full_name":"Schwarzmayr, Thomas","last_name":"Schwarzmayr"},{"first_name":"Macarena Moronta","last_name":"Gines","full_name":"Gines, Macarena Moronta"},{"last_name":"Van Staveren","full_name":"Van Staveren, Thomas","first_name":"Thomas"},{"full_name":"Van Ijcken, Wilfred F.J.","last_name":"Van Ijcken","first_name":"Wilfred F.J."},{"first_name":"Tim M.","last_name":"Strom","full_name":"Strom, Tim M."},{"last_name":"Pié","full_name":"Pié, Juan","first_name":"Juan"},{"full_name":"Watrin, Erwan","last_name":"Watrin","first_name":"Erwan"},{"full_name":"Kaiser, Frank J.","last_name":"Kaiser","first_name":"Frank J."},{"full_name":"Wendt, Kerstin S.","last_name":"Wendt","first_name":"Kerstin S."}],"title":"MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome","citation":{"ista":"Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, Van Staveren T, Van Ijcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. 2020. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 31(7), 107647.","chicago":"Parenti, Ilaria, Farah Diab, Sara Ruiz Gil, Eskeatnaf Mulugeta, Valentina Casa, Riccardo Berutti, Rutger W.W. Brouwer, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.107647.","ama":"Parenti I, Diab F, Gil SR, et al. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 2020;31(7). doi:10.1016/j.celrep.2020.107647","apa":"Parenti, I., Diab, F., Gil, S. R., Mulugeta, E., Casa, V., Berutti, R., … Wendt, K. S. (2020). MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.107647","short":"I. Parenti, F. Diab, S.R. Gil, E. Mulugeta, V. Casa, R. Berutti, R.W.W. Brouwer, V. Dupé, J. Eckhold, E. Graf, B. Puisac, F. Ramos, T. Schwarzmayr, M.M. Gines, T. Van Staveren, W.F.J. Van Ijcken, T.M. Strom, J. Pié, E. Watrin, F.J. Kaiser, K.S. Wendt, Cell Reports 31 (2020).","ieee":"I. Parenti et al., “MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome,” Cell Reports, vol. 31, no. 7. Elsevier, 2020.","mla":"Parenti, Ilaria, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell Reports, vol. 31, no. 7, 107647, Elsevier, 2020, doi:10.1016/j.celrep.2020.107647."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 31","month":"05","abstract":[{"text":"The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication inNIPBL, engineered in two different cell lines,alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interactwith MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protectiveagainst out-of-frame mutations that is potentially relevant for other genetic conditions.","lang":"eng"}],"oa_version":"Published Version","issue":"7","volume":31,"publication_status":"published","publication_identifier":{"eissn":["22111247"]},"language":[{"iso":"eng"}],"file":[{"checksum":"64d8f7467731ee5c166b10b939b8310b","file_id":"7892","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-05-26T11:05:01Z","file_name":"2020_CellReports_Parenti.pdf","date_updated":"2020-07-14T12:48:04Z","file_size":4695682,"creator":"dernst"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","_id":"7877","file_date_updated":"2020-07-14T12:48:04Z","department":[{"_id":"GaNo"}],"date_updated":"2023-08-21T06:27:47Z","ddc":["570"]},{"file_date_updated":"2020-07-14T12:48:04Z","department":[{"_id":"RySh"}],"date_updated":"2023-08-21T06:26:50Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"7878","volume":9,"publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":4832050,"date_updated":"2020-07-14T12:48:04Z","file_name":"2020_eLife_Bao.pdf","date_created":"2020-05-26T09:34:54Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7891","checksum":"8ea99bb6660cc407dbdb00c173b01683"}],"scopus_import":"1","intvolume":" 9","month":"05","abstract":[{"text":"Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal signaling. While their function is well documented in slices, requirements for their activation in vivo are poorly understood. We examine this question in adult mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons (MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases Cai rises associated with locomotion. In vitro studies and freeze-fracture electron microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by close association of the two classes of receptors. Altogether our results suggest that mGluR1s, acting in synergy with iGluRs, potently contribute to processing cerebellar neuronal signaling under physiological conditions.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","external_id":{"isi":["000535191600001"],"pmid":["32401196"]},"article_processing_charge":"No","author":[{"full_name":"Bao, Jin","last_name":"Bao","first_name":"Jin"},{"first_name":"Michael","full_name":"Graupner, Michael","last_name":"Graupner"},{"full_name":"Astorga, Guadalupe","last_name":"Astorga","first_name":"Guadalupe"},{"first_name":"Thibault","last_name":"Collin","full_name":"Collin, Thibault"},{"first_name":"Abdelali","last_name":"Jalil","full_name":"Jalil, Abdelali"},{"first_name":"Dwi Wahyu","last_name":"Indriati","full_name":"Indriati, Dwi Wahyu"},{"last_name":"Bradley","full_name":"Bradley, Jonathan","first_name":"Jonathan"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"last_name":"Llano","full_name":"Llano, Isabel","first_name":"Isabel"}],"title":"Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo","citation":{"chicago":"Bao, Jin, Michael Graupner, Guadalupe Astorga, Thibault Collin, Abdelali Jalil, Dwi Wahyu Indriati, Jonathan Bradley, Ryuichi Shigemoto, and Isabel Llano. