[{"type":"conference","conference":{"name":"ICLR: International Conference on Learning Representations","start_date":"2020-04-26","end_date":"2020-05-01","location":"Virtual ; Addis Ababa, Ethiopia"},"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)"},"status":"public","_id":"10672","file_date_updated":"2022-01-26T07:35:17Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"date_updated":"2023-04-03T07:33:40Z","ddc":["000"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://openreview.net/forum?id=Bke61krFvS"}],"month":"03","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","publication_status":"published","file":[{"success":1,"file_id":"10677","checksum":"ea13d42dd4541ddb239b6a75821fd6c9","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"iclr_2020.pdf","date_created":"2022-01-26T07:35:17Z","file_size":249431,"date_updated":"2022-01-26T07:35:17Z","creator":"mlechner"}],"language":[{"iso":"eng"}],"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","full_name":"Lechner, Mathias","last_name":"Lechner"}],"article_processing_charge":"No","title":"Learning representations for binary-classification without backpropagation","citation":{"mla":"Lechner, Mathias. “Learning Representations for Binary-Classification without Backpropagation.” 8th International Conference on Learning Representations, ICLR, 2020.","short":"M. Lechner, in:, 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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ICLR","quality_controlled":"1","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","date_published":"2020-03-11T00:00:00Z","date_created":"2022-01-25T15:50:00Z","has_accepted_license":"1","year":"2020","day":"11","publication":"8th International Conference on Learning Representations"},{"date_created":"2020-07-31T16:59:19Z","date_published":"2020-07-07T00:00:00Z","page":"3106–3117","publication":"34th Conference on Neural Information Processing Systems","day":"07","year":"2020","oa":1,"quality_controlled":"1","publisher":"Curran Associates","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.","title":"Unsupervised object-centric video generation and decomposition in 3D","article_processing_charge":"No","external_id":{"arxiv":["2007.06705"]},"author":[{"first_name":"Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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."},"volume":33,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781713829546"]},"intvolume":" 33","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06705"}],"oa_version":"Preprint","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"}],"department":[{"_id":"ChLa"}],"date_updated":"2023-04-25T09:49:58Z","status":"public","conference":{"start_date":"2020-12-06","location":"Vancouver, Canada","end_date":"2020-12-12","name":"NeurIPS: Neural Information Processing Systems"},"type":"conference","_id":"8188"},{"citation":{"chicago":"Bloomer, Rebecca H., Claire E. Hutchison, Isabel Bäurle, James Walker, Xiaofeng Fang, Pumi Perera, Christos N. Velanis, et al. “The Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1920621117.","ista":"Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN, Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, Dean C. 2020. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 117(28), 16660–16666.","mla":"Bloomer, Rebecca H., et al. “The Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences, vol. 117, no. 28, Proceedings of the National Academy of Sciences, 2020, pp. 16660–66, doi:10.1073/pnas.1920621117.","ieee":"R. H. Bloomer et al., “The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2,” Proceedings of the National Academy of Sciences, vol. 117, no. 28. Proceedings of the National Academy of Sciences, pp. 16660–16666, 2020.","short":"R.H. Bloomer, C.E. Hutchison, I. Bäurle, J. Walker, X. Fang, P. Perera, C.N. Velanis, S. Gümüs, C. Spanos, J. Rappsilber, X. Feng, J. Goodrich, C. Dean, Proceedings of the National Academy of Sciences 117 (2020) 16660–16666.","ama":"Bloomer RH, Hutchison CE, Bäurle I, et al. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 2020;117(28):16660-16666. doi:10.1073/pnas.1920621117","apa":"Bloomer, R. H., Hutchison, C. E., Bäurle, I., Walker, J., Fang, X., Perera, P., … Dean, C. (2020). The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1920621117"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["32601198"]},"article_processing_charge":"No","author":[{"first_name":"Rebecca H.","last_name":"Bloomer","full_name":"Bloomer, Rebecca H."},{"last_name":"Hutchison","full_name":"Hutchison, Claire E.","first_name":"Claire E."},{"first_name":"Isabel","full_name":"Bäurle, Isabel","last_name":"Bäurle"},{"full_name":"Walker, James","last_name":"Walker","first_name":"James"},{"last_name":"Fang","full_name":"Fang, Xiaofeng","first_name":"Xiaofeng"},{"first_name":"Pumi","full_name":"Perera, Pumi","last_name":"Perera"},{"first_name":"Christos N.","last_name":"Velanis","full_name":"Velanis, Christos N."},{"first_name":"Serin","last_name":"Gümüs","full_name":"Gümüs, Serin"},{"full_name":"Spanos, Christos","last_name":"Spanos","first_name":"Christos"},{"last_name":"Rappsilber","full_name":"Rappsilber, Juri","first_name":"Juri"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"},{"first_name":"Justin","full_name":"Goodrich, Justin","last_name":"Goodrich"},{"last_name":"Dean","full_name":"Dean, Caroline","first_name":"Caroline"}],"title":"The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2","year":"2020","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences","day":"22","page":"16660-16666","date_created":"2023-01-16T09:15:44Z","date_published":"2020-05-22T00:00:00Z","doi":"10.1073/pnas.1920621117","acknowledgement":"We would like to thank Scott Berry for help with ICU-GFP nuclear localization microscopy, Hao Yu and Lisha Shen for assistance with 6mA DNA methylation analysis, Donna Gibson for graphic design assistance, and members of the C.D. and Howard laboratories for helpful discussions. This work was funded by the European Research Council grants to “MEXTIM” (to C.D.) and “SexMeth” (to X. Feng), by the Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programmes GRO (BB/J004588/1), GEN (BB/P013511/1), BBSRC grant (to X. Feng) (BB/S009620/1), and the Marie Sklodowska–Curie Postdoctoral Fellowships “UNRAVEL” (to R.H.B.) and \"WISDOM\" (to X. Fang). Additional funding via the Wellcome Trust through a Senior Research Fellowship (to J.R.) (103139) and a multiuser equipment grant (108504). The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust (203149).","oa":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","date_updated":"2023-05-08T10:53:55Z","ddc":["580"],"extern":"1","department":[{"_id":"XiFe"}],"file_date_updated":"2023-02-07T11:29:55Z","_id":"12188","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","keyword":["Multidisciplinary"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"12526","checksum":"cedee184cb12f454f2fba4158ff47db9","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PNAS_Bloomer.pdf","date_created":"2023-02-07T11:29:55Z","creator":"alisjak","file_size":1105414,"date_updated":"2023-02-07T11:29:55Z"}],"issue":"28","volume":117,"abstract":[{"lang":"eng","text":"Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states."}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/"}],"scopus_import":"1","intvolume":" 117","month":"05"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics, vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:10.1371/journal.pgen.1008894.","short":"N. Christophorou, W. She, J. Long, A. Hurel, S. Beaubiat, Y. Idir, M. Tagliaro-Jahns, A. Chambon, V. Solier, D. Vezon, M. Grelon, X. Feng, N. Bouché, C. Mézard, PLOS Genetics 16 (2020).","ieee":"N. Christophorou et al., “AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization,” PLOS Genetics, vol. 16, no. 6. Public Library of Science (PLoS), 2020.","ama":"Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 2020;16(6). doi:10.1371/journal.pgen.1008894","apa":"Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., … Mézard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1008894","chicago":"Christophorou, Nicolas, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics. Public Library of Science (PLoS), 2020. https://doi.org/10.1371/journal.pgen.1008894.","ista":"Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. 2020. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 16(6), e1008894."},"title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","article_processing_charge":"No","external_id":{"pmid":["32598340"]},"author":[{"full_name":"Christophorou, Nicolas","last_name":"Christophorou","first_name":"Nicolas"},{"last_name":"She","full_name":"She, Wenjing","first_name":"Wenjing"},{"last_name":"Long","full_name":"Long, Jincheng","first_name":"Jincheng"},{"first_name":"Aurélie","full_name":"Hurel, Aurélie","last_name":"Hurel"},{"first_name":"Sébastien","full_name":"Beaubiat, Sébastien","last_name":"Beaubiat"},{"first_name":"Yassir","last_name":"Idir","full_name":"Idir, Yassir"},{"first_name":"Marina","last_name":"Tagliaro-Jahns","full_name":"Tagliaro-Jahns, Marina"},{"full_name":"Chambon, Aurélie","last_name":"Chambon","first_name":"Aurélie"},{"last_name":"Solier","full_name":"Solier, Victor","first_name":"Victor"},{"first_name":"Daniel","last_name":"Vezon","full_name":"Vezon, Daniel"},{"first_name":"Mathilde","full_name":"Grelon, Mathilde","last_name":"Grelon"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"},{"full_name":"Bouché, Nicolas","last_name":"Bouché","first_name":"Nicolas"},{"first_name":"Christine","full_name":"Mézard, Christine","last_name":"Mézard"}],"article_number":"e1008894","publication":"PLOS Genetics","day":"29","year":"2020","date_created":"2023-01-16T09:16:10Z","date_published":"2020-06-29T00:00:00Z","doi":"10.1371/journal.pgen.1008894","acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","oa":1,"publisher":"Public Library of Science (PLoS)","quality_controlled":"1","extern":"1","date_updated":"2023-05-08T10:54:39Z","department":[{"_id":"XiFe"}],"_id":"12189","keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1553-7404"]},"issue":"6","volume":16,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells."}],"intvolume":" 16","month":"06","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/","open_access":"1"}],"scopus_import":"1"},{"date_created":"2023-01-16T11:45:07Z","date_published":"2020-04-01T00:00:00Z","doi":"10.1016/j.jnt.2019.09.003","page":"378-390","publication":"Journal of Number Theory","day":"01","year":"2020","oa":1,"quality_controlled":"1","publisher":"Elsevier","title":"Primitive divisors of sequences associated to elliptic curves","article_processing_charge":"No","external_id":{"arxiv":["1906.00632"]},"author":[{"full_name":"Verzobio, Matteo","orcid":"0000-0002-0854-0306","last_name":"Verzobio","first_name":"Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Verzobio, “Primitive divisors of sequences associated to elliptic curves,” Journal of Number Theory, vol. 209, no. 4. Elsevier, pp. 378–390, 2020.","short":"M. Verzobio, Journal of Number Theory 209 (2020) 378–390.","ama":"Verzobio M. Primitive divisors of sequences associated to elliptic curves. Journal of Number Theory. 2020;209(4):378-390. doi:10.1016/j.jnt.2019.09.003","apa":"Verzobio, M. (2020). Primitive divisors of sequences associated to elliptic curves. Journal of Number Theory. Elsevier. https://doi.org/10.1016/j.jnt.2019.09.003","mla":"Verzobio, Matteo. “Primitive Divisors of Sequences Associated to Elliptic Curves.” Journal of Number Theory, vol. 209, no. 4, Elsevier, 2020, pp. 378–90, doi:10.1016/j.jnt.2019.09.003.","ista":"Verzobio M. 2020. Primitive divisors of sequences associated to elliptic curves. Journal of Number Theory. 209(4), 378–390.","chicago":"Verzobio, Matteo. “Primitive Divisors of Sequences Associated to Elliptic Curves.” Journal of Number Theory. Elsevier, 2020. https://doi.org/10.1016/j.jnt.2019.09.003."},"volume":209,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-314X"]},"intvolume":" 209","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1906.00632"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Let be a sequence of points on an elliptic curve defined over a number field K. In this paper, we study the denominators of the x-coordinates of this sequence. We prove that, if Q is a torsion point of prime order, then for n large enough there always exists a primitive divisor. Later on, we show the link between the study of the primitive divisors and a Lang-Trotter conjecture. Indeed, given two points P and Q on the elliptic curve, we prove a lower bound for the number of primes p such that P is in the orbit of Q modulo p.","lang":"eng"}],"extern":"1","date_updated":"2023-05-10T11:14:56Z","keyword":["Algebra and Number Theory"],"status":"public","type":"journal_article","article_type":"original","_id":"12310"},{"abstract":[{"text":"We investigate the structural similarities between liquid water and 53 ices, including 20 known crystalline phases. We base such similarity comparison on the local environments that consist of atoms within a certain cutoff radius of a central atom. We reveal that liquid water explores the local environments of the diverse ice phases, by directly comparing the environments in these phases using general atomic descriptors, and also by demonstrating that a machine-learning potential trained on liquid water alone can predict the densities, the lattice energies, and vibrational properties of the\r\nices. The finding that the local environments characterising the different ice phases are found in water sheds light on water phase behaviors, and rationalizes the transferability of water models between different phases.","lang":"eng"}],"oa_version":"Submitted Version","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2006.13316","open_access":"1"}],"month":"06","year":"2020","publication_status":"submitted","day":"23","language":[{"iso":"eng"}],"publication":"arXiv","doi":"10.48550/arXiv.2006.13316","date_published":"2020-06-23T00:00:00Z","date_created":"2021-07-20T11:25:15Z","_id":"9699","article_number":"2006.13316","type":"preprint","status":"public","citation":{"chicago":"Monserrat, Bartomeu, Jan Gerit Brandenburg, Edgar A. Engel, and Bingqing Cheng. “Extracting Ice Phases from Liquid Water: Why a Machine-Learning Water Model Generalizes so Well.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2006.13316.","ista":"Monserrat B, Brandenburg JG, Engel EA, Cheng B. Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well. arXiv, 2006.13316.","mla":"Monserrat, Bartomeu, et al. “Extracting Ice Phases from Liquid Water: Why a Machine-Learning Water Model Generalizes so Well.” ArXiv, 2006.13316, doi:10.48550/arXiv.2006.13316.","ama":"Monserrat B, Brandenburg JG, Engel EA, Cheng B. Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well. arXiv. doi:10.48550/arXiv.2006.13316","apa":"Monserrat, B., Brandenburg, J. G., Engel, E. A., & Cheng, B. (n.d.). Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well. arXiv. https://doi.org/10.48550/arXiv.2006.13316","ieee":"B. Monserrat, J. G. Brandenburg, E. A. Engel, and B. Cheng, “Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well,” arXiv. .","short":"B. Monserrat, J.G. Brandenburg, E.A. Engel, B. Cheng, ArXiv (n.d.)."},"date_updated":"2023-05-10T10:17:48Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Monserrat","full_name":"Monserrat, Bartomeu","first_name":"Bartomeu"},{"last_name":"Brandenburg","full_name":"Brandenburg, Jan Gerit","first_name":"Jan Gerit"},{"first_name":"Edgar A.","last_name":"Engel","full_name":"Engel, Edgar A."},{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"external_id":{"arxiv":["2006.13316"]},"article_processing_charge":"No","title":"Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well"},{"status":"public","keyword":["Analytical Chemistry"],"type":"journal_article","article_type":"letter_note","_id":"12940","extern":"1","date_updated":"2023-05-15T08:01:20Z","month":"10","intvolume":" 92","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1021/acs.analchem.0c02615","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Desorption electrospray ionization (DESI), easy ambient sonic-spray ionization (EASI) and low-temperature plasma (LTP) ionization are powerful ambient ionization techniques for mass spectrometry. However, every single method has its limitation in terms of polarity and molecular weight of analyte molecules. After the miniaturization of every possible component of the different ion sources, we finally were able to embed two emitters and an ion transfer tubing into a small, hand-held device. The pen-like interface is connected to the mass spectrometer and a separate control unit via a bundle of flexible tubing and cables. The novel device allows the user to ionize an extended range of chemicals by simple switching between DESI, voltage-free EASI, or LTP ionization as well as to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The interface was successfully tested using different types of chemicals, pharmaceuticals, and real life samples. Moreover, the combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging mass spectrometry, which we name “interactive mass spectrometry imaging (IMSI)”.","lang":"eng"}],"issue":"21","volume":92,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0003-2700","1520-6882"]},"publication_status":"published","title":"A 3-in-1 hand-held ambient mass spectrometry interface for identification and 2D localization of chemicals on surfaces","author":[{"first_name":"Christina","full_name":"Meisenbichler, Christina","last_name":"Meisenbichler"},{"last_name":"Kluibenschedl","full_name":"Kluibenschedl, Florian","first_name":"Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9"},{"full_name":"Müller, Thomas","last_name":"Müller","first_name":"Thomas"}],"article_processing_charge":"No","external_id":{"pmid":["33063994"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Meisenbichler C, Kluibenschedl F, Müller T. 2020. A 3-in-1 hand-held ambient mass spectrometry interface for identification and 2D localization of chemicals on surfaces. Analytical Chemistry. 92(21), 14314–14318.","chicago":"Meisenbichler, Christina, Florian Kluibenschedl, and Thomas Müller. “A 3-in-1 Hand-Held Ambient Mass Spectrometry Interface for Identification and 2D Localization of Chemicals on Surfaces.” Analytical Chemistry. American Chemical Society, 2020. https://doi.org/10.1021/acs.analchem.0c02615.","ama":"Meisenbichler C, Kluibenschedl F, Müller T. A 3-in-1 hand-held ambient mass spectrometry interface for identification and 2D localization of chemicals on surfaces. Analytical Chemistry. 2020;92(21):14314-14318. doi:10.1021/acs.analchem.0c02615","apa":"Meisenbichler, C., Kluibenschedl, F., & Müller, T. (2020). A 3-in-1 hand-held ambient mass spectrometry interface for identification and 2D localization of chemicals on surfaces. Analytical Chemistry. 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Müller, Analytical Chemistry 92 (2020) 14314–14318.","mla":"Meisenbichler, Christina, et al. “A 3-in-1 Hand-Held Ambient Mass Spectrometry Interface for Identification and 2D Localization of Chemicals on Surfaces.” Analytical Chemistry, vol. 92, no. 21, American Chemical Society, 2020, pp. 14314–18, doi:10.1021/acs.analchem.0c02615."},"quality_controlled":"1","publisher":"American Chemical Society","oa":1,"date_published":"2020-10-16T00:00:00Z","doi":"10.1021/acs.analchem.0c02615","date_created":"2023-05-10T14:50:19Z","page":"14314-14318","day":"16","publication":"Analytical Chemistry","year":"2020"},{"publication":"European Journal of Organic Chemistry","day":"09","year":"2020","date_created":"2023-05-10T14:49:30Z","doi":"10.1002/ejoc.202000692","date_published":"2020-08-09T00:00:00Z","page":"4499-4509","oa":1,"quality_controlled":"1","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Karg, Cornelia A., et al. “Phylloxanthobilins Are Abundant Linear Tetrapyrroles from Chlorophyll Breakdown with Activities against Cancer Cells.” European Journal of Organic Chemistry, vol. 2020, no. 29, Wiley, 2020, pp. 4499–509, doi:10.1002/ejoc.202000692.","apa":"Karg, C. A., Wang, P., Kluibenschedl, F., Müller, T., Allmendinger, L., Vollmar, A. M., & Moser, S. (2020). Phylloxanthobilins are abundant linear tetrapyrroles from chlorophyll breakdown with activities against cancer cells. European Journal of Organic Chemistry. Wiley. https://doi.org/10.1002/ejoc.202000692","ama":"Karg CA, Wang P, Kluibenschedl F, et al. Phylloxanthobilins are abundant linear tetrapyrroles from chlorophyll breakdown with activities against cancer cells. European Journal of Organic Chemistry. 2020;2020(29):4499-4509. doi:10.1002/ejoc.202000692","short":"C.A. Karg, P. Wang, F. Kluibenschedl, T. Müller, L. Allmendinger, A.M. Vollmar, S. Moser, European Journal of Organic Chemistry 2020 (2020) 4499–4509.","ieee":"C. A. Karg et al., “Phylloxanthobilins are abundant linear tetrapyrroles from chlorophyll breakdown with activities against cancer cells,” European Journal of Organic Chemistry, vol. 2020, no. 29. Wiley, pp. 4499–4509, 2020.","chicago":"Karg, Cornelia A., Pengyu Wang, Florian Kluibenschedl, Thomas Müller, Lars Allmendinger, Angelika M. Vollmar, and Simone Moser. “Phylloxanthobilins Are Abundant Linear Tetrapyrroles from Chlorophyll Breakdown with Activities against Cancer Cells.” European Journal of Organic Chemistry. Wiley, 2020. https://doi.org/10.1002/ejoc.202000692.","ista":"Karg CA, Wang P, Kluibenschedl F, Müller T, Allmendinger L, Vollmar AM, Moser S. 2020. Phylloxanthobilins are abundant linear tetrapyrroles from chlorophyll breakdown with activities against cancer cells. European Journal of Organic Chemistry. 2020(29), 4499–4509."},"title":"Phylloxanthobilins are abundant linear tetrapyrroles from chlorophyll breakdown with activities against cancer cells","article_processing_charge":"No","author":[{"first_name":"Cornelia A.","full_name":"Karg, Cornelia A.","last_name":"Karg"},{"last_name":"Wang","full_name":"Wang, Pengyu","first_name":"Pengyu"},{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl"},{"first_name":"Thomas","full_name":"Müller, Thomas","last_name":"Müller"},{"full_name":"Allmendinger, Lars","last_name":"Allmendinger","first_name":"Lars"},{"full_name":"Vollmar, Angelika M.","last_name":"Vollmar","first_name":"Angelika M."},{"last_name":"Moser","full_name":"Moser, Simone","first_name":"Simone"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1434-193X","1099-0690"]},"issue":"29","volume":2020,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Linear tetrapyrroles, called phyllobilins, are obtained as major catabolites upon chlorophyll degradation. Primarily, colorless phylloleucobilins featuring four deconjugated pyrrole units were identified. Their yellow counterparts, phylloxanthobilins, were discovered more recently. Although the two catabolites differ only by one double bond, physicochemical properties are very distinct. Moreover, the presence of the double bond seems to enhance physiologically relevant bioactivities: in contrast to phylloleucobilin, we identified a potent anti-proliferative activity for a phylloxanthobilin, and show that this natural product induces apoptotic cell death and a cell cycle arrest in cancer cells. Interestingly, upon modifying inactive phylloleucobilin by esterification, an anti-proliferative activity can be observed that increases with the chain lengths of the alkyl esters. We provide first evidence for anti-cancer activity of phyllobilins, report a novel plant source for a phylloxanthobilin, and by using paper spray MS, show that these bioactive yellow chlorophyll catabolites are more prevalent in Nature than previously assumed."}],"intvolume":" 2020","month":"08","main_file_link":[{"url":"https://doi.org/10.1002/ejoc.202000692","open_access":"1"}],"scopus_import":"1","extern":"1","date_updated":"2023-05-15T07:57:14Z","_id":"12939","keyword":["Organic Chemistry","Physical and Theoretical Chemistry"],"status":"public","article_type":"original","type":"journal_article"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This booklet is a collection of abstracts presented at the AHPC conference."}],"month":"02","place":"Klosterneuburg, Austria","file":[{"creator":"schloegl","file_size":90899507,"date_updated":"2020-07-14T12:47:59Z","file_name":"BOOKLET_AHPC2020.final.pdf","date_created":"2020-02-19T06:53:38Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7504","checksum":"49798edb9e57bbd6be18362d1d7b18a9"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-004-6"]},"publication_status":"published","_id":"7474","status":"public","type":"book_editor","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":"AHPC: Austrian High-Performance-Computing Meeting","location":"Klosterneuburg, Austria","end_date":"2020-02-21","start_date":"2020-02-19"},"ddc":["000"],"date_updated":"2023-05-16T07:48:28Z","department":[{"_id":"ScienComp"}],"file_date_updated":"2020-07-14T12:47:59Z","publisher":"IST Austria","quality_controlled":"1","oa":1,"day":"19","has_accepted_license":"1","year":"2020","date_published":"2020-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:7474","date_created":"2020-02-11T07:59:04Z","page":"72","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","mla":"Schlögl, Alois, et al., editors. Austrian High-Performance-Computing Meeting (AHPC2020). 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","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","ieee":"A. Schlögl, J. Kiss, and S. Elefante, Eds., Austrian High-Performance-Computing meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020.","short":"A. Schlögl, J. Kiss, S. Elefante, eds., Austrian High-Performance-Computing Meeting (AHPC2020), IST Austria, Klosterneuburg, Austria, 2020."},"title":"Austrian High-Performance-Computing meeting (AHPC2020)","editor":[{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","first_name":"Janos","last_name":"Kiss","full_name":"Kiss, Janos"},{"first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano","last_name":"Elefante"}],"article_processing_charge":"No"},{"title":"How many bits does it take to quantize your neural network?","author":[{"id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco","last_name":"Giacobbe"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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.","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.","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."},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_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"}],"date_published":"2020-04-17T00:00:00Z","doi":"10.1007/978-3-030-45237-7_5","date_created":"2020-05-10T22:00:49Z","page":"79-97","day":"17","publication":"International Conference on Tools and Algorithms for the Construction and Analysis of Systems","has_accepted_license":"1","year":"2020","publisher":"Springer Nature","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-06-23T07:01:11Z","status":"public","type":"conference","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Dublin, Ireland","end_date":"2020-04-30","start_date":"2020-04-25"},"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":"7808","related_material":{"record":[{"relation":"dissertation_contains","id":"11362","status":"public"}]},"volume":12079,"file":[{"checksum":"f19905a42891fe5ce93d69143fa3f6fb","file_id":"7893","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-26T12:48:15Z","file_name":"2020_TACAS_Giacobbe.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:03Z","file_size":2744030}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["16113349"],"isbn":["9783030452360"],"issn":["03029743"]},"publication_status":"published","month":"04","intvolume":" 12079","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}]},{"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","year":"2020","has_accepted_license":"1","publication":"36th International Symposium on Computational Geometry","day":"01","date_created":"2020-06-09T07:24:11Z","date_published":"2020-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2020.20","article_number":"20:1-20:18","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"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","short":"J.-D. Boissonnat, M. Wintraecken, in:, 36th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"title":"The topological correctness of PL-approximations of isomanifolds","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. "}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":"1","intvolume":" 164","month":"06","publication_status":"published","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-143-6"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:48:06Z","file_size":1009739,"creator":"dernst","date_created":"2020-06-17T10:13:34Z","file_name":"2020_LIPIcsSoCG_Boissonnat.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"38cbfa4f5d484d267a35d44d210df044","file_id":"7969"}],"ec_funded":1,"related_material":{"record":[{"id":"9649","status":"public","relation":"later_version"}]},"volume":164,"_id":"7952","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":{"end_date":"2020-06-26","location":"Zürich, Switzerland","start_date":"2020-06-22","name":"SoCG: Symposium on Computational Geometry"},"type":"conference","status":"public","date_updated":"2023-08-02T06:49:16Z","ddc":["510"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:48:06Z"},{"oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1","year":"2020","publication":"Nanoscale","day":"10","page":"3174-3182","date_created":"2023-08-01T08:27:12Z","doi":"10.1039/C9NR08578E","date_published":"2020-01-10T00:00:00Z","citation":{"mla":"Anahory, Y., et al. “SQUID-on-Tip with Single-Electron Spin Sensitivity for High-Field and Ultra-Low Temperature Nanomagnetic Imaging.” Nanoscale, vol. 12, no. 5, Royal Society of Chemistry, 2020, pp. 3174–82, doi:10.1039/C9NR08578E.","ama":"Anahory Y, Naren HR, Lachman EO, et al. SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging. Nanoscale. 2020;12(5):3174-3182. doi:10.1039/C9NR08578E","apa":"Anahory, Y., Naren, H. R., Lachman, E. O., Sinai, S. B., Uri, A., Embon, L., … Zeldov, E. (2020). SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging. Nanoscale. Royal Society of Chemistry. https://doi.org/10.1039/C9NR08578E","short":"Y. Anahory, H.R. Naren, E.O. Lachman, S.B. Sinai, A. Uri, L. Embon, E. Yaakobi, Y. Myasoedov, M.E. Huber, R. Klajn, E. Zeldov, Nanoscale 12 (2020) 3174–3182.","ieee":"Y. Anahory et al., “SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging,” Nanoscale, vol. 12, no. 5. Royal Society of Chemistry, pp. 3174–3182, 2020.","chicago":"Anahory, Y., H. R. Naren, E. O. Lachman, S. Buhbut Sinai, A. Uri, L. Embon, E. Yaakobi, et al. “SQUID-on-Tip with Single-Electron Spin Sensitivity for High-Field and Ultra-Low Temperature Nanomagnetic Imaging.” Nanoscale. Royal Society of Chemistry, 2020. https://doi.org/10.1039/C9NR08578E.","ista":"Anahory Y, Naren HR, Lachman EO, Sinai SB, Uri A, Embon L, Yaakobi E, Myasoedov Y, Huber ME, Klajn R, Zeldov E. 2020. SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging. Nanoscale. 12(5), 3174–3182."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2001.03342"]},"author":[{"first_name":"Y.","last_name":"Anahory","full_name":"Anahory, Y."},{"first_name":"H. R.","full_name":"Naren, H. R.","last_name":"Naren"},{"full_name":"Lachman, E. O.","last_name":"Lachman","first_name":"E. O."},{"last_name":"Sinai","full_name":"Sinai, S. Buhbut","first_name":"S. Buhbut"},{"last_name":"Uri","full_name":"Uri, A.","first_name":"A."},{"first_name":"L.","last_name":"Embon","full_name":"Embon, L."},{"first_name":"E.","last_name":"Yaakobi","full_name":"Yaakobi, E."},{"first_name":"Y.","full_name":"Myasoedov, Y.","last_name":"Myasoedov"},{"first_name":"M. E.","full_name":"Huber, M. E.","last_name":"Huber"},{"full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"},{"first_name":"E.","full_name":"Zeldov, E.","last_name":"Zeldov"}],"title":"SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging","abstract":[{"text":"Scanning nanoscale superconducting quantum interference devices (nanoSQUIDs)\r\nare of growing interest for highly sensitive quantitative imaging of magnetic,\r\nspintronic, and transport properties of low-dimensional systems. Utilizing\r\nspecifically designed grooved quartz capillaries pulled into a sharp pipette,\r\nwe have fabricated the smallest SQUID-on-tip (SOT) devices with effective\r\ndiameters down to 39 nm. Integration of a resistive shunt in close proximity to\r\nthe pipette apex combined with self-aligned deposition of In and Sn, have\r\nresulted in SOT with a flux noise of 42 n$\\Phi_0$Hz$^{-1/2}$, yielding a record\r\nlow spin noise of 0.29 $\\mu_B$Hz$^{-1/2}$. In addition, the new SOTs function\r\nat sub-Kelvin temperatures and in high magnetic fields of over 2.5 T.\r\nIntegrating the SOTs into a scanning probe microscope allowed us to image the\r\nstray field of a single Fe$_3$O$_4$ nanocube at 300 mK. Our results show that\r\nthe easy magnetization axis direction undergoes a transition from the (111)\r\ndirection at room temperature to an in-plane orientation, which could be\r\nattributed to the Verwey phase transition in Fe$_3$O$_4$.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2001.03342"}],"scopus_import":"1","intvolume":" 12","month":"01","publication_status":"published","publication_identifier":{"eissn":["2040-3372"]},"language":[{"iso":"eng"}],"volume":12,"issue":"5","_id":"13341","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-02T09:35:52Z","extern":"1"},{"doi":"10.4230/LIPIcs.SoCG.2020.67","date_published":"2020-06-01T00:00:00Z","date_created":"2020-06-22T09:14:19Z","has_accepted_license":"1","year":"2020","day":"01","publication":"36th International Symposium on Computational Geometry","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"author":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"},{"full_name":"Welzl, Emo","last_name":"Welzl","first_name":"Emo"}],"external_id":{"arxiv":["2003.13557"]},"article_processing_charge":"No","title":"Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)","citation":{"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.","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","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","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.","short":"U. Wagner, E. Welzl, in:, 36th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"67:1 - 67:16","related_material":{"record":[{"status":"public","id":"12129","relation":"later_version"}]},"volume":164,"publication_identifier":{"isbn":["9783959771436"],"issn":["18688969"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8003","checksum":"3f6925be5f3dcdb3b14cab92f410edf7","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"}],"language":[{"iso":"eng"}],"scopus_import":1,"alternative_title":["LIPIcs"],"month":"06","intvolume":" 164","abstract":[{"lang":"eng","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)."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:06Z","department":[{"_id":"UlWa"}],"date_updated":"2023-08-04T08:51:07Z","ddc":["510"],"type":"conference","conference":{"start_date":"2020-06-22","location":"Zürich, Switzerland","end_date":"2020-06-26","name":"SoCG: Symposium on Computational Geometry"},"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":"7990"},{"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"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":[{"relation":"later_version","id":"12129","status":"public"}]},"volume":"2020-January","_id":"7807","status":"public","type":"conference","conference":{"start_date":"2020-01-05","end_date":"2020-01-08","location":"Salt Lake City, UT, United States","name":"SODA: Symposium on Discrete Algorithms"},"date_updated":"2023-08-04T08:51:07Z","department":[{"_id":"UlWa"}],"quality_controlled":"1","publisher":"SIAM","oa":1,"day":"01","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","year":"2020","doi":"10.1137/1.9781611975994.172","date_published":"2020-01-01T00:00:00Z","date_created":"2020-05-10T22:00:48Z","page":"2823-2841","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","short":"U. Wagner, E. Welzl, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2020, pp. 2823–2841.","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."},"title":"Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)","author":[{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"},{"first_name":"Emo","full_name":"Welzl, Emo","last_name":"Welzl"}],"external_id":{"arxiv":["2003.13557"]},"article_processing_charge":"No"},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"publisher":"Dryad","month":"09","year":"2020","day":"22","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-23T16:48:27Z","related_material":{"record":[{"id":"8708","status":"public","relation":"used_in_publication"}]},"date_published":"2020-09-22T00:00:00Z","doi":"10.5061/DRYAD.R4XGXD29N","_id":"13073","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","status":"public","citation":{"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.","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.","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","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","ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020)."},"date_updated":"2023-08-04T11:04:11Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Alexis","full_name":"Simon, Alexis","last_name":"Simon"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"El Ayari","full_name":"El Ayari, Tahani","first_name":"Tahani"},{"last_name":"Liautard-Haag","full_name":"Liautard-Haag, Cathy","first_name":"Cathy"},{"full_name":"Strelkov, Petr","last_name":"Strelkov","first_name":"Petr"},{"full_name":"Welch, John","last_name":"Welch","first_name":"John"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","department":[{"_id":"NiBa"}]},{"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","department":[{"_id":"NiBa"}],"author":[{"last_name":"Arnoux","full_name":"Arnoux, Stephanie","first_name":"Stephanie"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"first_name":"Christopher","full_name":"Sauvage, Christopher","last_name":"Sauvage"}],"article_processing_charge":"No","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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."},"date_updated":"2023-08-04T11:19:26Z","status":"public","type":"research_data_reference","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)"},"_id":"13065","date_published":"2020-10-19T00:00:00Z","doi":"10.5061/DRYAD.Q2BVQ83HD","related_material":{"link":[{"relation":"software","url":"https://github.com/starnoux/arnoux_et_al_2019"}],"record":[{"relation":"used_in_publication","id":"8928","status":"public"}]},"date_created":"2023-05-23T16:30:20Z","day":"19","year":"2020","month":"10","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}]},{"quality_controlled":"1","publisher":"American Chemical Society","oa":1,"doi":"10.1021/acs.accounts.0c00434","date_published":"2020-11-17T00:00:00Z","date_created":"2023-08-01T09:35:50Z","page":"2600-2610","day":"17","publication":"Accounts of Chemical Research","year":"2020","title":"Molecular photoswitching in confined spaces","author":[{"first_name":"Angela B.","last_name":"Grommet","full_name":"Grommet, Angela B."},{"last_name":"Lee","full_name":"Lee, Lucia M.","first_name":"Lucia M."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"external_id":{"pmid":["32969638"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A.B. Grommet, L.M. Lee, R. Klajn, Accounts of Chemical Research 53 (2020) 2600–2610.","ieee":"A. B. Grommet, L. M. Lee, and R. Klajn, “Molecular photoswitching in confined spaces,” Accounts of Chemical Research, vol. 53, no. 11. American Chemical Society, pp. 2600–2610, 2020.","apa":"Grommet, A. B., Lee, L. M., & Klajn, R. (2020). Molecular photoswitching in confined spaces. Accounts of Chemical Research. American Chemical Society. https://doi.org/10.1021/acs.accounts.0c00434","ama":"Grommet AB, Lee LM, Klajn R. Molecular photoswitching in confined spaces. Accounts of Chemical Research. 2020;53(11):2600-2610. doi:10.1021/acs.accounts.0c00434","mla":"Grommet, Angela B., et al. “Molecular Photoswitching in Confined Spaces.” Accounts of Chemical Research, vol. 53, no. 11, American Chemical Society, 2020, pp. 2600–10, doi:10.1021/acs.accounts.0c00434.","ista":"Grommet AB, Lee LM, Klajn R. 2020. Molecular photoswitching in confined spaces. Accounts of Chemical Research. 53(11), 2600–2610.","chicago":"Grommet, Angela B., Lucia M. Lee, and Rafal Klajn. “Molecular Photoswitching in Confined Spaces.” Accounts of Chemical Research. American Chemical Society, 2020. https://doi.org/10.1021/acs.accounts.0c00434."},"month":"11","intvolume":" 53","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1021/acs.accounts.0c00434","open_access":"1"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"In nature, light is harvested by photoactive proteins to drive a range of biological processes, including photosynthesis, phototaxis, vision, and ultimately life. Bacteriorhodopsin, for example, is a protein embedded within archaeal cell membranes that binds the chromophore retinal within its hydrophobic pocket. Exposure to light triggers regioselective photoisomerization of the confined retinal, which in turn initiates a cascade of conformational changes within the protein, triggering proton flux against the concentration gradient, providing the microorganisms with the energy to live. We are inspired by these functions in nature to harness light energy using synthetic photoswitches under confinement. Like retinal, synthetic photoswitches require some degree of conformational flexibility to isomerize. In nature, the conformational change associated with retinal isomerization is accommodated by the structural flexibility of the opsin host, yet it results in steric communication between the chromophore and the protein. Similarly, we strive to design systems wherein isomerization of confined photoswitches results in steric communication between a photoswitch and its confining environment. To achieve this aim, a balance must be struck between molecular crowding and conformational freedom under confinement: too much crowding prevents switching, whereas too much freedom resembles switching of isolated molecules in solution, preventing communication.\r\n\r\nIn this Account, we discuss five classes of synthetic light-switchable compounds—diarylethenes, anthracenes, azobenzenes, spiropyrans, and donor–acceptor Stenhouse adducts—comparing their behaviors under confinement and in solution. The environments employed to confine these photoswitches are diverse, ranging from planar surfaces to nanosized cavities within coordination cages, nanoporous frameworks, and nanoparticle aggregates. The trends that emerge are primarily dependent on the nature of the photoswitch and not on the material used for confinement. In general, we find that photoswitches requiring less conformational freedom for switching are, as expected, more straightforward to isomerize reversibly under confinement. Because these compounds undergo only small structural changes upon isomerization, however, switching does not propagate into communication with their environment. Conversely, photoswitches that require more conformational freedom are more challenging to switch under confinement but also can influence system-wide behavior.\r\n\r\nAlthough we are primarily interested in the effects of geometric constraints on photoswitching under confinement, additional effects inevitably emerge when a compound is removed from solution and placed within a new, more crowded environment. For instance, we have found that compounds that convert to zwitterionic isomers upon light irradiation often experience stabilization of these forms under confinement. This effect results from the mutual stabilization of zwitterions that are brought into close proximity on surfaces or within cavities. Furthermore, photoswitches can experience preorganization under confinement, influencing the selectivity and efficiency of their photoreactions. Because intermolecular interactions arising from confinement cannot be considered independently from the effects of geometric constraints, we describe all confinement effects concurrently throughout this Account."}],"volume":53,"issue":"11","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-4898"],"issn":["0001-4842"]},"publication_status":"published","status":"public","keyword":["General Medicine","General Chemistry"],"article_type":"original","type":"journal_article","_id":"13361","extern":"1","date_updated":"2023-08-07T10:06:46Z"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"volume":142,"issue":"41","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Aggregation of organic molecules can drastically affect their physicochemical properties. For instance, the optical properties of BODIPY dyes are inherently related to the degree of aggregation and the mutual orientation of BODIPY units within these aggregates. Whereas the noncovalent aggregation of various BODIPY dyes has been studied in diverse media, the ill-defined nature of these aggregates has made it difficult to elucidate the structure–property relationships. Here, we studied the encapsulation of three structurally simple BODIPY derivatives within the hydrophobic cavity of a water-soluble, flexible PdII6L4 coordination cage. The cavity size allowed for the selective encapsulation of two dye molecules, irrespective of the substitution pattern on the BODIPY core. Working with a model, a pentamethyl-substituted derivative, we found that the mutual orientation of two BODIPY units in the cage’s cavity was remarkably similar to that in the crystalline state of the free dye, allowing us to isolate and characterize the smallest possible noncovalent H-type BODIPY aggregate, namely, an H-dimer. Interestingly, a CF3-substituted BODIPY, known for forming J-type aggregates, was also encapsulated as an H-dimer. Taking advantage of the dynamic nature of encapsulation, we developed a system in which reversible switching between H- and J-aggregates can be induced for multiple cycles simply by addition and subsequent destruction of the cage. We expect that the ability to rapidly and reversibly manipulate the optical properties of supramolecular inclusion complexes in aqueous media will open up avenues for developing detection systems that operate within biological environments.","lang":"eng"}],"intvolume":" 142","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.0c08589"}],"scopus_import":"1","extern":"1","date_updated":"2023-08-07T10:09:54Z","_id":"13362","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","article_type":"original","type":"journal_article","publication":"Journal of the American Chemical Society","day":"04","year":"2020","date_created":"2023-08-01T09:36:10Z","doi":"10.1021/jacs.0c08589","date_published":"2020-10-04T00:00:00Z","page":"17721-17729","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Gemen, J. Ahrens, L. J. W. Shimon, and R. Klajn, “Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage,” Journal of the American Chemical Society, vol. 142, no. 41. American Chemical Society, pp. 17721–17729, 2020.","short":"J. Gemen, J. Ahrens, L.J.W. Shimon, R. Klajn, Journal of the American Chemical Society 142 (2020) 17721–17729.","apa":"Gemen, J., Ahrens, J., Shimon, L. J. W., & Klajn, R. (2020). Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.0c08589","ama":"Gemen J, Ahrens J, Shimon LJW, Klajn R. Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage. Journal of the American Chemical Society. 2020;142(41):17721-17729. doi:10.1021/jacs.0c08589","mla":"Gemen, Julius, et al. “Modulating the Optical Properties of BODIPY Dyes by Noncovalent Dimerization within a Flexible Coordination Cage.” Journal of the American Chemical Society, vol. 142, no. 41, American Chemical Society, 2020, pp. 17721–29, doi:10.1021/jacs.0c08589.","ista":"Gemen J, Ahrens J, Shimon LJW, Klajn R. 2020. Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage. Journal of the American Chemical Society. 142(41), 17721–17729.","chicago":"Gemen, Julius, Johannes Ahrens, Linda J. W. Shimon, and Rafal Klajn. “Modulating the Optical Properties of BODIPY Dyes by Noncovalent Dimerization within a Flexible Coordination Cage.” Journal of the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.0c08589."