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56839.","ista":"Bao J, Graupner M, Astorga G, Collin T, Jalil A, Indriati DW, Bradley J, Shigemoto R, Llano I. 2020. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife. 9, e56839.","mla":"Bao, Jin, et al. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” ELife, vol. 9, e56839, eLife Sciences Publications, 2020, doi:10.7554/eLife.56839.","ama":"Bao J, Graupner M, Astorga G, et al. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife. 2020;9. doi:10.7554/eLife.56839","apa":"Bao, J., Graupner, M., Astorga, G., Collin, T., Jalil, A., Indriati, D. W., … Llano, I. (2020). Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56839","short":"J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley, R. Shigemoto, I. Llano, ELife 9 (2020).","ieee":"J. Bao et al., “Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo,” eLife, vol. 9. eLife Sciences Publications, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e56839","date_created":"2020-05-24T22:00:58Z","date_published":"2020-05-13T00:00:00Z","doi":"10.7554/eLife.56839","year":"2020","isi":1,"has_accepted_license":"1","publication":"eLife","day":"13","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1"},{"author":[{"full_name":"Fagan, Rita R.","last_name":"Fagan","first_name":"Rita R."},{"last_name":"Kearney","full_name":"Kearney, Patrick J.","first_name":"Patrick J."},{"last_name":"Sweeney","full_name":"Sweeney, Carolyn G.","first_name":"Carolyn G."},{"first_name":"Dino","last_name":"Luethi","full_name":"Luethi, Dino"},{"last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","first_name":"Florianne E"},{"first_name":"Klaus","full_name":"Schicker, Klaus","last_name":"Schicker"},{"first_name":"Brian S.","last_name":"Alejandro","full_name":"Alejandro, Brian S."},{"last_name":"O'Connor","full_name":"O'Connor, Lauren C.","first_name":"Lauren C."},{"last_name":"Sitte","full_name":"Sitte, Harald H.","first_name":"Harald H."},{"last_name":"Melikian","full_name":"Melikian, Haley E.","first_name":"Haley E."}],"external_id":{"isi":["000530288000006"],"pmid":["32132171"]},"article_processing_charge":"No","title":"Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact","citation":{"ista":"Fagan RR, Kearney PJ, Sweeney CG, Luethi D, Schoot Uiterkamp FE, Schicker K, Alejandro BS, O’Connor LC, Sitte HH, Melikian HE. 2020. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 295(16), 5229–5244.","chicago":"Fagan, Rita R., Patrick J. Kearney, Carolyn G. Sweeney, Dino Luethi, Florianne E Schoot Uiterkamp, Klaus Schicker, Brian S. Alejandro, Lauren C. O’Connor, Harald H. Sitte, and Haley E. Melikian. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry. ASBMB Publications, 2020. https://doi.org/10.1074/jbc.RA120.012628.","ama":"Fagan RR, Kearney PJ, Sweeney CG, et al. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 2020;295(16):5229-5244. doi:10.1074/jbc.RA120.012628","apa":"Fagan, R. R., Kearney, P. J., Sweeney, C. G., Luethi, D., Schoot Uiterkamp, F. E., Schicker, K., … Melikian, H. E. (2020). Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. ASBMB Publications. https://doi.org/10.1074/jbc.RA120.012628","ieee":"R. R. Fagan et al., “Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact,” Journal of Biological Chemistry, vol. 295, no. 16. ASBMB Publications, pp. 5229–5244, 2020.","short":"R.R. Fagan, P.J. Kearney, C.G. Sweeney, D. Luethi, F.E. Schoot Uiterkamp, K. Schicker, B.S. Alejandro, L.C. O’Connor, H.H. Sitte, H.E. Melikian, Journal of Biological Chemistry 295 (2020) 5229–5244.","mla":"Fagan, Rita R., et al. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry, vol. 295, no. 16, ASBMB Publications, 2020, pp. 5229–44, doi:10.1074/jbc.RA120.012628."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"5229-5244","doi":"10.1074/jbc.RA120.012628","date_published":"2020-04-17T00:00:00Z","date_created":"2020-05-24T22:00:59Z","isi":1,"year":"2020","day":"17","publication":"Journal of Biological Chemistry","publisher":"ASBMB Publications","quality_controlled":"1","oa":1,"department":[{"_id":"SaSi"}],"date_updated":"2023-08-21T06:26:22Z","type":"journal_article","article_type":"original","status":"public","_id":"7880","volume":295,"issue":"16","publication_identifier":{"eissn":["1083351X"],"issn":["00219258"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://escholarship.umassmed.edu/oapubs/4187","open_access":"1"}],"month":"04","intvolume":" 295","abstract":[{"lang":"eng","text":"Following its evoked release, dopamine (DA) signaling is rapidly terminated by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT). DAT surface availability is