},"title":"Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage","external_id":{"pmid":["33006898"]},"article_processing_charge":"No","author":[{"full_name":"Gemen, Julius","last_name":"Gemen","first_name":"Julius"},{"last_name":"Ahrens","full_name":"Ahrens, Johannes","first_name":"Johannes"},{"full_name":"Shimon, Linda J. W.","last_name":"Shimon","first_name":"Linda J. W."},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}]},{"date_updated":"2023-08-07T10:15:38Z","extern":"1","_id":"13364","type":"journal_article","article_type":"original","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","publication_status":"published","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"language":[{"iso":"eng"}],"issue":"34","volume":142,"abstract":[{"text":"Photochromic molecules undergo reversible isomerization upon irradiation with light at different wavelengths, a process that can alter their physical and chemical properties. For instance, dihydropyrene (DHP) is a deep-colored compound that isomerizes to light-brown cyclophanediene (CPD) upon irradiation with visible light. CPD can then isomerize back to DHP upon irradiation with UV light or thermally in the dark. Conversion between DHP and CPD is thought to proceed via a biradical intermediate; bimolecular events involving this unstable intermediate thus result in rapid decomposition and poor cycling performance. Here, we show that the reversible isomerization of DHP can be stabilized upon confinement within a PdII6L4 coordination cage. By protecting this reactive intermediate using the cage, each isomerization reaction proceeds to higher yield, which significantly decreases the fatigue experienced by the system upon repeated photocycling. Although molecular confinement is known to help stabilize reactive species, this effect is not typically employed to protect reactive intermediates and thus improve reaction yields. We envisage that performing reactions under confinement will not only improve the cyclic performance of photochromic molecules, but may also increase the amount of product obtainable from traditionally low-yielding organic reactions.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.0c06146"}],"scopus_import":"1","intvolume":" 142","month":"08","citation":{"ista":"Canton M, Grommet AB, Pesce L, Gemen J, Li S, Diskin-Posner Y, Credi A, Pavan GM, Andréasson J, Klajn R. 2020. Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage. Journal of the American Chemical Society. 142(34), 14557–14565.","chicago":"Canton, Martina, Angela B. Grommet, Luca Pesce, Julius Gemen, Shiming Li, Yael Diskin-Posner, Alberto Credi, Giovanni M. Pavan, Joakim Andréasson, and Rafal Klajn. “Improving Fatigue Resistance of Dihydropyrene by Encapsulation within a Coordination Cage.” Journal of the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.0c06146.","short":"M. Canton, A.B. Grommet, L. Pesce, J. Gemen, S. Li, Y. Diskin-Posner, A. Credi, G.M. Pavan, J. Andréasson, R. Klajn, Journal of the American Chemical Society 142 (2020) 14557–14565.","ieee":"M. Canton et al., “Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage,” Journal of the American Chemical Society, vol. 142, no. 34. American Chemical Society, pp. 14557–14565, 2020.","apa":"Canton, M., Grommet, A. B., Pesce, L., Gemen, J., Li, S., Diskin-Posner, Y., … Klajn, R. (2020). Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.0c06146","ama":"Canton M, Grommet AB, Pesce L, et al. Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage. Journal of the American Chemical Society. 2020;142(34):14557-14565. doi:10.1021/jacs.0c06146","mla":"Canton, Martina, et al. “Improving Fatigue Resistance of Dihydropyrene by Encapsulation within a Coordination Cage.” Journal of the American Chemical Society, vol. 142, no. 34, American Chemical Society, 2020, pp. 14557–65, doi:10.1021/jacs.0c06146."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["32791832"]},"article_processing_charge":"No","author":[{"last_name":"Canton","full_name":"Canton, Martina","first_name":"Martina"},{"full_name":"Grommet, Angela B.","last_name":"Grommet","first_name":"Angela B."},{"full_name":"Pesce, Luca","last_name":"Pesce","first_name":"Luca"},{"last_name":"Gemen","full_name":"Gemen, Julius","first_name":"Julius"},{"last_name":"Li","full_name":"Li, Shiming","first_name":"Shiming"},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"last_name":"Credi","full_name":"Credi, Alberto","first_name":"Alberto"},{"full_name":"Pavan, Giovanni M.","last_name":"Pavan","first_name":"Giovanni M."},{"first_name":"Joakim","last_name":"Andréasson","full_name":"Andréasson, Joakim"},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"title":"Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage","year":"2020","publication":"Journal of the American Chemical Society","day":"14","page":"14557-14565","date_created":"2023-08-01T09:36:59Z","doi":"10.1021/jacs.0c06146","date_published":"2020-08-14T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"American Chemical Society"},{"title":"Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage","article_processing_charge":"No","external_id":{"pmid":["32353237"]},"author":[{"first_name":"Luca","last_name":"Pesce","full_name":"Pesce, Luca"},{"first_name":"Claudio","full_name":"Perego, Claudio","last_name":"Perego"},{"first_name":"Angela B.","full_name":"Grommet, Angela B.","last_name":"Grommet"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"},{"first_name":"Giovanni M.","last_name":"Pavan","full_name":"Pavan, Giovanni M."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Pesce L, Perego C, Grommet AB, Klajn R, Pavan GM. 2020. Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage. Journal of the American Chemical Society. 142(21), 9792–9802.","chicago":"Pesce, Luca, Claudio Perego, Angela B. Grommet, Rafal Klajn, and Giovanni M. Pavan. “Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage.” Journal of the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.0c03444.","short":"L. Pesce, C. Perego, A.B. Grommet, R. Klajn, G.M. Pavan, Journal of the American Chemical Society 142 (2020) 9792–9802.","ieee":"L. Pesce, C. Perego, A. B. Grommet, R. Klajn, and G. M. Pavan, “Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage,” Journal of the American Chemical Society, vol. 142, no. 21. American Chemical Society, pp. 9792–9802, 2020.","apa":"Pesce, L., Perego, C., Grommet, A. B., Klajn, R., & Pavan, G. M. (2020). Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.0c03444","ama":"Pesce L, Perego C, Grommet AB, Klajn R, Pavan GM. Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage. Journal of the American Chemical Society. 2020;142(21):9792-9802. doi:10.1021/jacs.0c03444","mla":"Pesce, Luca, et al. “Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage.” Journal of the American Chemical Society, vol. 142, no. 21, American Chemical Society, 2020, pp. 9792–802, doi:10.1021/jacs.0c03444."},"oa":1,"publisher":"American Chemical Society","quality_controlled":"1","date_created":"2023-08-01T09:37:12Z","doi":"10.1021/jacs.0c03444","date_published":"2020-04-30T00:00:00Z","page":"9792-9802","publication":"Journal of the American Chemical Society","day":"30","year":"2020","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","type":"journal_article","article_type":"original","_id":"13365","extern":"1","date_updated":"2023-08-07T10:18:53Z","intvolume":" 142","month":"04","main_file_link":[{"url":"https://doi.org/10.1021/jacs.0c03444","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Photoswitchable molecules are employed for many applications, from the development of active materials to the design of stimuli-responsive molecular systems and light-powered molecular machines. To fully exploit their potential, we must learn ways to control the mechanism and kinetics of their photoinduced isomerization. One possible strategy involves confinement of photoresponsive switches such as azobenzenes or spiropyrans within crowded molecular environments, which may allow control over their light-induced conversion. However, the molecular factors that influence and control the switching process under realistic conditions and within dynamic molecular regimes often remain difficult to ascertain. As a case study, here we have employed molecular models to probe the isomerization of azobenzene guests within a Pd(II)-based coordination cage host in water. Atomistic molecular dynamics and metadynamics simulations allow us to characterize the flexibility of the cage in the solvent, the (rare) guest encapsulation and release events, and the relative probability/kinetics of light-induced isomerization of azobenzene analogues in these host–guest systems. In this way, we can reconstruct the mechanism of azobenzene switching inside the cage cavity and explore key molecular factors that may control this event. We obtain a molecular-level insight on the effects of crowding and host–guest interactions on azobenzene isomerization. The detailed picture elucidated by this study may enable the rational design of photoswitchable systems whose reactivity can be controlled via host–guest interactions.","lang":"eng"}],"issue":"21","volume":142,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]}},{"quality_controlled":"1","publisher":"Royal Society of Chemistry","day":"10","publication":"Nanoscale","year":"2020","doi":"10.1039/c9nr08578e","date_published":"2020-01-10T00:00:00Z","date_created":"2023-08-01T09:37:53Z","page":"3174-3182","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Anahory, Y., H. R. Naren, E. O. Lachman, S. Buhbut Sinai, A. Uri, L. Embon, E. Yaakobi, et al. “SQUID-on-Tip with Single-Electron Spin Sensitivity for High-Field and Ultra-Low Temperature Nanomagnetic Imaging.” Nanoscale. Royal Society of Chemistry, 2020. https://doi.org/10.1039/c9nr08578e.","ista":"Anahory Y, Naren HR, Lachman EO, Buhbut Sinai S, Uri A, Embon L, Yaakobi E, Myasoedov Y, Huber ME, Klajn R, Zeldov E. 2020. SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging. Nanoscale. 12(5), 3174–3182.","mla":"Anahory, Y., et al. “SQUID-on-Tip with Single-Electron Spin Sensitivity for High-Field and Ultra-Low Temperature Nanomagnetic Imaging.” Nanoscale, vol. 12, no. 5, Royal Society of Chemistry, 2020, pp. 3174–82, doi:10.1039/c9nr08578e.","apa":"Anahory, Y., Naren, H. R., Lachman, E. O., Buhbut Sinai, S., Uri, A., Embon, L., … Zeldov, E. (2020). SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging. Nanoscale. Royal Society of Chemistry. https://doi.org/10.1039/c9nr08578e","ama":"Anahory Y, Naren HR, Lachman EO, et al. SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging. Nanoscale. 2020;12(5):3174-3182. doi:10.1039/c9nr08578e","short":"Y. Anahory, H.R. Naren, E.O. Lachman, S. Buhbut Sinai, A. Uri, L. Embon, E. Yaakobi, Y. Myasoedov, M.E. Huber, R. Klajn, E. Zeldov, Nanoscale 12 (2020) 3174–3182.","ieee":"Y. Anahory et al., “SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging,” Nanoscale, vol. 12, no. 5. Royal Society of Chemistry, pp. 3174–3182, 2020."},"title":"SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging","author":[{"first_name":"Y.","full_name":"Anahory, Y.","last_name":"Anahory"},{"full_name":"Naren, H. R.","last_name":"Naren","first_name":"H. R."},{"last_name":"Lachman","full_name":"Lachman, E. O.","first_name":"E. O."},{"first_name":"S.","full_name":"Buhbut Sinai, S.","last_name":"Buhbut Sinai"},{"last_name":"Uri","full_name":"Uri, A.","first_name":"A."},{"first_name":"L.","full_name":"Embon, L.","last_name":"Embon"},{"full_name":"Yaakobi, E.","last_name":"Yaakobi","first_name":"E."},{"first_name":"Y.","last_name":"Myasoedov","full_name":"Myasoedov, Y."},{"first_name":"M. E.","last_name":"Huber","full_name":"Huber, M. E."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"},{"first_name":"E.","last_name":"Zeldov","full_name":"Zeldov, E."}],"external_id":{"pmid":["31967152"],"arxiv":["2001.03342"]},"article_processing_charge":"No","pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Scanning nanoscale superconducting quantum interference devices (nanoSQUIDs) are of growing interest for highly sensitive quantitative imaging of magnetic, spintronic, and transport properties of low-dimensional systems. Utilizing specifically designed grooved quartz capillaries pulled into a sharp pipette, we have fabricated the smallest SQUID-on-tip (SOT) devices with effective diameters down to 39 nm. Integration of a resistive shunt in close proximity to the pipette apex combined with self-aligned deposition of In and Sn, has resulted in SOTs with a flux noise of 42 nΦ0 Hz−1/2, yielding a record low spin noise of 0.29 μB Hz−1/2. In addition, the new SOTs function at sub-Kelvin temperatures and in high magnetic fields of over 2.5 T. Integrating the SOTs into a scanning probe microscope allowed us to image the stray field of a single Fe3O4 nanocube at 300 mK. Our results show that the easy magnetization axis direction undergoes a transition from the 〈111〉 direction at room temperature to an in-plane orientation, which could be attributed to the Verwey phase transition in Fe3O4."}],"month":"01","intvolume":" 12","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2001.03342"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2040-3372"],"issn":["2040-3364"]},"publication_status":"published","volume":12,"issue":"5","_id":"13368","status":"public","keyword":["General Materials Science"],"type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-07T10:32:15Z"},{"article_number":"2002135","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Moreno, Silvia, et al. “Light‐driven Proton Transfer for Cyclic and Temporal Switching of Enzymatic Nanoreactors.” Small, vol. 16, no. 37, 2002135, Wiley, 2020, doi:10.1002/smll.202002135.","ieee":"S. Moreno et al., “Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors,” Small, vol. 16, no. 37. Wiley, 2020.","short":"S. Moreno, P. Sharan, J. Engelke, H. Gumz, S. Boye, U. Oertel, P. Wang, S. Banerjee, R. Klajn, B. Voit, A. Lederer, D. Appelhans, Small 16 (2020).","ama":"Moreno S, Sharan P, Engelke J, et al. Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors. Small. 2020;16(37). doi:10.1002/smll.202002135","apa":"Moreno, S., Sharan, P., Engelke, J., Gumz, H., Boye, S., Oertel, U., … Appelhans, D. (2020). Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors. Small. Wiley. https://doi.org/10.1002/smll.202002135","chicago":"Moreno, Silvia, Priyanka Sharan, Johanna Engelke, Hannes Gumz, Susanne Boye, Ulrich Oertel, Peng Wang, et al. “Light‐driven Proton Transfer for Cyclic and Temporal Switching of Enzymatic Nanoreactors.” Small. Wiley, 2020. https://doi.org/10.1002/smll.202002135.","ista":"Moreno S, Sharan P, Engelke J, Gumz H, Boye S, Oertel U, Wang P, Banerjee S, Klajn R, Voit B, Lederer A, Appelhans D. 2020. Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors. Small. 16(37), 2002135."},"title":"Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors","external_id":{"pmid":["32783385"]},"article_processing_charge":"No","author":[{"first_name":"Silvia","last_name":"Moreno","full_name":"Moreno, Silvia"},{"first_name":"Priyanka","last_name":"Sharan","full_name":"Sharan, Priyanka"},{"first_name":"Johanna","last_name":"Engelke","full_name":"Engelke, Johanna"},{"last_name":"Gumz","full_name":"Gumz, Hannes","first_name":"Hannes"},{"full_name":"Boye, Susanne","last_name":"Boye","first_name":"Susanne"},{"first_name":"Ulrich","last_name":"Oertel","full_name":"Oertel, Ulrich"},{"last_name":"Wang","full_name":"Wang, Peng","first_name":"Peng"},{"last_name":"Banerjee","full_name":"Banerjee, Susanta","first_name":"Susanta"},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"full_name":"Voit, Brigitte","last_name":"Voit","first_name":"Brigitte"},{"last_name":"Lederer","full_name":"Lederer, Albena","first_name":"Albena"},{"first_name":"Dietmar","full_name":"Appelhans, Dietmar","last_name":"Appelhans"}],"oa":1,"publisher":"Wiley","quality_controlled":"1","publication":"Small","day":"11","year":"2020","date_created":"2023-08-01T09:36:48Z","doi":"10.1002/smll.202002135","date_published":"2020-08-11T00:00:00Z","_id":"13363","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-07T10:11:41Z","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Temporal activation of biological processes by visible light and subsequent return to an inactive state in the absence of light is an essential characteristic of photoreceptor cells. Inspired by these phenomena, light-responsive materials are very attractive due to the high spatiotemporal control of light irradiation, with light being able to precisely orchestrate processes repeatedly over many cycles. Herein, it is reported that light-driven proton transfer triggered by a merocyanine-based photoacid can be used to modulate the permeability of pH-responsive polymersomes through cyclic, temporally controlled protonation and deprotonation of the polymersome membrane. The membranes can undergo repeated light-driven swelling–contraction cycles without losing functional effectiveness. When applied to enzyme loaded-nanoreactors, this membrane responsiveness is used for the reversible control of enzymatic reactions. This combination of the merocyanine-based photoacid and pH-switchable nanoreactors results in rapidly responding and versatile supramolecular systems successfully used to switch enzymatic reactions ON and OFF on demand.","lang":"eng"}],"intvolume":" 16","month":"08","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/smll.202002135"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1613-6829"],"issn":["1613-6810"]},"volume":16,"issue":"37"},{"extern":"1","date_updated":"2023-08-07T10:29:06Z","_id":"13367","keyword":["Electrical and Electronic Engineering","Condensed Matter Physics","General Materials Science","Biomedical Engineering","Atomic and Molecular Physics","and Optics","Bioengineering"],"status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1748-3387"],"eissn":["1748-3395"]},"volume":15,"pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Confining molecules can fundamentally change their chemical and physical properties. Confinement effects are considered instrumental at various stages of the origins of life, and life continues to rely on layers of compartmentalization to maintain an out-of-equilibrium state and efficiently synthesize complex biomolecules under mild conditions. As interest in synthetic confined systems grows, we are realizing that the principles governing reactivity under confinement are the same in abiological systems as they are in nature. In this Review, we categorize the ways in which nanoconfinement effects impact chemical reactivity in synthetic systems. Under nanoconfinement, chemical properties can be modulated to increase reaction rates, enhance selectivity and stabilize reactive species. Confinement effects also lead to changes in physical properties. The fluorescence of light emitters, the colours of dyes and electronic communication between electroactive species can all be tuned under confinement. Within each of these categories, we elucidate design principles and strategies that are widely applicable across a range of confined systems, specifically highlighting examples of different nanocompartments that influence reactivity in similar ways."}],"intvolume":" 15","month":"04","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Grommet, Angela B., Moran Feller, and Rafal Klajn. “Chemical Reactivity under Nanoconfinement.” Nature Nanotechnology. Springer Nature, 2020. https://doi.org/10.1038/s41565-020-0652-2.","ista":"Grommet AB, Feller M, Klajn R. 2020. Chemical reactivity under nanoconfinement. Nature Nanotechnology. 15, 256–271.","mla":"Grommet, Angela B., et al. “Chemical Reactivity under Nanoconfinement.” Nature Nanotechnology, vol. 15, Springer Nature, 2020, pp. 256–71, doi:10.1038/s41565-020-0652-2.","ieee":"A. B. Grommet, M. Feller, and R. Klajn, “Chemical reactivity under nanoconfinement,” Nature Nanotechnology, vol. 15. Springer Nature, pp. 256–271, 2020.","short":"A.B. Grommet, M. Feller, R. Klajn, Nature Nanotechnology 15 (2020) 256–271.","apa":"Grommet, A. B., Feller, M., & Klajn, R. (2020). Chemical reactivity under nanoconfinement. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-020-0652-2","ama":"Grommet AB, Feller M, Klajn R. Chemical reactivity under nanoconfinement. Nature Nanotechnology. 2020;15:256-271. doi:10.1038/s41565-020-0652-2"},"title":"Chemical reactivity under nanoconfinement","article_processing_charge":"No","external_id":{"pmid":["32303705"]},"author":[{"first_name":"Angela B.","last_name":"Grommet","full_name":"Grommet, Angela B."},{"last_name":"Feller","full_name":"Feller, Moran","first_name":"Moran"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"publication":"Nature Nanotechnology","day":"17","year":"2020","date_created":"2023-08-01T09:37:39Z","date_published":"2020-04-17T00:00:00Z","doi":"10.1038/s41565-020-0652-2","page":"256-271","quality_controlled":"1","publisher":"Springer Nature"},{"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.","oa":1,"publisher":"IEEE","quality_controlled":"1","publication":"IEEE International Symposium on Information Theory - Proceedings","day":"01","year":"2020","date_created":"2020-09-20T22:01:37Z","doi":"10.1109/ISIT44484.2020.9174141","date_published":"2020-06-01T00:00:00Z","article_number":"401-406","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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. Simplified successive cancellation decoding of polar codes has sublinear latency. In: IEEE International Symposium on Information Theory - Proceedings. Vol 2020-June. IEEE; 2020. doi:10.1109/ISIT44484.2020.9174141","ieee":"M. Mondelli, S. A. Hashemi, J. Cioffi, and A. Goldsmith, “Simplified successive cancellation decoding of polar codes has sublinear latency,” in IEEE International Symposium on Information Theory - Proceedings, Los Angeles, CA, United States, 2020, vol. 2020–June.","short":"M. Mondelli, S.A. Hashemi, J. Cioffi, A. Goldsmith, in:, IEEE International Symposium on Information Theory - Proceedings, IEEE, 2020.","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.","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.","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."},"title":"Simplified successive cancellation decoding of polar codes has sublinear latency","article_processing_charge":"No","external_id":{"arxiv":["1909.04892"]},"author":[{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"full_name":"Cioffi, John","last_name":"Cioffi","first_name":"John"},{"first_name":"Andrea","last_name":"Goldsmith","full_name":"Goldsmith, Andrea"}],"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."}],"month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.04892"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["21578095"],"isbn":["9781728164328"]},"related_material":{"record":[{"id":"9047","status":"public","relation":"later_version"}]},"volume":"2020-June","_id":"8536","status":"public","conference":{"name":"ISIT: Internation Symposium on Information Theory","end_date":"2020-06-26","location":"Los Angeles, CA, United States","start_date":"2020-06-21"},"type":"conference","date_updated":"2023-08-07T13:36:24Z","department":[{"_id":"MaMo"}]},{"article_number":"A51","article_processing_charge":"No","external_id":{"arxiv":["1911.03477"]},"author":[{"first_name":"J.","last_name":"Bodensteiner","full_name":"Bodensteiner, J."},{"last_name":"Sana","full_name":"Sana, H.","first_name":"H."},{"last_name":"Mahy","full_name":"Mahy, L.","first_name":"L."},{"last_name":"Patrick","full_name":"Patrick, L. R.","first_name":"L. R."},{"last_name":"de Koter","full_name":"de Koter, A.","first_name":"A."},{"first_name":"S. E.","full_name":"de Mink, S. E.","last_name":"de Mink"},{"first_name":"C. J.","last_name":"Evans","full_name":"Evans, C. J."},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg"},{"full_name":"Langer, N.","last_name":"Langer","first_name":"N."},{"first_name":"D. J.","full_name":"Lennon, D. J.","last_name":"Lennon"},{"first_name":"F. R. N.","full_name":"Schneider, F. R. N.","last_name":"Schneider"},{"first_name":"F.","full_name":"Tramper, F.","last_name":"Tramper"}],"title":"The young massive SMC cluster NGC 330 seen by MUSE","citation":{"mla":"Bodensteiner, J., et al. “The Young Massive SMC Cluster NGC 330 Seen by MUSE.” Astronomy & Astrophysics, vol. 634, A51, EDP Sciences, 2020, doi:10.1051/0004-6361/201936743.","apa":"Bodensteiner, J., Sana, H., Mahy, L., Patrick, L. R., de Koter, A., de Mink, S. E., … Tramper, F. (2020). The young massive SMC cluster NGC 330 seen by MUSE. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201936743","ama":"Bodensteiner J, Sana H, Mahy L, et al. The young massive SMC cluster NGC 330 seen by MUSE. Astronomy & Astrophysics. 2020;634. doi:10.1051/0004-6361/201936743","short":"J. Bodensteiner, H. Sana, L. Mahy, L.R. Patrick, A. de Koter, S.E. de Mink, C.J. Evans, Y.L.L. Götberg, N. Langer, D.J. Lennon, F.R.N. Schneider, F. Tramper, Astronomy & Astrophysics 634 (2020).","ieee":"J. Bodensteiner et al., “The young massive SMC cluster NGC 330 seen by MUSE,” Astronomy & Astrophysics, vol. 634. EDP Sciences, 2020.","chicago":"Bodensteiner, J., H. Sana, L. Mahy, L. R. Patrick, A. de Koter, S. E. de Mink, C. J. Evans, et al. “The Young Massive SMC Cluster NGC 330 Seen by MUSE.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/201936743.","ista":"Bodensteiner J, Sana H, Mahy L, Patrick LR, de Koter A, de Mink SE, Evans CJ, Götberg YLL, Langer N, Lennon DJ, Schneider FRN, Tramper F. 2020. The young massive SMC cluster NGC 330 seen by MUSE. Astronomy & Astrophysics. 634, A51."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"EDP Sciences","quality_controlled":"1","date_created":"2023-08-03T10:13:29Z","date_published":"2020-02-05T00:00:00Z","doi":"10.1051/0004-6361/201936743","year":"2020","publication":"Astronomy & Astrophysics","day":"05","article_type":"original","type":"journal_article","keyword":["stars: massive / stars: emission-line / Be / binaries: spectroscopic / blue stragglers / Magellanic Clouds"],"status":"public","_id":"13466","date_updated":"2023-08-09T12:50:01Z","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201936743"}],"scopus_import":"1","intvolume":" 634","month":"02","abstract":[{"text":"Context. A majority of massive stars are part of binary systems, a large fraction of which will inevitably interact during their lives. Binary-interaction products (BiPs), that is, stars affected by such interaction, are expected to be commonly present in stellar populations. BiPs are thus a crucial ingredient in the understanding of stellar evolution.\r\nAims. We aim to identify and characterize a statistically significant sample of BiPs by studying clusters of 10 − 40 Myr, an age at which binary population models predict the abundance of BiPs to be highest. One example of such a cluster is NGC 330 in the Small Magellanic Cloud.\r\nMethods. Using MUSE WFM-AO observations of NGC 330, we resolved the dense cluster core for the first time and were able to extract spectra of its entire massive star population. We developed an automated spectral classification scheme based on the equivalent widths of spectral lines in the red part of the spectrum.\r\nResults. We characterize the massive star content of the core of NGC 330, which contains more than 200 B stars, 2 O stars, 6 A-type supergiants, and 11 red supergiants. We find a lower limit on the Be star fraction of 32 ± 3% in the whole sample. It increases to at least 46 ± 10% when we only consider stars brighter than V = 17 mag. We estimate an age of the cluster core between 35 and 40 Myr and a total cluster mass of 88−18+17 × 103 M⊙.\r\nConclusions. We find that the population in the cluster core is different than the population in the outskirts: while the stellar content in the core appears to be older than the stars in the outskirts, the Be star fraction and the observed binary fraction are significantly higher. Furthermore, we detect several BiP candidates that will be subject of future studies.","lang":"eng"}],"oa_version":"Published Version","volume":634,"publication_status":"published","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"language":[{"iso":"eng"}]},{"date_updated":"2023-08-09T12:53:37Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"_id":"13465","issue":"3","volume":493,"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1093/mnras/staa549","open_access":"1"}],"month":"04","intvolume":" 493","abstract":[{"lang":"eng","text":"Gravitational-wave detections are now probing the black hole (BH) mass distribution, including the predicted pair-instability mass gap. These data require robust quantitative predictions, which are challenging to obtain. The most massive BH progenitors experience episodic mass ejections on time-scales shorter than the convective turnover time-scale. This invalidates the steady-state assumption on which the classic mixing length theory relies. We compare the final BH masses computed with two different versions of the stellar evolutionary code MESA\r\n: (i) using the default implementation of Paxton et al. (2018) and (ii) solving an additional equation accounting for the time-scale for convective deceleration. In the second grid, where stronger convection develops during the pulses and carries part of the energy, we find weaker pulses. This leads to lower amounts of mass being ejected and thus higher final BH masses of up to ∼5M⊙\r\n. The differences are much smaller for the progenitors that determine the maximum mass of BHs below the gap. This prediction is robust at MBH,max≃48M⊙\r\n, at least within the idealized context of this study. This is an encouraging indication that current models are robust enough for comparison with the present-day gravitational-wave detections. However, the large differences between individual models emphasize the importance of improving the treatment of convection in stellar models, especially in the light of the data anticipated from the third generation of gravitational-wave detectors."}],"oa_version":"Published Version","author":[{"last_name":"Renzo","full_name":"Renzo, M","first_name":"M"},{"first_name":"R J","last_name":"Farmer","full_name":"Farmer, R J"},{"full_name":"Justham, S","last_name":"Justham","first_name":"S"},{"first_name":"S E","full_name":"de Mink, S E","last_name":"de Mink"},{"full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"last_name":"Marchant","full_name":"Marchant, P","first_name":"P"}],"article_processing_charge":"No","external_id":{"arxiv":["2002.08200"]},"title":"Sensitivity of the lower edge of the pair-instability black hole mass gap to the treatment of time-dependent convection","citation":{"chicago":"Renzo, M, R J Farmer, S Justham, S E de Mink, Ylva Louise Linsdotter Götberg, and P Marchant. “Sensitivity of the Lower Edge of the Pair-Instability Black Hole Mass Gap to the Treatment of Time-Dependent Convection.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa549.","ista":"Renzo M, Farmer RJ, Justham S, de Mink SE, Götberg YLL, Marchant P. 2020. Sensitivity of the lower edge of the pair-instability black hole mass gap to the treatment of time-dependent convection. Monthly Notices of the Royal Astronomical Society. 493(3), 4333–4341.","mla":"Renzo, M., et al. “Sensitivity of the Lower Edge of the Pair-Instability Black Hole Mass Gap to the Treatment of Time-Dependent Convection.” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 3, Oxford University Press, 2020, pp. 4333–41, doi:10.1093/mnras/staa549.","short":"M. Renzo, R.J. Farmer, S. Justham, S.E. de Mink, Y.L.L. Götberg, P. Marchant, Monthly Notices of the Royal Astronomical Society 493 (2020) 4333–4341.","ieee":"M. Renzo, R. J. Farmer, S. Justham, S. E. de Mink, Y. L. L. Götberg, and P. Marchant, “Sensitivity of the lower edge of the pair-instability black hole mass gap to the treatment of time-dependent convection,” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 3. Oxford University Press, pp. 4333–4341, 2020.","ama":"Renzo M, Farmer RJ, Justham S, de Mink SE, Götberg YLL, Marchant P. Sensitivity of the lower edge of the pair-instability black hole mass gap to the treatment of time-dependent convection. Monthly Notices of the Royal Astronomical Society. 2020;493(3):4333-4341. doi:10.1093/mnras/staa549","apa":"Renzo, M., Farmer, R. J., Justham, S., de Mink, S. E., Götberg, Y. L. L., & Marchant, P. (2020). Sensitivity of the lower edge of the pair-instability black hole mass gap to the treatment of time-dependent convection. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa549"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"4333-4341","doi":"10.1093/mnras/staa549","date_published":"2020-04-04T00:00:00Z","date_created":"2023-08-03T10:13:20Z","year":"2020","day":"04","publication":"Monthly Notices of the Royal Astronomical Society","quality_controlled":"1","publisher":"Oxford University Press","oa":1},{"quality_controlled":"1","publisher":"EDP Sciences","oa":1,"doi":"10.1051/0004-6361/201936669","date_published":"2020-02-25T00:00:00Z","date_created":"2023-08-03T10:13:43Z","day":"25","publication":"Astronomy & Astrophysics","year":"2020","article_number":"A134","title":"Contribution from stars stripped in binaries to cosmic reionization of hydrogen and helium","author":[{"first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","last_name":"Götberg","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter"},{"full_name":"de Mink, S. E.","last_name":"de Mink","first_name":"S. E."},{"full_name":"McQuinn, M.","last_name":"McQuinn","first_name":"M."},{"last_name":"Zapartas","full_name":"Zapartas, E.","first_name":"E."},{"first_name":"J. H.","last_name":"Groh","full_name":"Groh, J. H."},{"first_name":"C.","last_name":"Norman","full_name":"Norman, C."}],"article_processing_charge":"No","external_id":{"arxiv":["1911.00543"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"Y.L.L. Götberg, S.E. de Mink, M. McQuinn, E. Zapartas, J.H. Groh, C. Norman, Astronomy & Astrophysics 634 (2020).","ieee":"Y. L. L. Götberg, S. E. de Mink, M. McQuinn, E. Zapartas, J. H. Groh, and C. Norman, “Contribution from stars stripped in binaries to cosmic reionization of hydrogen and helium,” Astronomy & Astrophysics, vol. 634. EDP Sciences, 2020.","ama":"Götberg YLL, de Mink SE, McQuinn M, Zapartas E, Groh JH, Norman C. Contribution from stars stripped in binaries to cosmic reionization of hydrogen and helium. Astronomy & Astrophysics. 2020;634. doi:10.1051/0004-6361/201936669","apa":"Götberg, Y. L. L., de Mink, S. E., McQuinn, M., Zapartas, E., Groh, J. H., & Norman, C. (2020). Contribution from stars stripped in binaries to cosmic reionization of hydrogen and helium. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201936669","mla":"Götberg, Ylva Louise Linsdotter, et al. “Contribution from Stars Stripped in Binaries to Cosmic Reionization of Hydrogen and Helium.” Astronomy & Astrophysics, vol. 634, A134, EDP Sciences, 2020, doi:10.1051/0004-6361/201936669.","ista":"Götberg YLL, de Mink SE, McQuinn M, Zapartas E, Groh JH, Norman C. 2020. Contribution from stars stripped in binaries to cosmic reionization of hydrogen and helium. Astronomy & Astrophysics. 634, A134.","chicago":"Götberg, Ylva Louise Linsdotter, S. E. de Mink, M. McQuinn, E. Zapartas, J. H. Groh, and C. Norman. “Contribution from Stars Stripped in Binaries to Cosmic Reionization of Hydrogen and Helium.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/201936669."},"month":"02","intvolume":" 634","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201936669"}],"oa_version":"Published Version","abstract":[{"text":"Massive stars are often found in binary systems, and it has been argued that binary products boost the ionizing radiation of stellar populations. Accurate predictions for binary products are needed to understand and quantify their contribution to cosmic reionization. We investigate the contribution of stars stripped in binaries because (1) they are, arguably, the best-understood products of binary evolution, (2) we recently produced the first radiative transfer calculations for the atmospheres of these stripped stars that predict their ionizing spectra, and (3) they are very promising sources because they boost the ionizing emission of stellar populations at late times. This allows stellar feedback to clear the surroundings such that a higher fraction of their photons can escape and ionize the intergalactic medium. Combining our detailed predictions for the ionizing spectra with a simple cosmic reionization model, we estimate that stripped stars contributed tens of percent of the photons that caused cosmic reionization of hydrogen, depending on the assumed escape fractions. More importantly, stripped stars harden the ionizing emission. We estimate that the spectral index for the ionizing part of the spectrum can increase to −1 compared to ≲ − 2 for single stars. At high redshift, stripped stars and massive single stars combined dominate the He II-ionizing emission, but we expect that active galactic nuclei drive cosmic helium reionization. Further observational consequences we expect are (1) high ionization states for the intergalactic gas surrounding stellar systems, such as C IV and Si IV, and (2) additional heating of the intergalactic medium of up to a few thousand Kelvin. Quantifying these warrants the inclusion of accurate models for stripped stars and other binary products in full cosmological simulations.","lang":"eng"}],"volume":634,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"publication_status":"published","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"article_type":"original","type":"journal_article","_id":"13467","extern":"1","date_updated":"2023-08-09T12:46:05Z"},{"article_number":"A56","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Renzo, M., R. Farmer, S. Justham, Ylva Louise Linsdotter Götberg, S. E. de Mink, E. Zapartas, P. Marchant, and N. Smith. “Predictions for the Hydrogen-Free Ejecta of Pulsational Pair-Instability Supernovae.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/202037710.","ista":"Renzo M, Farmer R, Justham S, Götberg YLL, de Mink SE, Zapartas E, Marchant P, Smith N. 2020. Predictions for the hydrogen-free ejecta of pulsational pair-instability supernovae. Astronomy & Astrophysics. 640, A56.","mla":"Renzo, M., et al. “Predictions for the Hydrogen-Free Ejecta of Pulsational Pair-Instability Supernovae.” Astronomy & Astrophysics, vol. 640, A56, EDP Sciences, 2020, doi:10.1051/0004-6361/202037710.","ieee":"M. Renzo et al., “Predictions for the hydrogen-free ejecta of pulsational pair-instability supernovae,” Astronomy & Astrophysics, vol. 640. EDP Sciences, 2020.","short":"M. Renzo, R. Farmer, S. Justham, Y.L.L. Götberg, S.E. de Mink, E. Zapartas, P. Marchant, N. Smith, Astronomy & Astrophysics 640 (2020).","apa":"Renzo, M., Farmer, R., Justham, S., Götberg, Y. L. L., de Mink, S. E., Zapartas, E., … Smith, N. (2020). Predictions for the hydrogen-free ejecta of pulsational pair-instability supernovae. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202037710","ama":"Renzo M, Farmer R, Justham S, et al. Predictions for the hydrogen-free ejecta of pulsational pair-instability supernovae. Astronomy & Astrophysics. 2020;640. doi:10.1051/0004-6361/202037710"},"title":"Predictions for the hydrogen-free ejecta of pulsational pair-instability supernovae","author":[{"first_name":"M.","last_name":"Renzo","full_name":"Renzo, M."},{"first_name":"R.","last_name":"Farmer","full_name":"Farmer, R."},{"first_name":"S.","full_name":"Justham, S.","last_name":"Justham"},{"full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"first_name":"S. E.","full_name":"de Mink, S. E.","last_name":"de Mink"},{"full_name":"Zapartas, E.","last_name":"Zapartas","first_name":"E."},{"first_name":"P.","full_name":"Marchant, P.","last_name":"Marchant"},{"full_name":"Smith, N.","last_name":"Smith","first_name":"N."}],"external_id":{"arxiv":["2002.05077"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"EDP Sciences","oa":1,"day":"12","publication":"Astronomy & Astrophysics","year":"2020","date_published":"2020-08-12T00:00:00Z","doi":"10.1051/0004-6361/202037710","date_created":"2023-08-03T10:12:58Z","_id":"13463","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-09T12:58:41Z","oa_version":"Published Version","abstract":[{"text":"Present and upcoming time-domain astronomy efforts, in part driven by gravitational-wave follow-up campaigns, will unveil a variety of rare explosive transients in the sky. Here, we focus on pulsational pair-instability evolution, which can result in signatures that are observable with electromagnetic and gravitational waves. We simulated grids of bare helium stars to characterize the resulting black hole (BH) masses together with the ejecta composition, velocity, and thermal state. We find that the stars do not react “elastically” to the thermonuclear ignition in the core: there is not a one-to-one correspondence between pair-instability driven ignition and mass ejections, which causes ambiguity as to what is an observable pulse. In agreement with previous studies, we find that for initial helium core masses of 37.5 M⊙ ≲ MHe, init ≲ 41 M⊙, corresponding to carbon-oxygen core masses 27.5 M⊙ ≲ MCO ≲ 30.1 M⊙, the explosions are not strong enough to affect the surface. With increasing initial helium core mass, they become progressively stronger causing first large radial expansion (41 M⊙ ≲ MHe, init ≲ 42 M⊙, corresponding to 30.1 M⊙ ≲ MCO ≲ 30.8 M⊙) and, finally, also mass ejection episodes (for MHe, init ≳ 42 M⊙, or MCO ≳ 30.8 M⊙). The lowest mass helium core to be fully disrupted in a pair-instability supernova is MHe, init ≃ 80 M⊙, corresponding to MCO ≃ 55 M⊙. Models with MHe, init ≳ 200 M⊙ (MCO ≳ 114 M⊙) reach the photodisintegration regime, resulting in BHs with masses of MBH ≳ 125 M⊙. Although this is currently considered unlikely, if BHs from these models form via (weak) explosions, the previously-ejected material might be hit by the blast wave and convert kinetic energy into observable electromagnetic radiation. We characterize the hydrogen-free circumstellar material from the pulsational pair-instability of helium cores by simply assuming that the ejecta maintain a constant velocity after ejection. We find that our models produce helium-rich ejecta with mass of 10−3 M⊙ ≲ MCSM ≲ 40 M⊙, the larger values corresponding to the more massive progenitor stars. These ejecta are typically launched at a few thousand km s−1 and reach distances of ∼1012 − 1015 cm before the core-collapse of the star. The delays between mass ejection events and the final collapse span a wide and mass-dependent range (from subhour to 104 years), and the shells ejected can also collide with each other, powering supernova impostor events before the final core-collapse. The range of properties we find suggests a possible connection with (some) type Ibn supernovae.","lang":"eng"}],"month":"08","intvolume":" 640","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/202037710","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"publication_status":"published","volume":640},{"date_updated":"2023-08-09T13:01:45Z","extern":"1","type":"journal_article","article_type":"original","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"_id":"13461","issue":"1","volume":901,"publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3847/1538-4357/abaefa"}],"month":"09","intvolume":" 901","abstract":[{"lang":"eng","text":"High-resolution numerical simulations including feedback and aimed at calculating the escape fraction (fesc) of hydrogen-ionizing photons often assume stellar radiation based on single-stellar population synthesis models. However, strong evidence suggests the binary fraction of massive stars is ≳70%. Moreover, simulations so far have yielded values of fesc falling only on the lower end of the ∼10%–20% range, the amount presumed necessary to reionize the universe. Analyzing a high-resolution (4 pc) cosmological radiation-hydrodynamic simulation, we study how fesc changes when we include two different products of binary stellar evolution—stars stripped of their hydrogen envelopes and massive blue stragglers. Both produce significant amounts of ionizing photons 10–200 Myr after each starburst. We find the relative importance of these photons to be amplified with respect to escaped ionizing photons, because peaks in star formation rates (SFRs) and fesc are often out of phase by this 10–200 Myr. Additionally, low-mass, bursty galaxies emit Lyman continuum radiation primarily from binary products when SFRs are low. Observations of these galaxies by the James Webb Space Telescope could provide crucial information on the evolution of binary stars as a function of redshift. Overall, including stripped stars and massive blue stragglers increases our photon-weighted mean escape fraction ($\\langle {f}_{\\mathrm{esc}}\\rangle $) by ∼13% and ∼10%, respectively, resulting in $\\langle {f}_{\\mathrm{esc}}\\rangle =17 \\% $. Our results emphasize that using updated stellar population synthesis models with binary stellar evolution provides a more sound physical basis for stellar reionization."}],"oa_version":"Published Version","author":[{"first_name":"Amy","last_name":"Secunda","full_name":"Secunda, Amy"},{"last_name":"Cen","full_name":"Cen, Renyue","first_name":"Renyue"},{"first_name":"Taysun","last_name":"Kimm","full_name":"Kimm, Taysun"},{"orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"first_name":"Selma E.","full_name":"de Mink, Selma E.","last_name":"de Mink"}],"article_processing_charge":"No","external_id":{"arxiv":["2007.15012"]},"title":"Delayed photons from binary evolution help reionize the universe","citation":{"ieee":"A. Secunda, R. Cen, T. Kimm, Y. L. L. Götberg, and S. E. de Mink, “Delayed photons from binary evolution help reionize the universe,” The Astrophysical Journal, vol. 901, no. 1. American Astronomical Society, 2020.","short":"A. Secunda, R. Cen, T. Kimm, Y.L.L. Götberg, S.E. de Mink, The Astrophysical Journal 901 (2020).","apa":"Secunda, A., Cen, R., Kimm, T., Götberg, Y. L. L., & de Mink, S. E. (2020). Delayed photons from binary evolution help reionize the universe. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/abaefa","ama":"Secunda A, Cen R, Kimm T, Götberg YLL, de Mink SE. Delayed photons from binary evolution help reionize the universe. The Astrophysical Journal. 2020;901(1). doi:10.3847/1538-4357/abaefa","mla":"Secunda, Amy, et al. “Delayed Photons from Binary Evolution Help Reionize the Universe.” The Astrophysical Journal, vol. 901, no. 1, 72, American Astronomical Society, 2020, doi:10.3847/1538-4357/abaefa.","ista":"Secunda A, Cen R, Kimm T, Götberg YLL, de Mink SE. 2020. Delayed photons from binary evolution help reionize the universe. The Astrophysical Journal. 901(1), 72.","chicago":"Secunda, Amy, Renyue Cen, Taysun Kimm, Ylva Louise Linsdotter Götberg, and Selma E. de Mink. “Delayed Photons from Binary Evolution Help Reionize the Universe.” The Astrophysical Journal. American Astronomical Society, 2020. https://doi.org/10.3847/1538-4357/abaefa."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"72","date_published":"2020-09-23T00:00:00Z","doi":"10.3847/1538-4357/abaefa","date_created":"2023-08-03T10:12:16Z","year":"2020","day":"23","publication":"The Astrophysical Journal","publisher":"American Astronomical Society","quality_controlled":"1","oa":1},{"article_number":"A6","citation":{"ista":"Laplace E, Götberg YLL, de Mink SE, Justham S, Farmer R. 2020. The expansion of stripped-envelope stars: Consequences for supernovae and gravitational-wave progenitors. Astronomy & Astrophysics. 637, A6.","chicago":"Laplace, E., Ylva Louise Linsdotter Götberg, S. E. de Mink, S. Justham, and R. Farmer. “The Expansion of Stripped-Envelope Stars: Consequences for Supernovae and Gravitational-Wave Progenitors.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/201937300.","ieee":"E. Laplace, Y. L. L. Götberg, S. E. de Mink, S. Justham, and R. Farmer, “The expansion of stripped-envelope stars: Consequences for supernovae and gravitational-wave progenitors,” Astronomy & Astrophysics, vol. 637. EDP Sciences, 2020.","short":"E. Laplace, Y.L.L. Götberg, S.E. de Mink, S. Justham, R. Farmer, Astronomy & Astrophysics 637 (2020).","apa":"Laplace, E., Götberg, Y. L. L., de Mink, S. E., Justham, S., & Farmer, R. (2020). The expansion of stripped-envelope stars: Consequences for supernovae and gravitational-wave progenitors. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201937300","ama":"Laplace E, Götberg YLL, de Mink SE, Justham S, Farmer R. The expansion of stripped-envelope stars: Consequences for supernovae and gravitational-wave progenitors. Astronomy & Astrophysics. 