dynamically regulated by endocytic trafficking, and direct protein kinase C (PKC) activation acutely diminishes DAT surface expression by accelerating DAT internalization. Previous cell line studies demonstrated that PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT. However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis in DAergic terminals or whether there are region- and/or sex-dependent differences in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important questions. Ex vivo studies revealed that PKC activation acutely decreased DAT surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated, conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular distribution in DAergic terminals from female ventral, but not dorsal, striatum. Further, Rit2 was required for PKC-stimulated DAT internalization in both male and female ventral striatum. FRET and surface pulldown studies in cell lines revealed that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization. Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate PKC-stimulated DAT endocytosis. Together, our data provide greater insight into mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic terminals. "}],"pmid":1,"oa_version":"Submitted Version"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Sixt MK, Lämmermann T. 2020. T cells: Bridge-and-channel commute to the white pulp. Immunity. 52(5), 721–723.","chicago":"Sixt, Michael K, and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity. Elsevier, 2020. https://doi.org/10.1016/j.immuni.2020.04.020.","ama":"Sixt MK, Lämmermann T. T cells: Bridge-and-channel commute to the white pulp. Immunity. 2020;52(5):721-723. doi:10.1016/j.immuni.2020.04.020","apa":"Sixt, M. K., & Lämmermann, T. (2020). T cells: Bridge-and-channel commute to the white pulp. Immunity. Elsevier. https://doi.org/10.1016/j.immuni.2020.04.020","short":"M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723.","ieee":"M. K. Sixt and T. Lämmermann, “T cells: Bridge-and-channel commute to the white pulp,” Immunity, vol. 52, no. 5. Elsevier, pp. 721–723, 2020.","mla":"Sixt, Michael K., and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity, vol. 52, no. 5, Elsevier, 2020, pp. 721–23, doi:10.1016/j.immuni.2020.04.020."},"title":"T cells: Bridge-and-channel commute to the white pulp","article_processing_charge":"No","external_id":{"isi":["000535371100002"]},"author":[{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Tim","full_name":"Lämmermann, Tim","last_name":"Lämmermann"}],"oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Immunity","day":"19","year":"2020","isi":1,"date_created":"2020-05-24T22:00:57Z","doi":"10.1016/j.immuni.2020.04.020","date_published":"2020-05-19T00:00:00Z","page":"721-723","_id":"7876","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-21T06:27:18Z","department":[{"_id":"MiSi"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In contrast to lymph nodes, the lymphoid regions of the spleen—the white pulp—are located deep within the organ, yielding the trafficking paths of T cells in the white pulp largely invisible. In an intravital microscopy tour de force reported in this issue of Immunity, Chauveau et al. show that T cells perform unidirectional, perivascular migration through the enigmatic marginal zone bridging channels. "}],"intvolume":" 52","month":"05","main_file_link":[{"url":"https://pure.mpg.de/pubman/item/item_3265599_2/component/file_3265620/Sixt%20et%20al..pdf","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10974180"],"issn":["10747613"]},"volume":52,"issue":"5"},{"title":"Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion","article_processing_charge":"No","external_id":{"isi":["000537208000001"]},"author":[{"first_name":"Julia","full_name":"Damiano-Guercio, Julia","last_name":"Damiano-Guercio"},{"first_name":"Laëtitia","last_name":"Kurzawa","full_name":"Kurzawa, Laëtitia"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","full_name":"Müller, Jan","last_name":"Müller"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev"},{"first_name":"Matthias","full_name":"Schaks, Matthias","last_name":"Schaks"},{"first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria","last_name":"Nemethova"},{"first_name":"Thomas","full_name":"Pokrant, Thomas","last_name":"Pokrant"},{"first_name":"Stefan","last_name":"Brühmann","full_name":"Brühmann, Stefan"},{"last_name":"Linkner","full_name":"Linkner, Joern","first_name":"Joern"},{"full_name":"Blanchoin, Laurent","last_name":"Blanchoin","first_name":"Laurent"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife, vol. 9, e55351, eLife Sciences Publications, 2020, doi:10.7554/eLife.55351.","apa":"Damiano-Guercio, J., Kurzawa, L., Müller, J., Dimchev, G. A., Schaks, M., Nemethova, M., … Faix, J. (2020). Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.55351","ama":"Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 2020;9. doi:10.7554/eLife.55351","short":"J. Damiano-Guercio, L. Kurzawa, J. Müller, G.A. Dimchev, M. Schaks, M. Nemethova, T. Pokrant, S. Brühmann, J. Linkner, L. Blanchoin, M.K. Sixt, K. Rottner, J. Faix, ELife 9 (2020).","ieee":"J. Damiano-Guercio et al., “Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion,” eLife, vol. 9. eLife Sciences Publications, 2020.","chicago":"Damiano-Guercio, Julia, Laëtitia Kurzawa, Jan Müller, Georgi A Dimchev, Matthias Schaks, Maria Nemethova, Thomas Pokrant, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.55351.","ista":"Damiano-Guercio J, Kurzawa L, Müller J, Dimchev GA, Schaks M, Nemethova M, Pokrant T, Brühmann S, Linkner J, Blanchoin L, Sixt MK, Rottner K, Faix J. 2020. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 9, e55351."},"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373"}],"article_number":"e55351","date_created":"2020-05-31T22:00:49Z","date_published":"2020-05-11T00:00:00Z","doi":"10.7554/eLife.55351","publication":"eLife","day":"11","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:48:05Z","ddc":["570"],"date_updated":"2023-08-21T06:32:25Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"7909","ec_funded":1,"volume":9,"language":[{"iso":"eng"}],"file":[{"file_id":"7914","checksum":"d33bd4441b9a0195718ce1ba5d2c48a6","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-06-02T10:35:37Z","file_name":"2020_eLife_Damiano_Guercio.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:05Z","file_size":10535713}],"publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"intvolume":" 9","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration."}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Volatile anesthetics are widely used for surgery, but neuronal mechanisms of anesthesia remain unidentified. At the calyx of Held in brainstem slices from rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing the release probability and the number of readily releasable vesicles. In presynaptic recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization, whereas it inhibited exocytosis evoked by a prolonged depolarization via directly blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia is likely mediated by distinct dual mechanisms, depending on input frequencies. In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane impaired the fidelity of repetitive spike transmission, more strongly at higher frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited monosynaptic corticocortical spike transmission, preferentially at a higher frequency. We conclude that dual presynaptic mechanisms operate for the anesthetic action of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass filtering role in spike transmission at central excitatory synapses."}],"intvolume":" 40","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2020-06-02T09:12:16Z","file_name":"2020_JourNeuroscience_Wang.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:05Z","file_size":3817360,"checksum":"6571607ea9036154b67cc78e848a7f7d","file_id":"7912","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["15292401"]},"issue":"21","volume":40,"_id":"7908","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2023-08-21T06:31:25Z","file_date_updated":"2020-07-14T12:48:05Z","department":[{"_id":"RySh"}],"oa":1,"quality_controlled":"1","publisher":"Society for Neuroscience","publication":"Journal of Neuroscience","day":"20","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-05-31T22:00:48Z","doi":"10.1523/JNEUROSCI.2946-19.2020","date_published":"2020-05-20T00:00:00Z","page":"4103-4115","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 40(21), 4103–4115.","chicago":"Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.2946-19.2020.","ieee":"H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,” Journal of Neuroscience, vol. 40, no. 21. Society for Neuroscience, pp. 4103–4115, 2020.","short":"H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience 40 (2020) 4103–4115.","apa":"Wang, H. Y., Eguchi, K., Yamashita, T., & Takahashi, T. (2020). Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2946-19.2020","ama":"Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 2020;40(21):4103-4115. doi:10.1523/JNEUROSCI.2946-19.2020","mla":"Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience, vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:10.1523/JNEUROSCI.2946-19.2020."},"title":"Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms","external_id":{"isi":["000535694700004"]},"article_processing_charge":"No","author":[{"full_name":"Wang, Han Ying","last_name":"Wang","first_name":"Han Ying"},{"id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi"},{"last_name":"Yamashita","full_name":"Yamashita, Takayuki","first_name":"Takayuki"},{"first_name":"Tomoyuki","last_name":"Takahashi","full_name":"Takahashi, Tomoyuki"}]},{"file":[{"date_created":"2020-06-08T06:27:32Z","file_name":"2020_ScientificReports_Uroshlev.pdf","date_updated":"2020-07-14T12:48:05Z","file_size":1001724,"creator":"dernst","checksum":"099e51611a5b7ca04244d03b2faddf33","file_id":"7947","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20452322"]},"publication_status":"published","volume":10,"oa_version":"Published