2020;637. doi:10.1051/0004-6361/201937300","mla":"Laplace, E., et al. “The Expansion of Stripped-Envelope Stars: Consequences for Supernovae and Gravitational-Wave Progenitors.” Astronomy & Astrophysics, vol. 637, A6, EDP Sciences, 2020, doi:10.1051/0004-6361/201937300."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Laplace, E.","last_name":"Laplace","first_name":"E."},{"last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"full_name":"de Mink, S. E.","last_name":"de Mink","first_name":"S. E."},{"first_name":"S.","last_name":"Justham","full_name":"Justham, S."},{"full_name":"Farmer, R.","last_name":"Farmer","first_name":"R."}],"external_id":{"arxiv":["2003.01120"]},"article_processing_charge":"No","title":"The expansion of stripped-envelope stars: Consequences for supernovae and gravitational-wave progenitors","quality_controlled":"1","publisher":"EDP Sciences","oa":1,"year":"2020","day":"01","publication":"Astronomy & Astrophysics","date_published":"2020-05-01T00:00:00Z","doi":"10.1051/0004-6361/201937300","date_created":"2023-08-03T10:13:10Z","_id":"13464","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"date_updated":"2023-08-09T12:56:32Z","extern":"1","abstract":[{"text":"Massive binaries that merge as compact objects are the progenitors of gravitational-wave sources. Most of these binaries experience one or more phases of mass transfer, during which one of the stars loses all or part of its outer envelope and becomes a stripped-envelope star. The evolution of the size of these stripped stars is crucial in determining whether they experience further interactions and understanding their ultimate fate. We present new calculations of stripped-envelope stars based on binary evolution models computed with MESA. We use these to investigate their radius evolution as a function of mass and metallicity. We further discuss their pre-supernova observable characteristics and potential consequences of their evolution on the properties of supernovae from stripped stars. At high metallicity, we find that practically all of the hydrogen-rich envelope is removed, which is in agreement with earlier findings. Only progenitors with initial masses below 10 M⊙ expand to large radii (up to 100 R⊙), while more massive progenitors remain compact. At low metallicity, a substantial amount of hydrogen remains and the progenitors can, in principle, expand to giant sizes (> 400 R⊙) for all masses we consider. This implies that they can fill their Roche lobe anew. We show that the prescriptions commonly used in population synthesis models underestimate the stellar radii by up to two orders of magnitude. We expect that this has consequences for the predictions for gravitational-wave sources from double neutron star mergers, particularly with regard to their metallicity dependence.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201937300"}],"month":"05","intvolume":" 637","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":637},{"acknowledgement":"This research was carried out with the support of the Russian Foundation for Basic Research(grant no. 19-01-00169)","quality_controlled":"1","publisher":"IOP Publishing","oa":1,"day":"01","publication":"Russian Mathematical Surveys","isi":1,"year":"2020","doi":"10.1070/RM9943","date_published":"2020-12-01T00:00:00Z","date_created":"2021-04-04T22:01:22Z","page":"1156-1158","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” Russian Mathematical Surveys, vol. 75, no. 6, IOP Publishing, 2020, pp. 1156–58, doi:10.1070/RM9943.","apa":"Avvakumov, S., Wagner, U., Mabillard, I., & Skopenkov, A. B. (2020). Eliminating higher-multiplicity intersections, III. Codimension 2. Russian Mathematical Surveys. IOP Publishing. https://doi.org/10.1070/RM9943","ama":"Avvakumov S, Wagner U, Mabillard I, Skopenkov AB. Eliminating higher-multiplicity intersections, III. Codimension 2. Russian Mathematical Surveys. 2020;75(6):1156-1158. doi:10.1070/RM9943","short":"S. Avvakumov, U. Wagner, I. Mabillard, A.B. Skopenkov, Russian Mathematical Surveys 75 (2020) 1156–1158.","ieee":"S. Avvakumov, U. Wagner, I. Mabillard, and A. B. Skopenkov, “Eliminating higher-multiplicity intersections, III. Codimension 2,” Russian Mathematical Surveys, vol. 75, no. 6. IOP Publishing, pp. 1156–1158, 2020.","chicago":"Avvakumov, Sergey, Uli Wagner, Isaac Mabillard, and A. B. Skopenkov. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” Russian Mathematical Surveys. IOP Publishing, 2020. https://doi.org/10.1070/RM9943.","ista":"Avvakumov S, Wagner U, Mabillard I, Skopenkov AB. 2020. Eliminating higher-multiplicity intersections, III. Codimension 2. Russian Mathematical Surveys. 75(6), 1156–1158."},"title":"Eliminating higher-multiplicity intersections, III. Codimension 2","author":[{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"},{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"first_name":"A. B.","last_name":"Skopenkov","full_name":"Skopenkov, A. B."}],"external_id":{"isi":["000625983100001"],"arxiv":["1511.03501"]},"article_processing_charge":"No","oa_version":"Preprint","month":"12","intvolume":" 75","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0036-0279"]},"publication_status":"published","issue":"6","related_material":{"record":[{"relation":"earlier_version","id":"8183","status":"public"},{"relation":"later_version","status":"public","id":"10220"}]},"volume":75,"_id":"9308","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-14T11:43:54Z","department":[{"_id":"UlWa"}]},{"ddc":["500"],"date_updated":"2023-08-17T13:49:40Z","department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:28Z","_id":"6358","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_size":905538,"date_updated":"2020-07-14T12:47:28Z","creator":"dernst","file_name":"2019_JourStatistPhysics_Carlen.pdf","date_created":"2019-12-23T12:03:09Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7b04befbdc0d4982c0ee945d25d19872","file_id":"7209"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15729613"],"issn":["00224715"]},"publication_status":"published","issue":"2","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s10955-020-02671-4"}]},"volume":178,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study dynamical optimal transport metrics between density matricesassociated to symmetric Dirichlet forms on finite-dimensional C∗-algebras. Our settingcovers arbitrary skew-derivations and it provides a unified framework that simultaneously generalizes recently constructed transport metrics for Markov chains, Lindblad equations, and the Fermi Ornstein–Uhlenbeck semigroup. 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."}],"month":"01","intvolume":" 178","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Carlen, Eric A., and Jan Maas. “Non-Commutative Calculus, Optimal Transport and Functional Inequalities in Dissipative Quantum Systems.” Journal of Statistical Physics, vol. 178, no. 2, Springer Nature, 2020, pp. 319–78, doi:10.1007/s10955-019-02434-w.","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. Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems. Journal of Statistical Physics. 2020;178(2):319-378. doi:10.1007/s10955-019-02434-w","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.","short":"E.A. Carlen, J. Maas, Journal of Statistical Physics 178 (2020) 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.","ista":"Carlen EA, Maas J. 2020. Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems. Journal of Statistical Physics. 178(2), 319–378."},"title":"Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems","author":[{"first_name":"Eric A.","last_name":"Carlen","full_name":"Carlen, Eric A."},{"last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"external_id":{"isi":["000498933300001"],"arxiv":["1811.04572"]},"article_processing_charge":"Yes (via OA deal)","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Taming Complexity in Partial Di erential Systems","grant_number":" F06504"}],"day":"01","publication":"Journal of Statistical Physics","isi":1,"has_accepted_license":"1","year":"2020","date_published":"2020-01-01T00:00:00Z","doi":"10.1007/s10955-019-02434-w","date_created":"2019-04-30T07:34:18Z","page":"319-378","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"isi":1,"year":"2020","day":"21","publication":"Geometric Aspects of Functional Analysis","page":"1-27","date_published":"2020-06-21T00:00:00Z","doi":"10.1007/978-3-030-36020-7_1","date_created":"2018-12-11T11:44:29Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"mla":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” Geometric Aspects of Functional Analysis, edited by Bo’az Klartag and Emanuel Milman, vol. 2256, Springer Nature, 2020, pp. 1–27, doi:10.1007/978-3-030-36020-7_1.","ama":"Akopyan A, Karasev R. Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Klartag B, Milman E, eds. Geometric Aspects of Functional Analysis. Vol 2256. LNM. Springer Nature; 2020:1-27. doi:10.1007/978-3-030-36020-7_1","apa":"Akopyan, A., & Karasev, R. (2020). Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In B. Klartag & E. Milman (Eds.), Geometric Aspects of Functional Analysis (Vol. 2256, pp. 1–27). Springer Nature. https://doi.org/10.1007/978-3-030-36020-7_1","short":"A. Akopyan, R. Karasev, in:, B. Klartag, E. Milman (Eds.), Geometric Aspects of Functional Analysis, Springer Nature, 2020, pp. 1–27.","ieee":"A. Akopyan and R. Karasev, “Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures,” in Geometric Aspects of Functional Analysis, vol. 2256, B. Klartag and E. Milman, Eds. Springer Nature, 2020, pp. 1–27.","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. LNM. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-36020-7_1.","ista":"Akopyan A, Karasev R. 2020.Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Geometric Aspects of Functional Analysis. vol. 2256, 1–27."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"last_name":"Karasev","full_name":"Karasev, Roman","first_name":"Roman"}],"external_id":{"isi":["000557689300003"],"arxiv":["1808.07350"]},"article_processing_charge":"No","title":"Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures","editor":[{"first_name":"Bo'az","full_name":"Klartag, Bo'az","last_name":"Klartag"},{"first_name":"Emanuel","last_name":"Milman","full_name":"Milman, Emanuel"}],"project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_identifier":{"eisbn":["9783030360207"],"isbn":["9783030360191"],"eissn":["16179692"],"issn":["00758434"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":2256,"ec_funded":1,"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07350"}],"month":"06","intvolume":" 2256","date_updated":"2023-08-17T13:48:31Z","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"series_title":"LNM","_id":"74","type":"book_chapter","status":"public"},{"publication":"Annals of Mathematics","day":"01","year":"2020","isi":1,"date_created":"2018-12-11T11:45:02Z","doi":"10.4007/annals.2020.191.3.4","date_published":"2020-05-01T00:00:00Z","page":"893-948","oa":1,"publisher":"Princeton University","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Browning, Timothy D, and Will Sawin. “A Geometric Version of the Circle Method.” Annals of Mathematics. Princeton University, 2020. https://doi.org/10.4007/annals.2020.191.3.4.","ista":"Browning TD, Sawin W. 2020. A geometric version of the circle method. Annals of Mathematics. 191(3), 893–948.","mla":"Browning, Timothy D., and Will Sawin. “A Geometric Version of the Circle Method.” Annals of Mathematics, vol. 191, no. 3, Princeton University, 2020, pp. 893–948, doi:10.4007/annals.2020.191.3.4.","short":"T.D. Browning, W. Sawin, Annals of Mathematics 191 (2020) 893–948.","ieee":"T. D. Browning and W. Sawin, “A geometric version of the circle method,” Annals of Mathematics, vol. 191, no. 3. Princeton University, pp. 893–948, 2020.","apa":"Browning, T. D., & Sawin, W. (2020). A geometric version of the circle method. Annals of Mathematics. Princeton University. https://doi.org/10.4007/annals.2020.191.3.4","ama":"Browning TD, Sawin W. A geometric version of the circle method. Annals of Mathematics. 2020;191(3):893-948. doi:10.4007/annals.2020.191.3.4"},"title":"A geometric version of the circle method","article_processing_charge":"No","external_id":{"arxiv":["1711.10451"],"isi":["000526986300004"]},"publist_id":"7744","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177"},{"full_name":"Sawin, Will","last_name":"Sawin","first_name":"Will"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":191,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree."}],"intvolume":" 191","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.10451"}],"date_updated":"2023-08-17T07:12:37Z","department":[{"_id":"TiBr"}],"_id":"177","status":"public","type":"journal_article","article_type":"original"},{"publication":"Communications in Mathematical Physics","day":"01","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2019-07-18T13:30:04Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1007/s00220-019-03505-5","page":"2097–2150","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.","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.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Communications in Mathematical Physics 374 (2020) 2097–2150.","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. Communications in Mathematical Physics. 2020;374:2097–2150. doi:10.1007/s00220-019-03505-5","apa":"Benedikter, N. P., Nam, P. T., 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. Springer Nature. https://doi.org/10.1007/s00220-019-03505-5"},"title":"Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime","article_processing_charge":"No","external_id":{"arxiv":["1809.01902"],"isi":["000527910700019"]},"author":[{"id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P","last_name":"Benedikter","orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P"},{"first_name":"Phan Thành","full_name":"Nam, Phan Thành","last_name":"Nam"},{"last_name":"Porta","full_name":"Porta, Marcello","first_name":"Marcello"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"project":[{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6668","checksum":"f9dd6dd615a698f1d3636c4a092fed23","file_size":853289,"date_updated":"2020-07-14T12:47:35Z","creator":"dernst","file_name":"2019_CommMathPhysics_Benedikter.pdf","date_created":"2019-07-24T07:19:10Z"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"ec_funded":1,"volume":374,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. 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"}],"intvolume":" 374","month":"03","scopus_import":"1","ddc":["530"],"date_updated":"2023-08-17T13:51:50Z","file_date_updated":"2020-07-14T12:47:35Z","department":[{"_id":"RoSe"}],"_id":"6649","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"},{"date_published":"2020-04-01T00:00:00Z","doi":"10.1002/hipo.23144","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,"title":"Partial coherence and frustration in self-organizing spherical grids","author":[{"orcid":"0000-0001-9439-3148","full_name":"Stella, Federico","last_name":"Stella","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Urdapilleta, Eugenio","last_name":"Urdapilleta","first_name":"Eugenio"},{"first_name":"Yifan","full_name":"Luo, Yifan","last_name":"Luo"},{"first_name":"Alessandro","full_name":"Treves, Alessandro","last_name":"Treves"}],"external_id":{"isi":["000477299600001"],"pmid":["31339190"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"F. Stella, E. Urdapilleta, Y. Luo, A. Treves, Hippocampus 30 (2020) 302–313.","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","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","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.","ista":"Stella F, Urdapilleta E, Luo Y, Treves A. 2020. 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."},"issue":"4","volume":30,"file":[{"file_id":"6800","checksum":"7b54d22bfbfc0d1188a9ea24d985bfb2","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-08-12T07:53:33Z","file_name":"2019_Hippocampus_Stella.pdf","date_updated":"2020-07-14T12:47:40Z","file_size":2370658,"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"}],"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"},{"project":[{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425"}],"title":"Dynamic resource allocation games","external_id":{"isi":["000512219400004"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"G. Avni, T.A. Henzinger, O. Kupferman, Theoretical Computer Science 807 (2020) 42–55.","ieee":"G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” Theoretical Computer Science, vol. 807. Elsevier, pp. 42–55, 2020.","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","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","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."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","date_created":"2019-08-04T21:59:20Z","doi":"10.1016/j.tcs.2019.06.031","date_published":"2020-02-06T00:00:00Z","page":"42-55","publication":"Theoretical Computer Science","day":"06","year":"2020","isi":1,"has_accepted_license":"1","status":"public","type":"journal_article","article_type":"original","_id":"6761","file_date_updated":"2020-10-09T06:31:22Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-08-17T13:52:49Z","intvolume":" 807","month":"02","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"volume":807,"related_material":{"record":[{"relation":"earlier_version","id":"1341","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-10-09T06:31:22Z","file_size":1413001,"creator":"dernst","date_created":"2020-10-09T06:31:22Z","file_name":"2020_TheoreticalCS_Avni.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e86635417f45eb2cd75778f91382f737","file_id":"8639","success":1}],"publication_status":"published","publication_identifier":{"issn":["03043975"]}},{"oa_version":"Submitted Version","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."}],"intvolume":" 84","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2019-10-01T13:14:10Z","file_name":"ExtragradientMethodPaper.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:34Z","file_size":359654,"file_id":"6927","checksum":"bb1a1eb3ebb2df380863d0db594673ba","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1572-9265"],"issn":["1017-1398"]},"ec_funded":1,"volume":84,"_id":"6593","status":"public","article_type":"original","type":"journal_article","ddc":["000"],"date_updated":"2023-08-17T13:51:18Z","department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:47:34Z","acknowledgement":"The research of this author is supported by the ERC grant at the IST.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Numerical Algorithms","day":"01","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2019-06-27T20:09:33Z","doi":"10.1007/s11075-019-00758-y","date_published":"2020-05-01T00:00:00Z","page":"365-388","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","short":"Y. Shehu, X.-H. Li, Q.-L. Dong, Numerical Algorithms 84 (2020) 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.","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."},"title":"An efficient projection-type method for monotone variational inequalities in Hilbert spaces","external_id":{"isi":["000528979000015"]},"article_processing_charge":"No","author":[{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini","orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini","last_name":"Shehu"},{"first_name":"Xiao-Huan","full_name":"Li, Xiao-Huan","last_name":"Li"},{"first_name":"Qiao-Li","last_name":"Dong","full_name":"Dong, Qiao-Li"}]},{"department":[{"_id":"JoDa"}],"date_updated":"2023-08-17T13:59:57Z","status":"public","article_type":"original","type":"journal_article","_id":"6808","issue":"3","volume":174,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1046-2023"]},"intvolume":" 174","month":"03","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100895/","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"title":"Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens","external_id":{"isi":["000525860400005"],"pmid":["31344404"]},"article_processing_charge":"No","author":[{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","full_name":"Jahr, Wiebke"},{"first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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","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."},"project":[{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"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,"oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"date_published":"2020-04-01T00:00:00Z","doi":"10.1007/s10208-019-09419-x","date_created":"2019-06-16T21:59:14Z","page":"311-330","day":"01","publication":"Foundations of Computational Mathematics","isi":1,"year":"2020","publisher":"Springer Nature","quality_controlled":"1","oa":1,"title":"Are two given maps homotopic? An algorithmic viewpoint","author":[{"last_name":"Filakovský","full_name":"Filakovský, Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"},{"first_name":"Lukas","last_name":"Vokřínek","full_name":"Vokřínek, Lukas"}],"article_processing_charge":"No","external_id":{"isi":["000522437400004"],"arxiv":["1312.2337"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"M. Filakovský, L. Vokřínek, Foundations of Computational Mathematics 20 (2020) 311–330.","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.","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","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.","ista":"Filakovský M, Vokřínek L. 2020. Are two given maps homotopic? An algorithmic viewpoint. Foundations of Computational Mathematics. 20, 311–330."},"project":[{"grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425"}],"volume":20,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["16153375"],"eissn":["16153383"]},"publication_status":"published","month":"04","intvolume":" 20","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.2337"}],"oa_version":"Preprint","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."}],"department":[{"_id":"UlWa"}],"date_updated":"2023-08-17T13:50:44Z","status":"public","article_type":"original","type":"journal_article","_id":"6563"},{"department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:47:46Z","ddc":["004"],"date_updated":"2023-08-17T14:01:16Z","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":"6952","volume":128,"language":[{"iso":"eng"}],"file":[{"file_name":"2019_CompVision_Henderson.pdf","date_created":"2019-10-25T10:28:29Z","creator":"dernst","file_size":2243134,"date_updated":"2020-07-14T12:47:46Z","file_id":"6973","checksum":"a0f05dd4f5f64e4f713d8d9d4b5b1e3f","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]},"intvolume":" 128","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"title":"Learning single-image 3D reconstruction by generative modelling of shape, pose and shading","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1901.06447"],"isi":["000491042100002"]},"author":[{"first_name":"Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445"},{"full_name":"Ferrari, Vittorio","last_name":"Ferrari","first_name":"Vittorio"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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.","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."},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_created":"2019-10-17T13:38:20Z","date_published":"2020-04-01T00:00:00Z","doi":"10.1007/s11263-019-01219-8","page":"835-854","publication":"International Journal of Computer Vision","day":"01","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria)."},{"status":"public","type":"journal_article","article_type":"original","_id":"7148","department":[{"_id":"RySh"}],"ddc":["571","599"],"date_updated":"2023-08-17T14:06:50Z","month":"04","intvolume":" 528","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"text":"In the cerebellum, GluD2 is exclusively expressed in Purkinje cells, where it regulates synapse formation and regeneration, synaptic plasticity, and motor learning. Delayed cognitive development in humans with GluD2 gene mutations suggests extracerebellar functions of GluD2. However, extracerebellar expression of GluD2 and its relationship with that of GluD1 are poorly understood. GluD2 mRNA and protein were widely detected, with relatively high levels observed in the olfactory glomerular layer, medial prefrontal cortex, cingulate cortex, retrosplenial granular cortex, olfactory tubercle, subiculum, striatum, lateral septum, anterodorsal thalamic nucleus, and arcuate hypothalamic nucleus. These regions were also enriched for GluD1, and many individual neurons coexpressed the two GluDs. In the retrosplenial granular cortex, GluD1 and GluD2 were selectively expressed at PSD‐95‐expressing glutamatergic synapses, and their coexpression on the same synapses was shown by SDS‐digested freeze‐fracture replica labeling. Biochemically, GluD1 and GluD2 formed coimmunoprecipitable complex formation in HEK293T cells and in the cerebral cortex and hippocampus. We further estimated the relative protein amount by quantitative immunoblotting using GluA2/GluD2 and GluA2/GluD1 chimeric proteins as standards for titration of GluD1 and GluD2 antibodies. Intriguingly, the relative amount of GluD2 was almost comparable to that of GluD1 in the postsynaptic density fraction prepared from the cerebral cortex and hippocampus. In contrast, GluD2 was overwhelmingly predominant in the cerebellum. Thus, we have determined the relative extracerebellar expression of GluD1 and GluD2 at regional, neuronal, and synaptic levels. These data provide a molecular–anatomical basis for possible competitive and cooperative interactions of GluD family members at synapses in various brain regions.","lang":"eng"}],"issue":"6","volume":528,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9967"],"eissn":["1096-9861"]},"publication_status":"published","title":"Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain","author":[{"first_name":"Chihiro","last_name":"Nakamoto","full_name":"Nakamoto, Chihiro"},{"last_name":"Konno","full_name":"Konno, Kohtarou","first_name":"Kohtarou"},{"full_name":"Miyazaki, Taisuke","last_name":"Miyazaki","first_name":"Taisuke"},{"last_name":"Nakatsukasa","full_name":"Nakatsukasa, Ena","first_name":"Ena"},{"last_name":"Natsume","full_name":"Natsume, Rie","first_name":"Rie"},{"first_name":"Manabu","last_name":"Abe","full_name":"Abe, Manabu"},{"first_name":"Meiko","full_name":"Kawamura, Meiko","last_name":"Kawamura"},{"last_name":"Fukazawa","full_name":"Fukazawa, Yugo","first_name":"Yugo"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"full_name":"Yamasaki, Miwako","last_name":"Yamasaki","first_name":"Miwako"},{"full_name":"Sakimura, Kenji","last_name":"Sakimura","first_name":"Kenji"},{"last_name":"Watanabe","full_name":"Watanabe, Masahiko","first_name":"Masahiko"}],"external_id":{"isi":["000496410200001"],"pmid":["31625608"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Nakamoto C, Konno K, Miyazaki T, Nakatsukasa E, Natsume R, Abe M, Kawamura M, Fukazawa Y, Shigemoto R, Yamasaki M, Sakimura K, Watanabe M. 2020. Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain. Journal of Comparative Neurology. 528(6), 1003–1027.","chicago":"Nakamoto, Chihiro, Kohtarou Konno, Taisuke Miyazaki, Ena Nakatsukasa, Rie Natsume, Manabu Abe, Meiko Kawamura, et al. “Expression Mapping, Quantification, and Complex Formation of GluD1 and GluD2 Glutamate Receptors in Adult Mouse Brain.” Journal of Comparative Neurology. Wiley, 2020. https://doi.org/10.1002/cne.24792.","short":"C. Nakamoto, K. Konno, T. Miyazaki, E. Nakatsukasa, R. Natsume, M. Abe, M. Kawamura, Y. Fukazawa, R. Shigemoto, M. Yamasaki, K. Sakimura, M. Watanabe, Journal of Comparative Neurology 528 (2020) 1003–1027.","ieee":"C. Nakamoto et al., “Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain,” Journal of Comparative Neurology, vol. 528, no. 6. Wiley, pp. 1003–1027, 2020.","ama":"Nakamoto C, Konno K, Miyazaki T, et al. Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain. Journal of Comparative Neurology. 2020;528(6):1003-1027. doi:10.1002/cne.24792","apa":"Nakamoto, C., Konno, K., Miyazaki, T., Nakatsukasa, E., Natsume, R., Abe, M., … Watanabe, M. (2020). Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain. Journal of Comparative Neurology. Wiley. https://doi.org/10.1002/cne.24792","mla":"Nakamoto, Chihiro, et al. “Expression Mapping, Quantification, and Complex Formation of GluD1 and GluD2 Glutamate Receptors in Adult Mouse Brain.” Journal of Comparative Neurology, vol. 528, no. 6, Wiley, 2020, pp. 1003–27, doi:10.1002/cne.24792."},"quality_controlled":"1","publisher":"Wiley","acknowledgement":"This study was supported by Grants-in-Aid for Scientific Research to K.K. (18K06813), Y.M. (17K08503, 17H0631319), and K.S. (16H04650) and a grant for Scientific Research on Innovative Areas to K.S (16H06276) from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT). We thank K. Akashi, I. Watanabe-Iida, Y. Suzuki, and H. Azechi for technical assistance and advice, and H. Uchida for valuable discussions. We thank E. Kushiya,I. Yabe, C. Ohori, Y. Mochizuki, Y. Ishikawa, and N. Ishimoto for technical assistance in generating GluD1-KO mice.","date_published":"2020-04-01T00:00:00Z","doi":"10.1002/cne.24792","date_created":"2019-12-04T16:09:29Z","page":"1003-1027","day":"01","publication":"Journal of Comparative Neurology","isi":1,"has_accepted_license":"1","year":"2020"},{"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035206/"}],"scopus_import":"1","intvolume":" 57","month":"02","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","issue":"2","volume":57,"publication_status":"published","publication_identifier":{"eissn":["1559-1182"],"issn":["0893-7648"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"7033","department":[{"_id":"SaSi"}],"date_updated":"2023-08-17T14:05:48Z","oa":1,"publisher":"Springer Nature","quality_controlled":"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).","page":"1070–1084","date_created":"2019-11-18T14:18:39Z","doi":"10.1007/s12035-019-01783-7","date_published":"2020-02-01T00:00:00Z","year":"2020","isi":1,"publication":"Molecular Neurobiology","day":"01","article_processing_charge":"No","external_id":{"pmid":["31673950"],"isi":["000493754200001"]},"author":[{"first_name":"RJ","last_name":"Donahue","full_name":"Donahue, RJ"},{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","last_name":"Maes"},{"last_name":"Grosser","full_name":"Grosser, JA","first_name":"JA"},{"first_name":"RW","full_name":"Nickells, RW","last_name":"Nickells"}],"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.","short":"R. Donahue, M.E. Maes, J. Grosser, R. Nickells, Molecular Neurobiology 57 (2020) 1070–1084.","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.","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","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","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"},{"oa":1,"publisher":"Wiley","quality_controlled":"1","year":"2020","has_accepted_license":"1","isi":1,"publication":"New Phytologist","day":"01","page":"1049-1052","date_created":"2019-11-12T11:41:32Z","doi":"10.1111/nph.16203","date_published":"2020-02-01T00:00:00Z","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Zhang Y, Friml J. 2020. Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. 225(3), 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.","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.","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000489638800001"],"pmid":["31603260"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Zhang","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"title":"Auxin guides roots to avoid obstacles during gravitropic growth","pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 225","month":"02","publication_status":"published","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"cd42ffdb381fd52812b9583d4d407139","file_id":"8772","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_NewPhytologist_Zhang.pdf","date_created":"2020-11-18T16:42:48Z","creator":"dernst","file_size":717345,"date_updated":"2020-11-18T16:42:48Z"}],"ec_funded":1,"issue":"3","volume":225,"_id":"6997","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","date_updated":"2023-08-17T14:01:49Z","ddc":["580"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-11-18T16:42:48Z"},{"doi":"10.1111/cge.13674","date_published":"2020-01-01T00:00:00Z","date_created":"2019-12-04T16:10:59Z","page":"3-11","day":"01","publication":"Clinical Genetics","isi":1,"year":"2020","publisher":"Wiley","quality_controlled":"1","acknowledgement":" Dipartimento DiSS, Università degli Studi di Milano, Grant/Award Number: Linea 2; Fondazione Cariplo, Grant/Award Number: 2015-0783; German Federal Ministry of Education and Research (BMBF), Grant/Award Number: CHROMATIN-Net; Medical Faculty of the University of Lübeck, Grant/Award Number: J09-2017; Nickel & Co S.p.A.; Università degli Studi di Milano, Grant/Award Numbers: Molecular & Translational Medicine PhD Scholarship, Translational Medicine PhD Scholarship","title":"Chromatinopathies: A focus on Cornelia de Lange syndrome","author":[{"first_name":"Laura","full_name":"Avagliano, Laura","last_name":"Avagliano"},{"full_name":"Parenti, Ilaria","last_name":"Parenti","first_name":"Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425"},{"full_name":"Grazioli, Paolo","last_name":"Grazioli","first_name":"Paolo"},{"first_name":"Elisabetta","full_name":"Di Fede, Elisabetta","last_name":"Di Fede"},{"first_name":"Chiara","full_name":"Parodi, Chiara","last_name":"Parodi"},{"first_name":"Milena","full_name":"Mariani, Milena","last_name":"Mariani"},{"first_name":"Frank J.","full_name":"Kaiser, Frank J.","last_name":"Kaiser"},{"first_name":"Angelo","full_name":"Selicorni, Angelo","last_name":"Selicorni"},{"first_name":"Cristina","last_name":"Gervasini","full_name":"Gervasini, Cristina"},{"first_name":"Valentina","full_name":"Massa, Valentina","last_name":"Massa"}],"article_processing_charge":"No","external_id":{"isi":["000562561800001"],"pmid":["31721174"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Avagliano, Laura, Ilaria Parenti, Paolo Grazioli, Elisabetta Di Fede, Chiara Parodi, Milena Mariani, Frank J. Kaiser, Angelo Selicorni, Cristina Gervasini, and Valentina Massa. “Chromatinopathies: A Focus on Cornelia de Lange Syndrome.” Clinical Genetics. Wiley, 2020. https://doi.org/10.1111/cge.13674.","ista":"Avagliano L, Parenti I, Grazioli P, Di Fede E, Parodi C, Mariani M, Kaiser FJ, Selicorni A, Gervasini C, Massa V. 2020. Chromatinopathies: A focus on Cornelia de Lange syndrome. Clinical Genetics. 97(1), 3–11.","mla":"Avagliano, Laura, et al. “Chromatinopathies: A Focus on Cornelia de Lange Syndrome.” Clinical Genetics, vol. 97, no. 1, Wiley, 2020, pp. 3–11, doi:10.1111/cge.13674.","ama":"Avagliano L, Parenti I, Grazioli P, et al. Chromatinopathies: A focus on Cornelia de Lange syndrome. Clinical Genetics. 2020;97(1):3-11. doi:10.1111/cge.13674","apa":"Avagliano, L., Parenti, I., Grazioli, P., Di Fede, E., Parodi, C., Mariani, M., … Massa, V. (2020). Chromatinopathies: A focus on Cornelia de Lange syndrome. Clinical Genetics. Wiley. https://doi.org/10.1111/cge.13674","ieee":"L. Avagliano et al., “Chromatinopathies: A focus on Cornelia de Lange syndrome,” Clinical Genetics, vol. 97, no. 1. Wiley, pp. 3–11, 2020.","short":"L. Avagliano, I. Parenti, P. Grazioli, E. Di Fede, C. Parodi, M. Mariani, F.J. Kaiser, A. Selicorni, C. Gervasini, V. Massa, Clinical Genetics 97 (2020) 3–11."},"issue":"1","volume":97,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0009-9163"],"eissn":["1399-0004"]},"publication_status":"published","month":"01","intvolume":" 97","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"In recent years, many genes have been associated with chromatinopathies classified as “Cornelia de Lange Syndrome‐like.” It is known that the phenotype of these patients becomes less recognizable, overlapping to features characteristic of other syndromes caused by genetic variants affecting different regulators of chromatin structure and function. Therefore, Cornelia de Lange syndrome diagnosis might be arduous due to the seldom discordance between unexpected molecular diagnosis and clinical evaluation. Here, we review the molecular features of Cornelia de Lange syndrome, supporting the hypothesis that “CdLS‐like syndromes” are part of a larger “rare disease family” sharing multiple clinical features and common disrupted molecular pathways."}],"department":[{"_id":"GaNo"}],"date_updated":"2023-08-17T14:06:20Z","status":"public","type":"journal_article","article_type":"review","_id":"7149"},{"_id":"7004","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-17T14:02:59Z","department":[{"_id":"TaHa"}],"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"intvolume":" 376","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1810.10402","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"ec_funded":1,"volume":376,"project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","ista":"Rapcak M, Soibelman Y, Yang Y, Zhao G. 2020. Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. 376, 1803–1873.","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."},"title":"Cohomological Hall algebras, vertex algebras and instantons","external_id":{"arxiv":["1810.10402"],"isi":["000536255500004"]},"article_processing_charge":"No","author":[{"first_name":"Miroslav","full_name":"Rapcak, Miroslav","last_name":"Rapcak"},{"first_name":"Yan","last_name":"Soibelman","full_name":"Soibelman, Yan"},{"first_name":"Yaping","last_name":"Yang","full_name":"Yang, Yaping"},{"id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang","last_name":"Zhao","full_name":"Zhao, Gufang"}],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Communications in Mathematical Physics","day":"01","year":"2020","isi":1,"date_created":"2019-11-12T14:01:27Z","doi":"10.1007/s00220-019-03575-5","date_published":"2020-06-01T00:00:00Z","page":"1803-1873"},{"oa":1,"quality_controlled":"1","publisher":"Wiley","date_created":"2019-12-22T23:00:43Z","doi":"10.1002/advs.201901455","date_published":"2020-02-05T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Advanced Science","day":"05","article_number":"1901455","article_processing_charge":"No","external_id":{"isi":["000501912800001"],"pmid":["32042554"]},"author":[{"last_name":"Li","full_name":"Li, Yang","first_name":"Yang"},{"first_name":"Yaping","full_name":"Wang, Yaping","last_name":"Wang"},{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"first_name":"Zhen","full_name":"Li, Zhen","last_name":"Li"},{"first_name":"Zhi","full_name":"Yuan, Zhi","last_name":"Yuan"},{"full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","last_name":"Glanc","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"last_name":"Domjan","orcid":"0000-0003-2267-106X","full_name":"Domjan, David","first_name":"David","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F"},{"full_name":"Wang, Kai","last_name":"Wang","first_name":"Kai"},{"full_name":"Xuan, Wei","last_name":"Xuan","first_name":"Wei"},{"full_name":"Guo, Yan","last_name":"Guo","first_name":"Yan"},{"first_name":"Zhizhong","last_name":"Gong","full_name":"Gong, Zhizhong"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Zhang","full_name":"Zhang, Jing","first_name":"Jing"}],"title":"Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 7","month":"02","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","volume":7,"issue":"3","publication_status":"published","publication_identifier":{"eissn":["2198-3844"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-02-24T14:29:54Z","file_name":"2020_AdvScience_Li.pdf","date_updated":"2020-07-14T12:47:53Z","file_size":3586924,"creator":"dernst","checksum":"016eeab5860860af038e2da95ffe75c3","file_id":"7519","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"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":"7204","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:53Z","date_updated":"2023-08-17T14:13:17Z","ddc":["580"]},{"article_type":"original","type":"journal_article","status":"public","_id":"7220","department":[{"_id":"BeBi"}],"date_updated":"2023-08-17T14:14:23Z","scopus_import":"1","intvolume":" 134","month":"02","abstract":[{"text":"BACKGROUND:The introduction of image-guided methods to bypass surgery has resulted in optimized preoperative identification of the recipients and excellent patency rates. However, the recently presented methods have also been resource-consuming. In the present study, we have reported a cost-efficient planning workflow for extracranial-intracranial (EC-IC) revascularization combined with transdural indocyanine green videoangiography (tICG-VA). METHODS:We performed a retrospective review at a single tertiary referral center from 2011 to 2018. A novel software-derived workflow was applied for 25 of 92 bypass procedures during the study period. The precision and accuracy were assessed using tICG-VA identification of the cortical recipients and a comparison of the virtual and actual data. The data from a control group of 25 traditionally planned procedures were also matched. RESULTS:The intraoperative transfer time of the calculated coordinates averaged 0.8 minute (range, 0.4-1.9 minutes). The definitive recipients matched the targeted branches in 80%, and a neighboring branch was used in 16%. Our workflow led to a significant craniotomy size reduction in the study group compared with that in the control group (P = 0.005). tICG-VA was successfully applied in 19 cases. An average of 2 potential recipient arteries were identified transdurally, resulting in tailored durotomy and 3 craniotomy adjustments. Follow-up patency results were available for 49 bypass surgeries, comprising 54 grafts. The overall patency rate was 91% at a median follow-up period of 26 months. No significant difference was found in the patency rate between the study and control groups (P = 0.317). CONCLUSIONS:Our clinical results have validated the presented planning and surgical workflow and support the routine implementation of tICG-VA for recipient identification before durotomy.","lang":"eng"}],"pmid":1,"oa_version":"None","volume":134,"issue":"2","publication_status":"published","publication_identifier":{"issn":["1878-8750"],"eissn":["1878-8769"]},"language":[{"iso":"eng"}],"external_id":{"pmid":["31733380"],"isi":["000512878200104"]},"article_processing_charge":"No","author":[{"first_name":"Philippe","last_name":"Dodier","full_name":"Dodier, Philippe"},{"last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gabriel","full_name":"Mistelbauer, Gabriel","last_name":"Mistelbauer"},{"first_name":"Wei Te","full_name":"Wang, Wei Te","last_name":"Wang"},{"last_name":"Ferraz-Leite","full_name":"Ferraz-Leite, Heber","first_name":"Heber"},{"first_name":"Andreas","last_name":"Gruber","full_name":"Gruber, Andreas"},{"full_name":"Marik, Wolfgang","last_name":"Marik","first_name":"Wolfgang"},{"first_name":"Fabian","full_name":"Winter, Fabian","last_name":"Winter"},{"first_name":"Gerrit","last_name":"Fischer","full_name":"Fischer, Gerrit"},{"first_name":"Josa M.","last_name":"Frischer","full_name":"Frischer, Josa M."},{"first_name":"Gerhard","last_name":"Bavinzski","full_name":"Bavinzski, Gerhard"}],"title":"Novel software-derived workflow in extracranial–intracranial bypass surgery validated by transdural indocyanine green videoangiography","citation":{"ista":"Dodier P, Auzinger T, Mistelbauer G, Wang WT, Ferraz-Leite H, Gruber A, Marik W, Winter F, Fischer G, Frischer JM, Bavinzski G. 2020. Novel software-derived workflow in extracranial–intracranial bypass surgery validated by transdural indocyanine green videoangiography. World Neurosurgery. 134(2), e892–e902.","chicago":"Dodier, Philippe, Thomas Auzinger, Gabriel Mistelbauer, Wei Te Wang, Heber Ferraz-Leite, Andreas Gruber, Wolfgang Marik, et al. “Novel Software-Derived Workflow in Extracranial–Intracranial Bypass Surgery Validated by Transdural Indocyanine Green Videoangiography.” World Neurosurgery. Elsevier, 2020. https://doi.org/10.1016/j.wneu.2019.11.038.","apa":"Dodier, P., Auzinger, T., Mistelbauer, G., Wang, W. T., Ferraz-Leite, H., Gruber, A., … Bavinzski, G. (2020). Novel software-derived workflow in extracranial–intracranial bypass surgery validated by transdural indocyanine green videoangiography. World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2019.11.038","ama":"Dodier P, Auzinger T, Mistelbauer G, et al. Novel software-derived workflow in extracranial–intracranial bypass surgery validated by transdural indocyanine green videoangiography. World Neurosurgery. 2020;134(2):e892-e902. doi:10.1016/j.wneu.2019.11.038","ieee":"P. Dodier et al., “Novel software-derived workflow in extracranial–intracranial bypass surgery validated by transdural indocyanine green videoangiography,” World Neurosurgery, vol. 134, no. 2. Elsevier, pp. e892–e902, 2020.","short":"P. Dodier, T. Auzinger, G. Mistelbauer, W.T. Wang, H. Ferraz-Leite, A. Gruber, W. Marik, F. Winter, G. Fischer, J.M. Frischer, G. Bavinzski, World Neurosurgery 134 (2020) e892–e902.","mla":"Dodier, Philippe, et al. “Novel Software-Derived Workflow in Extracranial–Intracranial Bypass Surgery Validated by Transdural Indocyanine Green Videoangiography.” World Neurosurgery, vol. 134, no. 2, Elsevier, 2020, pp. e892–902, doi:10.1016/j.wneu.2019.11.038."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","quality_controlled":"1","page":"e892-e902","date_created":"2019-12-29T23:00:48Z","doi":"10.1016/j.wneu.2019.11.038","date_published":"2020-02-01T00:00:00Z","year":"2020","isi":1,"publication":"World Neurosurgery","day":"01"},{"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"article_processing_charge":"No","external_id":{"isi":["000521120600007"],"pmid":["31760231"]},"author":[{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368"},{"first_name":"Christian","full_name":"Luschnig, Christian","last_name":"Luschnig"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"title":"Auxin signalling in growth: Schrödinger's cat out of the bag","citation":{"mla":"Gallei, Michelle C., et al. “Auxin Signalling in Growth: Schrödinger’s Cat out of the Bag.” Current Opinion in Plant Biology, vol. 53, no. 2, Elsevier, 2020, pp. 43–49, doi:10.1016/j.pbi.2019.10.003.","ama":"Gallei MC, Luschnig C, Friml J. Auxin signalling in growth: Schrödinger’s cat out of the bag. Current Opinion in Plant Biology. 2020;53(2):43-49. doi:10.1016/j.pbi.2019.10.003","apa":"Gallei, M. C., Luschnig, C., & Friml, J. (2020). Auxin signalling in growth: Schrödinger’s cat out of the bag. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.10.003","short":"M.C. Gallei, C. Luschnig, J. Friml, Current Opinion in Plant Biology 53 (2020) 43–49.","ieee":"M. C. Gallei, C. Luschnig, and J. Friml, “Auxin signalling in growth: Schrödinger’s cat out of the bag,” Current Opinion in Plant Biology, vol. 53, no. 2. Elsevier, pp. 43–49, 2020.","chicago":"Gallei, Michelle C, Christian Luschnig, and Jiří Friml. “Auxin Signalling in Growth: Schrödinger’s Cat out of the Bag.” Current Opinion in Plant Biology. Elsevier, 2020. https://doi.org/10.1016/j.pbi.2019.10.003.","ista":"Gallei MC, Luschnig C, Friml J. 2020. Auxin signalling in growth: Schrödinger’s cat out of the bag. Current Opinion in Plant Biology. 53(2), 43–49."