Version","abstract":[{"text":"In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data.","lang":"eng"}],"month":"05","intvolume":" 10","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-21T07:00:17Z","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:48:05Z","_id":"7931","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"25","publication":"Scientific Reports","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1038/s41598-020-65406-1","date_published":"2020-05-25T00:00:00Z","date_created":"2020-06-07T22:00:51Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020.","short":"L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020).","apa":"Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1","ama":"Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1","mla":"Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.","ista":"Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635.","chicago":"Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-65406-1."},"title":"A method for identification of the methylation level of CpG islands from NGS data","author":[{"full_name":"Uroshlev, Leonid A.","last_name":"Uroshlev","first_name":"Leonid A."},{"first_name":"Eldar T.","full_name":"Abdullaev, Eldar T.","last_name":"Abdullaev"},{"first_name":"Iren R.","full_name":"Umarova, Iren R.","last_name":"Umarova"},{"full_name":"Il’Icheva, Irina A.","last_name":"Il’Icheva","first_name":"Irina A."},{"full_name":"Panchenko, Larisa A.","last_name":"Panchenko","first_name":"Larisa A."},{"first_name":"Robert V.","full_name":"Polozov, Robert V.","last_name":"Polozov"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"last_name":"Nechipurenko","full_name":"Nechipurenko, Yury D.","first_name":"Yury D."},{"last_name":"Grokhovsky","full_name":"Grokhovsky, Sergei L.","first_name":"Sergei L."}],"article_processing_charge":"No","external_id":{"isi":["000560774200007"]},"article_number":"8635"},{"citation":{"mla":"Maslov, Mikhail, et al. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B, vol. 101, no. 18, 184104, American Physical Society, 2020, doi:10.1103/PhysRevB.101.184104.","ama":"Maslov M, Lemeshko M, Yakaboylu E. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 2020;101(18). doi:10.1103/PhysRevB.101.184104","apa":"Maslov, M., Lemeshko, M., & Yakaboylu, E. (2020). Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.184104","short":"M. Maslov, M. Lemeshko, E. Yakaboylu, Physical Review B 101 (2020).","ieee":"M. Maslov, M. Lemeshko, and E. Yakaboylu, “Synthetic spin-orbit coupling mediated by a bosonic environment,” Physical Review B, vol. 101, no. 18. American Physical Society, 2020.","chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Enderalp Yakaboylu. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.184104.","ista":"Maslov M, Lemeshko M, Yakaboylu E. 2020. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 101(18), 184104."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["1912.03092"],"isi":["000530754700003"]},"author":[{"last_name":"Maslov","orcid":"0000-0003-4074-2570","full_name":"Maslov, Mikhail","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"}],"title":"Synthetic spin-orbit coupling mediated by a bosonic environment","article_number":"184104 ","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"year":"2020","isi":1,"publication":"Physical Review B","day":"01","date_created":"2020-06-07T22:00:52Z","date_published":"2020-05-01T00:00:00Z","doi":"10.1103/PhysRevB.101.184104","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_updated":"2023-08-21T07:05:15Z","department":[{"_id":"MiLe"}],"_id":"7933","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":101,"issue":"18","abstract":[{"text":"We study a mobile quantum impurity, possessing internal rotational degrees of freedom, confined to a ring in the presence of a many-particle bosonic bath. By considering the recently introduced rotating polaron problem, we define the Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied by means of a variational ansatz in the truncated Fock space. The corresponding spectrum indicates that there emerges a coupling between the internal and orbital angular momenta of the impurity as a consequence of the phonon exchange. We interpret the coupling as a phonon-mediated spin-orbit coupling and quantify it by using a correlation function between the internal and the orbital angular momentum operators. The strong-coupling regime is investigated within the Pekar approach, and it is shown that the correlation function of the ground state shows a kink at a critical coupling, that is explained by a sharp transition from the noninteracting state to the states that exhibit strong interaction with the surroundings. The results might find applications in such fields as spintronics or topological insulators where spin-orbit coupling is of crucial importance.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.03092"}],"scopus_import":"1","intvolume":" 101","month":"05"}]