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Elsevier","acknowledgement":"Research in J.F. laboratory is funded by the European Union's Horizon 2020 program (ERC grant agreement n° 742985); C.L. is supported by the Austrian Science Fund (FWF grant P 31493).","page":"43-49","date_created":"2019-12-02T12:05:26Z","doi":"10.1016/j.pbi.2019.10.003","date_published":"2020-02-01T00:00:00Z","year":"2020","isi":1,"publication":"Current Opinion in Plant Biology","day":"01","article_type":"original","type":"journal_article","status":"public","_id":"7142","department":[{"_id":"JiFr"}],"date_updated":"2023-08-17T14:07:22Z","scopus_import":"1","intvolume":" 53","month":"02","abstract":[{"text":"The phytohormone auxin acts as an amazingly versatile coordinator of plant growth and development. With its morphogen-like properties, auxin controls sites and timing of differentiation and/or growth responses both, in quantitative and qualitative terms. Specificity in the auxin response depends largely on distinct modes of signal transmission, by which individual cells perceive and convert auxin signals into a remarkable diversity of responses. The best understood, or so-called canonical mechanism of auxin perception ultimately results in variable adjustments of the cellular transcriptome, via a short, nuclear signal transduction pathway. Additional findings that accumulated over decades implied that an additional, presumably, cell surface-based auxin perception mechanism mediates very rapid cellular responses and decisively contributes to the cell's overall hormonal response. Recent investigations into both, nuclear and cell surface auxin signalling challenged this assumed partition of roles for different auxin signalling pathways and revealed an unexpected complexity in transcriptional and non-transcriptional cellular responses mediated by auxin.","lang":"eng"}],"oa_version":"None","pmid":1,"ec_funded":1,"volume":53,"issue":"2","related_material":{"record":[{"id":"11626","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"eissn":["1879-0356"],"issn":["1369-5266"]},"language":[{"iso":"eng"}]},{"_id":"7166","type":"journal_article","article_type":"letter_note","status":"public","date_updated":"2023-08-17T14:07:52Z","department":[{"_id":"EdHa"}],"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."}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.nanolett.9b04445"}],"scopus_import":"1","intvolume":" 20","month":"01","publication_status":"published","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"language":[{"iso":"eng"}],"volume":20,"issue":"1","related_material":{"record":[{"relation":"research_data","id":"9726","status":"public"},{"relation":"research_data","id":"9885","status":"public"}]},"citation":{"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","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.","short":"M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 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.","ista":"Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 20(1), 669–676.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000507151600087"],"pmid":["31797672"]},"article_processing_charge":"No","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"first_name":"Reinhard","last_name":"Lipowsky","full_name":"Lipowsky, Reinhard"}],"title":"Collective force generation by molecular motors is determined by strain-induced unbinding","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","year":"2020","isi":1,"publication":"Nano Letters","day":"08","page":"669-676","date_created":"2019-12-10T15:36:05Z","date_published":"2020-01-08T00:00:00Z","doi":"10.1021/acs.nanolett.9b04445"},{"citation":{"ieee":"M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society , 2020.","short":"M.C. Ucar, R. Lipowsky, (2020).","apa":"Ucar, M. C., & Lipowsky, R. (2020). MURL_Dataz. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s002","ama":"Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:10.1021/acs.nanolett.9b04445.s002","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. MURL_Dataz. American Chemical Society , 2020, doi:10.1021/acs.nanolett.9b04445.s002.","ista":"Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society , 10.1021/acs.nanolett.9b04445.s002.","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical Society , 2020. https://doi.org/10.1021/acs.nanolett.9b04445.s002."},"date_updated":"2023-08-17T14:07:52Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar"},{"first_name":"Reinhard","full_name":"Lipowsky, Reinhard","last_name":"Lipowsky"}],"department":[{"_id":"EdHa"}],"title":"MURL_Dataz","_id":"9885","type":"research_data_reference","status":"public","year":"2020","day":"08","date_created":"2021-08-11T13:16:03Z","related_material":{"record":[{"status":"public","id":"7166","relation":"used_in_publication"}]},"doi":"10.1021/acs.nanolett.9b04445.s002","date_published":"2020-01-08T00:00:00Z","abstract":[{"text":"Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)","lang":"eng"}],"oa_version":"Published Version","publisher":"American Chemical Society ","month":"01"},{"issue":"8","volume":49,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0901-5027"],"eissn":["1399-0020"]},"intvolume":" 49","month":"08","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"The combined resection of skull-infiltrating tumours and immediate cranioplastic reconstruction predominantly relies on freehand-moulded solutions. Techniques that enable this procedure to be performed easily in routine clinical practice would be useful. A cadaveric study was developed in which a new software tool was used to perform single-stage reconstructions with prefabricated implants after the resection of skull-infiltrating pathologies. A novel 3D visualization and interaction framework was developed to create 10 virtual craniotomies in five cadaveric specimens. Polyether ether ketone (PEEK) implants were manufactured according to the bone defects. The image-guided craniotomy was reconstructed with PEEK and compared to polymethyl methacrylate (PMMA). Navigational accuracy and surgical precision were assessed. The PEEK workflow resulted in up to 10-fold shorter reconstruction times than the standard technique. Surgical precision was reflected by the mean 1.1 ± 0.29 mm distance between the virtual and real craniotomy, with submillimetre precision in 50%. Assessment of the global offset between virtual and actual craniotomy revealed an average shift of 4.5 ± 3.6 mm. The results validated the ‘elective single-stage cranioplasty’ technique as a state-of-the-art virtual planning method and surgical workflow. This patient-tailored workflow could significantly reduce surgical times compared to the traditional, intraoperative acrylic moulding method and may be an option for the reconstruction of bone defects in the craniofacial region."}],"department":[{"_id":"BeBi"}],"date_updated":"2023-08-17T14:15:22Z","status":"public","type":"journal_article","article_type":"original","_id":"7218","date_created":"2019-12-29T23:00:47Z","doi":"10.1016/j.ijom.2019.11.011","date_published":"2020-08-01T00:00:00Z","page":"P1007-1015","publication":"International Journal of Oral and Maxillofacial Surgery","day":"01","year":"2020","isi":1,"publisher":"Elsevier","quality_controlled":"1","title":"Single-stage bone resection and cranioplastic reconstruction: Comparison of a novel software-derived PEEK workflow with the standard reconstructive method","external_id":{"isi":["000556819800005"],"pmid":["31866145"]},"article_processing_charge":"No","author":[{"first_name":"Philippe","full_name":"Dodier, Philippe","last_name":"Dodier"},{"full_name":"Winter, Fabian","last_name":"Winter","first_name":"Fabian"},{"last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Gabriel","last_name":"Mistelbauer","full_name":"Mistelbauer, Gabriel"},{"first_name":"Josa M.","last_name":"Frischer","full_name":"Frischer, Josa M."},{"first_name":"Wei Te","full_name":"Wang, Wei Te","last_name":"Wang"},{"first_name":"Ammar","full_name":"Mallouhi, Ammar","last_name":"Mallouhi"},{"first_name":"Wolfgang","last_name":"Marik","full_name":"Marik, Wolfgang"},{"first_name":"Stefan","full_name":"Wolfsberger, Stefan","last_name":"Wolfsberger"},{"first_name":"Lukas","last_name":"Reissig","full_name":"Reissig, Lukas"},{"first_name":"Firas","full_name":"Hammadi, Firas","last_name":"Hammadi"},{"last_name":"Matula","full_name":"Matula, Christian","first_name":"Christian"},{"first_name":"Arnulf","full_name":"Baumann, Arnulf","last_name":"Baumann"},{"last_name":"Bavinzski","full_name":"Bavinzski, Gerhard","first_name":"Gerhard"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Dodier, Philippe, et al. “Single-Stage Bone Resection and Cranioplastic Reconstruction: Comparison of a Novel Software-Derived PEEK Workflow with the Standard Reconstructive Method.” International Journal of Oral and Maxillofacial Surgery, vol. 49, no. 8, Elsevier, 2020, pp. P1007-1015, doi:10.1016/j.ijom.2019.11.011.","short":"P. Dodier, F. Winter, T. Auzinger, G. Mistelbauer, J.M. Frischer, W.T. Wang, A. Mallouhi, W. Marik, S. Wolfsberger, L. Reissig, F. Hammadi, C. Matula, A. Baumann, G. Bavinzski, International Journal of Oral and Maxillofacial Surgery 49 (2020) P1007-1015.","ieee":"P. Dodier et al., “Single-stage bone resection and cranioplastic reconstruction: Comparison of a novel software-derived PEEK workflow with the standard reconstructive method,” International Journal of Oral and Maxillofacial Surgery, vol. 49, no. 8. Elsevier, pp. P1007-1015, 2020.","ama":"Dodier P, Winter F, Auzinger T, et al. Single-stage bone resection and cranioplastic reconstruction: Comparison of a novel software-derived PEEK workflow with the standard reconstructive method. International Journal of Oral and Maxillofacial Surgery. 2020;49(8):P1007-1015. doi:10.1016/j.ijom.2019.11.011","apa":"Dodier, P., Winter, F., Auzinger, T., Mistelbauer, G., Frischer, J. M., Wang, W. T., … Bavinzski, G. (2020). Single-stage bone resection and cranioplastic reconstruction: Comparison of a novel software-derived PEEK workflow with the standard reconstructive method. International Journal of Oral and Maxillofacial Surgery. Elsevier. https://doi.org/10.1016/j.ijom.2019.11.011","chicago":"Dodier, Philippe, Fabian Winter, Thomas Auzinger, Gabriel Mistelbauer, Josa M. Frischer, Wei Te Wang, Ammar Mallouhi, et al. “Single-Stage Bone Resection and Cranioplastic Reconstruction: Comparison of a Novel Software-Derived PEEK Workflow with the Standard Reconstructive Method.” International Journal of Oral and Maxillofacial Surgery. Elsevier, 2020. https://doi.org/10.1016/j.ijom.2019.11.011.","ista":"Dodier P, Winter F, Auzinger T, Mistelbauer G, Frischer JM, Wang WT, Mallouhi A, Marik W, Wolfsberger S, Reissig L, Hammadi F, Matula C, Baumann A, Bavinzski G. 2020. Single-stage bone resection and cranioplastic reconstruction: Comparison of a novel software-derived PEEK workflow with the standard reconstructive method. International Journal of Oral and Maxillofacial Surgery. 49(8), P1007-1015."}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Xiao, Guanghui, and Yuzhou Zhang. “Adaptive Growth: Shaping Auxin-Mediated Root System Architecture.” Trends in Plant Science. Elsevier, 2020. https://doi.org/10.1016/j.tplants.2019.12.001.","ista":"Xiao G, Zhang Y. 2020. Adaptive growth: Shaping auxin-mediated root system architecture. Trends in Plant Science. 25(2), P121-123.","mla":"Xiao, Guanghui, and Yuzhou Zhang. “Adaptive Growth: Shaping Auxin-Mediated Root System Architecture.” Trends in Plant Science, vol. 25, no. 2, Elsevier, 2020, pp. P121-123, doi:10.1016/j.tplants.2019.12.001.","ama":"Xiao G, Zhang Y. Adaptive growth: Shaping auxin-mediated root system architecture. Trends in Plant Science. 2020;25(2):P121-123. doi:10.1016/j.tplants.2019.12.001","apa":"Xiao, G., & Zhang, Y. (2020). Adaptive growth: Shaping auxin-mediated root system architecture. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2019.12.001","ieee":"G. Xiao and Y. Zhang, “Adaptive growth: Shaping auxin-mediated root system architecture,” Trends in Plant Science, vol. 25, no. 2. Elsevier, pp. P121-123, 2020.","short":"G. Xiao, Y. Zhang, Trends in Plant Science 25 (2020) P121-123."},"title":"Adaptive growth: Shaping auxin-mediated root system architecture","external_id":{"pmid":["31843370"],"isi":["000508637500001"]},"article_processing_charge":"No","author":[{"first_name":"Guanghui","last_name":"Xiao","full_name":"Xiao, Guanghui"},{"last_name":"Zhang","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","publisher":"Elsevier","publication":"Trends in Plant Science","day":"01","year":"2020","isi":1,"date_created":"2019-12-29T23:00:48Z","doi":"10.1016/j.tplants.2019.12.001","date_published":"2020-02-01T00:00:00Z","page":"P121-123","_id":"7219","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-17T14:14:50Z","department":[{"_id":"JiFr"}],"oa_version":"None","pmid":1,"abstract":[{"text":"Root system architecture (RSA), governed by the phytohormone auxin, endows plants with an adaptive advantage in particular environments. Using geographically representative arabidopsis (Arabidopsis thaliana) accessions as a resource for GWA mapping, Waidmann et al. and Ogura et al. recently identified two novel components involved in modulating auxin-mediated RSA and conferring plant fitness in particular habitats.","lang":"eng"}],"intvolume":" 25","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["13601385"]},"issue":"2","volume":25},{"publisher":"Wiley","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Immunology and Cell Biology","page":"93-113","doi":"10.1111/imcb.12304","date_published":"2020-02-01T00:00:00Z","date_created":"2020-01-05T23:00:48Z","citation":{"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.","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.","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Peyman","last_name":"Obeidy","full_name":"Obeidy, Peyman"},{"first_name":"Lining A.","full_name":"Ju, Lining A.","last_name":"Ju"},{"full_name":"Oehlers, Stefan H.","last_name":"Oehlers","first_name":"Stefan H."},{"last_name":"Zulkhernain","full_name":"Zulkhernain, Nursafwana S.","first_name":"Nursafwana S."},{"first_name":"Quintin","last_name":"Lee","full_name":"Lee, Quintin"},{"first_name":"Jorge L.","full_name":"Galeano Niño, Jorge L.","last_name":"Galeano Niño"},{"full_name":"Kwan, Rain Y.Q.","last_name":"Kwan","first_name":"Rain Y.Q."},{"last_name":"Tikoo","full_name":"Tikoo, Shweta","first_name":"Shweta"},{"full_name":"Cavanagh, Lois L.","last_name":"Cavanagh","first_name":"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."},{"first_name":"Shaun P.","last_name":"Jackson","full_name":"Jackson, Shaun P."},{"first_name":"Maté","last_name":"Biro","full_name":"Biro, Maté"},{"last_name":"Roediger","full_name":"Roediger, Ben","first_name":"Ben"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Weninger, Wolfgang","last_name":"Weninger","first_name":"Wolfgang"}],"external_id":{"isi":["000503885600001"],"pmid":["31698518"]},"article_processing_charge":"No","title":"Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes","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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 98","publication_identifier":{"issn":["08189641"],"eissn":["14401711"]},"publication_status":"published","file":[{"date_created":"2020-11-19T11:22:33Z","file_name":"2020_ImmunologyCellBio_Obeidy.pdf","date_updated":"2020-11-19T11:22:33Z","file_size":8569945,"creator":"dernst","file_id":"8775","checksum":"c389477b4b52172ef76afff8a06c6775","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"2","volume":98,"_id":"7234","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":"2023-08-17T14:21:12Z","ddc":["570"],"file_date_updated":"2020-11-19T11:22:33Z","department":[{"_id":"MiSi"}]},{"oa_version":"Published Version","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."}],"acknowledged_ssus":[{"_id":"PreCl"}],"intvolume":" 11","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"checksum":"ebf1ed522f4e0be8d94c939c1806a709","file_id":"7261","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"}],"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-function-for-potential-tumour-suppressor-in-brain-development/","relation":"press_release"}]},"volume":11,"_id":"7253","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":"2023-08-17T14:23:41Z","file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"SiHi"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature Communications","day":"10","year":"2020","isi":1,"has_accepted_license":"1","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":[{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031"},{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","short":"S. Laukoter, R.J. Beattie, F. Pauler, N. Amberg, K.I. Nakayama, S. Hippenmeyer, Nature Communications 11 (2020).","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.","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."},"title":"Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development","article_processing_charge":"No","external_id":{"isi":["000551459000005"]},"author":[{"first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010"},{"last_name":"Beattie","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg"},{"full_name":"Nakayama, Keiichi I.","last_name":"Nakayama","first_name":"Keiichi I."},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}]},{"_id":"7339","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":"2023-08-17T14:25:23Z","ddc":["570"],"department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:56Z","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 40","month":"01","publication_status":"published","publication_identifier":{"eissn":["15292401"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2020_JourNeuroscience_Piriya.pdf","date_created":"2020-01-20T14:44:10Z","file_size":4460781,"date_updated":"2020-07-14T12:47:56Z","creator":"dernst","file_id":"7345","checksum":"92f5e8a47f454fc131fb94cd7f106e60","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":40,"issue":"1","citation":{"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.","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.","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","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","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.","short":"L. Piriya Ananda Babu, H.Y. Wang, K. Eguchi, L. Guillaud, T. Takahashi, Journal of Neuroscience 40 (2020) 131–142."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["31767677"],"isi":["000505167600013"]},"author":[{"full_name":"Piriya Ananda Babu, Lashmi","last_name":"Piriya Ananda Babu","first_name":"Lashmi"},{"last_name":"Wang","full_name":"Wang, Han Ying","first_name":"Han Ying"},{"last_name":"Eguchi","orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Guillaud","full_name":"Guillaud, Laurent"},{"first_name":"Tomoyuki","last_name":"Takahashi","full_name":"Takahashi, Tomoyuki"}],"title":"Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission","oa":1,"quality_controlled":"1","publisher":"Society for Neuroscience","year":"2020","isi":1,"has_accepted_license":"1","publication":"Journal of neuroscience","day":"02","page":"131-142","date_created":"2020-01-19T23:00:38Z","doi":"10.1523/JNEUROSCI.1571-19.2019","date_published":"2020-01-02T00:00:00Z"},{"date_created":"2020-01-22T15:23:57Z","doi":"10.3389/fpls.2019.01680","date_published":"2020-01-22T00:00:00Z","publication":"Frontiers in Plant Science","day":"22","year":"2020","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Frontiers Media","quality_controlled":"1","title":"Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2","external_id":{"isi":["000511376000001"]},"article_processing_charge":"No","author":[{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"last_name":"Gallemi","full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal"},{"last_name":"Dadarou","full_name":"Dadarou, Despoina","first_name":"Despoina"},{"first_name":"John H.","last_name":"Doonan","full_name":"Doonan, John H."},{"first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola","last_name":"Cavallari"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","short":"C. Nibau, M. Gallemi, D. Dadarou, J.H. Doonan, N. Cavallari, Frontiers in Plant Science 10 (2020).","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.","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.","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."},"article_number":"1680","volume":10,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1951438,"date_updated":"2020-07-14T12:47:56Z","file_name":"2020_FrontiersPlantScience_Nibau.pdf","date_created":"2020-01-27T09:07:02Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"d1f92e60a713fbd15097ce895e5c7ccb","file_id":"7366"}],"publication_status":"published","publication_identifier":{"issn":["1664-462X"]},"intvolume":" 10","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:47:56Z","ddc":["580"],"date_updated":"2023-08-17T14:21:45Z","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":"7350"},{"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"author":[{"full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero","first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"first_name":"Matteo","full_name":"Marsili, Matteo","last_name":"Marsili"},{"full_name":"Roudi, Yasser","last_name":"Roudi","first_name":"Yasser"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000515321800006"]},"title":"Multiscale relevance and informative encoding in neuronal spike trains","citation":{"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.","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.","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","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","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.","ista":"Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 48, 85–102."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","page":"85-102","doi":"10.1007/s10827-020-00740-x","date_published":"2020-02-01T00:00:00Z","date_created":"2020-01-28T10:34:00Z","has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Journal of Computational Neuroscience","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","keyword":["Time series analysis","Multiple time scale analysis","Spike train data","Information theory","Bayesian decoding"],"_id":"7369","file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"SaSi"}],"date_updated":"2023-08-17T14:35:22Z","ddc":["004","519","570"],"scopus_import":"1","month":"02","intvolume":" 48","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","volume":48,"ec_funded":1,"publication_identifier":{"eissn":["1573-6873"],"issn":["0929-5313"]},"publication_status":"published","file":[{"relation":"supplementary_material","access_level":"open_access","content_type":"application/pdf","file_id":"7380","checksum":"036e9451d6cd0c190ad25791bf82393b","creator":"rcubero","file_size":1941355,"date_updated":"2020-07-14T12:47:56Z","file_name":"10827_2020_740_MOESM1_ESM.pdf","date_created":"2020-01-28T09:31:09Z"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"4dd8b1fd4b54486f79d82ac7b2a412b2","file_id":"7381","file_size":3257880,"date_updated":"2020-07-14T12:47:56Z","creator":"rcubero","file_name":"Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf","date_created":"2020-01-28T09:31:09Z"}],"language":[{"iso":"eng"}]},{"year":"2020","isi":1,"has_accepted_license":"1","publication":"SoftwareX","day":"17","date_created":"2020-01-26T23:00:35Z","date_published":"2020-01-17T00:00:00Z","doi":"10.1016/j.softx.2019.100395","oa":1,"quality_controlled":"1","publisher":"Elsevier","citation":{"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","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.","short":"J.M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, M. Avila, SoftwareX 11 (2020).","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000552271200011"],"arxiv":["1908.00587"]},"article_processing_charge":"No","author":[{"id":"40770848-F248-11E8-B48F-1D18A9856A87","first_name":"Jose M","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso"},{"last_name":"Feldmann","full_name":"Feldmann, Daniel","first_name":"Daniel"},{"last_name":"Rampp","full_name":"Rampp, Markus","first_name":"Markus"},{"first_name":"Alberto","last_name":"Vela-Martín","full_name":"Vela-Martín, Alberto"},{"full_name":"Shi, Liang","last_name":"Shi","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"}],"title":"nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow","article_number":"100395","publication_status":"published","publication_identifier":{"eissn":["23527110"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7365","checksum":"2af1a1a3cc33557b345145276f221668","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-01-27T07:32:46Z","file_name":"2020_SoftwareX_Lopez.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:56Z","file_size":679707}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":11,"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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 11","month":"01","date_updated":"2023-08-17T14:29:59Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"BjHo"}],"_id":"7364","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","status":"public"},{"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":[{"open_access":"1","url":"https://arxiv.org/abs/1903.10693"}],"month":"01","intvolume":" 17","publication_identifier":{"eissn":["17425662"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"162","volume":17,"_id":"7431","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-17T14:31:28Z","department":[{"_id":"EdHa"}],"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. ","quality_controlled":"1","publisher":"The Royal Society","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","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.","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","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)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Kolchinsky","full_name":"Kolchinsky, Artemy","first_name":"Artemy"},{"last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"}],"article_processing_charge":"No","external_id":{"arxiv":["1903.10693"],"isi":["000538369800002"],"pmid":["31964273"]},"title":"Decomposing information into copying versus transformation"},{"author":[{"last_name":"Geher","full_name":"Geher, Gyorgy Pal","first_name":"Gyorgy Pal"},{"full_name":"Titkos, Tamas","last_name":"Titkos","first_name":"Tamas"},{"orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel","last_name":"Virosztek","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2002.00859"],"isi":["000551418100018"]},"article_processing_charge":"No","title":"Isometric study of Wasserstein spaces - the real line","citation":{"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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Geometric study of Wasserstein spaces and free probability","grant_number":"846294","call_identifier":"H2020","_id":"26A455A6-B435-11E9-9278-68D0E5697425"}],"page":"5855-5883","doi":"10.1090/tran/8113","date_published":"2020-08-01T00:00:00Z","date_created":"2020-01-29T10:20:46Z","isi":1,"year":"2020","day":"01","publication":"Transactions of the American Mathematical Society","publisher":"American Mathematical Society","quality_controlled":"1","oa":1,"department":[{"_id":"LaEr"}],"date_updated":"2023-08-17T14:31:03Z","ddc":["515"],"type":"journal_article","article_type":"original","status":"public","keyword":["Wasserstein space","isometric embeddings","isometric rigidity","exotic isometry flow"],"_id":"7389","issue":"8","volume":373,"ec_funded":1,"publication_identifier":{"issn":["00029947"],"eissn":["10886850"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.00859"}],"month":"08","intvolume":" 373","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))."}],"oa_version":"Preprint"},{"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","scopus_import":"1","intvolume":" 3","month":"03","publication_status":"published","publication_identifier":{"eissn":["2574-0962"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"11942","checksum":"f23be731a766a480c77c962c1380315c","success":1,"creator":"dernst","date_updated":"2022-08-23T08:34:17Z","file_size":6423548,"date_created":"2022-08-23T08:34:17Z","file_name":"2020_ACSAppliedEnergyMat_Cadavid.pdf"}],"ec_funded":1,"volume":3,"issue":"3","_id":"7467","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-17T14:36:16Z","ddc":["540"],"file_date_updated":"2022-08-23T08:34:17Z","department":[{"_id":"MaIb"}],"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.","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","year":"2020","isi":1,"has_accepted_license":"1","publication":"ACS Applied Energy Materials","day":"01","page":"2120-2129","date_created":"2020-02-09T23:00:52Z","doi":"10.1021/acsaem.9b02137","date_published":"2020-03-01T00:00:00Z","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"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.","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.","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.","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","article_processing_charge":"No","external_id":{"isi":["000526598300012"]},"author":[{"full_name":"Cadavid, Doris","last_name":"Cadavid","first_name":"Doris"},{"first_name":"Silvia","full_name":"Ortega, Silvia","last_name":"Ortega"},{"full_name":"Illera, Sergio","last_name":"Illera","first_name":"Sergio"},{"first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"first_name":"Yu","full_name":"Zhang, Yu","last_name":"Zhang"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"first_name":"Antonio M.","last_name":"López","full_name":"López, Antonio M."},{"first_name":"Germán","full_name":"Noriega, Germán","last_name":"Noriega"},{"first_name":"Oscar Juan","last_name":"Durá","full_name":"Durá, Oscar Juan"},{"first_name":"M. A.","last_name":"López De La Torre","full_name":"López De La Torre, M. A."},{"last_name":"Prades","full_name":"Prades, Joan Daniel","first_name":"Joan Daniel"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"title":"Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials"},{"date_published":"2020-04-01T00:00:00Z","doi":"10.1016/j.plantsci.2020.110414","date_created":"2020-02-09T23:00:50Z","day":"01","publication":"Plant Science","isi":1,"has_accepted_license":"1","year":"2020","quality_controlled":"1","publisher":"Elsevier","oa":1,"title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","author":[{"first_name":"Ewa","full_name":"Mazur, Ewa","last_name":"Mazur"},{"last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski"},{"last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hélène S.","full_name":"Robert, Hélène S.","last_name":"Robert"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"article_processing_charge":"No","external_id":{"isi":["000520609800009"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","short":"E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020).","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.","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.","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."},"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"article_number":"110414","related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"}]},"issue":"4","volume":293,"ec_funded":1,"file":[{"checksum":"f7f27c6a8fea985ceb9279be2204461c","file_id":"7471","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"}],"publication_identifier":{"eissn":["18732259"],"issn":["01689452"]},"publication_status":"published","month":"04","intvolume":" 293","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:59Z","ddc":["580"],"date_updated":"2023-08-17T14:37:32Z","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":"7465"},{"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"day":"20","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.7554/eLife.51595","date_published":"2020-01-20T00:00:00Z","date_created":"2020-02-09T23:00:51Z","article_number":"e51595","project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen","grant_number":"P29638"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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).","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."},"title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","author":[{"full_name":"Kierdorf, Katrin","last_name":"Kierdorf","first_name":"Katrin"},{"first_name":"Fabian","full_name":"Hersperger, Fabian","last_name":"Hersperger"},{"first_name":"Jessica","last_name":"Sharrock","full_name":"Sharrock, Jessica"},{"first_name":"Crystal M.","last_name":"Vincent","full_name":"Vincent, Crystal M."},{"first_name":"Pinar","last_name":"Ustaoglu","full_name":"Ustaoglu, Pinar"},{"first_name":"Jiawen","full_name":"Dou, Jiawen","last_name":"Dou"},{"first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","full_name":"György, Attila","last_name":"György"},{"first_name":"Olaf","full_name":"Groß, Olaf","last_name":"Groß"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dionne","full_name":"Dionne, Marc S.","first_name":"Marc S."}],"article_processing_charge":"No","external_id":{"isi":["000512304800001"]},"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"01","intvolume":" 9","scopus_import":"1","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"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","volume":9,"_id":"7466","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"],"date_updated":"2023-08-17T14:36:39Z","department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:47:59Z"},{"project":[{"call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","grant_number":"607616","name":"Inter-and intracellular signalling in schizophrenia"}],"title":"Replay of behavioral sequences in the medial prefrontal cortex during rule switching","external_id":{"isi":["000525319300016"],"pmid":["32032512"]},"article_processing_charge":"No","author":[{"last_name":"Käfer","full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola"},{"orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"full_name":"Blahna, Karel","last_name":"Blahna","first_name":"Karel","id":"3EA859AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"K. Käfer, M. Nardin, K. Blahna, J.L. Csicsvari, Neuron 106 (2020) P154–165.e6.","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.","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"},"oa":1,"quality_controlled":"1","publisher":"Elsevier","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 ).","date_created":"2020-02-10T15:45:48Z","date_published":"2020-04-08T00:00:00Z","doi":"10.1016/j.neuron.2020.01.015","page":"P154-165.e6","publication":"Neuron","day":"08","year":"2020","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"7472","department":[{"_id":"JoCs"}],"date_updated":"2023-08-17T14:38:02Z","intvolume":" 106","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2020.01.015"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","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"}],"ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/this-brain-area-helps-us-decide/","relation":"press_release"}]},"volume":106,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0896-6273"]}},{"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.","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","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","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.","short":"M. Gerencser, Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire 37 (2020) 663–682.","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","author":[{"first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate","last_name":"Gerencser"}],"external_id":{"arxiv":["1902.07635"],"isi":["000531049800007"]},"article_processing_charge":"No","title":"Nondivergence form quasilinear heat equations driven by space-time white noise","publisher":"Elsevier","quality_controlled":"1","oa":1,"isi":1,"year":"2020","day":"01","publication":"Annales de l'Institut Henri Poincaré C, Analyse non linéaire","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","_id":"7388","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-17T14:35:46Z","department":[{"_id":"JaMa"}],"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","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07635"}],"month":"05","intvolume":" 37","publication_identifier":{"issn":["0294-1449"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":37,"issue":"3"},{"date_created":"2020-02-16T23:00:49Z","doi":"10.1038/s41598-020-58264-4","date_published":"2020-02-10T00:00:00Z","publication":"Scientific reports","day":"10","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","title":"Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation","external_id":{"isi":["000560694800012"],"pmid":["32042057"]},"article_processing_charge":"No","author":[{"first_name":"Amada R.","full_name":"López De La Oliva, Amada R.","last_name":"López De La Oliva"},{"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","last_name":"Cardona","full_name":"Cardona, Carolina"},{"first_name":"Mercedes","full_name":"Martín-Rufián, Mercedes","last_name":"Martín-Rufián"},{"first_name":"Fernando J.","last_name":"Sialana","full_name":"Sialana, Fernando J."},{"last_name":"Castilla","full_name":"Castilla, Laura","first_name":"Laura"},{"full_name":"Bae, Narkhyun","last_name":"Bae","first_name":"Narkhyun","id":"3A5F7CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lobo, Carolina","last_name":"Lobo","first_name":"Carolina"},{"full_name":"Peñalver, Ana","last_name":"Peñalver","first_name":"Ana"},{"first_name":"Marina","full_name":"García-Frutos, Marina","last_name":"García-Frutos"},{"first_name":"David","last_name":"Carro","full_name":"Carro, David"},{"last_name":"Enrique","full_name":"Enrique, Victoria","first_name":"Victoria"},{"first_name":"José C.","full_name":"Paz, José C.","last_name":"Paz"},{"first_name":"Raghavendra G.","last_name":"Mirmira","full_name":"Mirmira, Raghavendra G."},{"first_name":"Antonia","last_name":"Gutiérrez","full_name":"Gutiérrez, Antonia"},{"first_name":"Francisco J.","last_name":"Alonso","full_name":"Alonso, Francisco J."},{"full_name":"Segura, Juan A.","last_name":"Segura","first_name":"Juan A."},{"last_name":"Matés","full_name":"Matés, José M.","first_name":"José M."},{"full_name":"Lubec, Gert","last_name":"Lubec","first_name":"Gert"},{"full_name":"Márquez, Javier","last_name":"Márquez","first_name":"Javier"}],"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.","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","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","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."},"article_number":"2259","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-020-80651-0"}]},"issue":"1","volume":10,"language":[{"iso":"eng"}],"file":[{"file_name":"2020_ScientificReport_Lopez.pdf","date_created":"2020-02-18T07:43:21Z","file_size":4703751,"date_updated":"2020-07-14T12:47:59Z","creator":"dernst","file_id":"7495","checksum":"c780bd87476a9c9e12668ff66de3dc96","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["20452322"]},"intvolume":" 10","month":"02","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"department":[{"_id":"CaBe"}],"file_date_updated":"2020-07-14T12:47:59Z","ddc":["570"],"date_updated":"2023-08-18T06:35:13Z","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":"7487"},{"date_updated":"2023-08-18T06:33:07Z","ddc":["570","580"],"department":[{"_id":"JiFr"},{"_id":"GaTk"},{"_id":"EM-Fac"},{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:47:59Z","_id":"7490","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":["2050-084X"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7494","checksum":"2052daa4be5019534f3a42f200a09f32","creator":"dernst","file_size":7247468,"date_updated":"2020-07-14T12:47:59Z","file_name":"2020_eLife_Narasimhan.pdf","date_created":"2020-02-18T07:21:16Z"}],"language":[{"iso":"eng"}],"volume":9,"ec_funded":1,"abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 9","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","full_name":"Prizak, Roshan","last_name":"Prizak"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"external_id":{"pmid":["31971511"],"isi":["000514104100001"]},"article_processing_charge":"No","title":"Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants","article_number":"e52067","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"23","publication":"eLife","date_published":"2020-01-23T00:00:00Z","doi":"10.7554/eLife.52067","date_created":"2020-02-16T23:00:50Z","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1},{"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,"author":[{"first_name":"Ana","last_name":"Latorre-Pellicer","full_name":"Latorre-Pellicer, Ana"},{"full_name":"Ascaso, Ángela","last_name":"Ascaso","first_name":"Ángela"},{"full_name":"Trujillano, Laura","last_name":"Trujillano","first_name":"Laura"},{"first_name":"Marta","full_name":"Gil-Salvador, Marta","last_name":"Gil-Salvador"},{"first_name":"Maria","last_name":"Arnedo","full_name":"Arnedo, Maria"},{"last_name":"Lucia-Campos","full_name":"Lucia-Campos, Cristina","first_name":"Cristina"},{"first_name":"Rebeca","full_name":"Antoñanzas-Pérez, Rebeca","last_name":"Antoñanzas-Pérez"},{"full_name":"Marcos-Alcalde, Iñigo","last_name":"Marcos-Alcalde","first_name":"Iñigo"},{"full_name":"Parenti, Ilaria","last_name":"Parenti","first_name":"Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425"},{"first_name":"Gloria","last_name":"Bueno-Lozano","full_name":"Bueno-Lozano, Gloria"},{"first_name":"Antonio","full_name":"Musio, Antonio","last_name":"Musio"},{"first_name":"Beatriz","last_name":"Puisac","full_name":"Puisac, Beatriz"},{"first_name":"Frank J.","full_name":"Kaiser, Frank J.","last_name":"Kaiser"},{"full_name":"Ramos, Feliciano J.","last_name":"Ramos","first_name":"Feliciano J."},{"full_name":"Gómez-Puertas, Paulino","last_name":"Gómez-Puertas","first_name":"Paulino"},{"full_name":"Pié, Juan","last_name":"Pié","first_name":"Juan"}],"article_processing_charge":"No","external_id":{"isi":["000522551606028"]},"title":"Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes","citation":{"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.","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","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","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).","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"1042","issue":"3","volume":21,"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:59Z","file_size":4271234,"creator":"dernst","date_created":"2020-02-18T07:49:22Z","file_name":"2020_IntMolecSciences_Latorre.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0e6658c4fe329d55d4d9bef01c5b15d0","file_id":"7496"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"02","intvolume":" 21","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"GaNo"}],"date_updated":"2023-08-18T06:35:41Z","ddc":["570"],"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":"7488"},{"status":"public","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)"},"conference":{"name":"ECAI: European Conference on Artificial Intelligence","start_date":"2020-08-29","end_date":"2020-09-08","location":"Santiago de Compostela, Spain"},"type":"conference","_id":"7505","file_date_updated":"2020-09-21T07:12:32Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-08-18T06:38:16Z","intvolume":" 325","month":"02","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"oa_version":"Published Version","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."}],"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":325,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8540","checksum":"80642fa0b6cd7da95dcd87d63789ad5e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_ECAI_Henzinger.pdf","date_created":"2020-09-21T07:12:32Z","creator":"dernst","file_size":1692214,"date_updated":"2020-09-21T07:12:32Z"}],"publication_status":"published","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"title":"Outside the box: Abstraction-based monitoring of neural networks","article_processing_charge":"No","external_id":{"isi":["000650971303002"],"arxiv":["1911.09032"]},"author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","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"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"T.A. Henzinger, A. Lukina, C. Schilling, in:, 24th European Conference on Artificial Intelligence, IOS Press, 2020, pp. 2433–2440.","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.","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","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."},"oa":1,"quality_controlled":"1","publisher":"IOS Press","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.","date_created":"2020-02-21T16:44:03Z","doi":"10.3233/FAIA200375","date_published":"2020-02-24T00:00:00Z","page":"2433-2440","publication":"24th European Conference on Artificial Intelligence","day":"24","year":"2020","has_accepted_license":"1","isi":1},{"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":"7508","department":[{"_id":"RoSe"}],"file_date_updated":"2020-11-20T09:26:46Z","date_updated":"2023-08-18T06:37:46Z","ddc":["510"],"scopus_import":"1","month":"02","intvolume":" 178","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."}],"oa_version":"Published Version","volume":178,"ec_funded":1,"publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"publication_status":"published","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"}],"language":[{"iso":"eng"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"author":[{"first_name":"Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","last_name":"Bossmann","orcid":"0000-0002-6854-1343","full_name":"Bossmann, Lea"},{"first_name":"Nataša","last_name":"Pavlović","full_name":"Pavlović, Nataša"},{"last_name":"Pickl","full_name":"Pickl, Peter","first_name":"Peter"},{"full_name":"Soffer, Avy","last_name":"Soffer","first_name":"Avy"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000516342200001"],"arxiv":["1905.06164"]},"title":"Higher order corrections to the mean-field description of the dynamics of interacting bosons","citation":{"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.","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.","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.","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","page":"1362-1396","date_published":"2020-02-21T00:00:00Z","doi":"10.1007/s10955-020-02500-8","date_created":"2020-02-23T09:45:51Z","isi":1,"has_accepted_license":"1","year":"2020","day":"21","publication":"Journal of Statistical Physics"},{"scopus_import":"1","intvolume":" 11","month":"02","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_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"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","checksum":"2c8d10475e1b0d397500760e28bdf561","file_id":"7517"}],"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":"7511","department":[{"_id":"FlSc"}],"file_date_updated":"2020-07-14T12:47:59Z","date_updated":"2023-08-18T06:36:41Z","ddc":["570"],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2020-02-23T23:00:35Z","date_published":"2020-02-13T00:00:00Z","doi":"10.1038/s41467-020-14535-2","year":"2020","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"13","article_number":"876","article_processing_charge":"No","external_id":{"isi":["000514928000017"]},"author":[{"first_name":"Beata","last_name":"Turoňová","full_name":"Turoňová, Beata"},{"last_name":"Hagen","full_name":"Hagen, Wim J.H.","first_name":"Wim J.H."},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Obr, Martin","orcid":"0000-0003-1756-6564","last_name":"Obr"},{"last_name":"Mosalaganti","full_name":"Mosalaganti, Shyamal","first_name":"Shyamal"},{"last_name":"Beugelink","full_name":"Beugelink, J. Wouter","first_name":"J. Wouter"},{"last_name":"Zimmerli","full_name":"Zimmerli, Christian E.","first_name":"Christian E."},{"last_name":"Kräusslich","full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg"},{"first_name":"Martin","last_name":"Beck","full_name":"Beck, Martin"}],"title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","citation":{"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","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","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.","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"},{"oa":1,"publisher":"Wiley","quality_controlled":"1","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).","date_created":"2020-02-18T10:02:25Z","date_published":"2020-09-01T00:00:00Z","doi":"10.1111/jipb.12905","page":"1433-1451","publication":"Journal of Integrative Plant Biology","day":"01","year":"2020","isi":1,"title":"Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid","article_processing_charge":"No","external_id":{"isi":["000515803000001"],"pmid":["31912615"]},"author":[{"full_name":"Han, L","last_name":"Han","first_name":"L"},{"full_name":"Zhou, X","last_name":"Zhou","first_name":"X"},{"first_name":"Y","full_name":"Zhao, Y","last_name":"Zhao"},{"first_name":"S","last_name":"Zhu","full_name":"Zhu, S"},{"last_name":"Wu","full_name":"Wu, L","first_name":"L"},{"full_name":"He, Y","last_name":"He","first_name":"Y"},{"full_name":"Ping, X","last_name":"Ping","first_name":"X"},{"full_name":"Lu, X","last_name":"Lu","first_name":"X"},{"full_name":"Huang, W","last_name":"Huang","first_name":"W"},{"first_name":"J","full_name":"Qian, J","last_name":"Qian"},{"first_name":"L","full_name":"Zhang, L","last_name":"Zhang"},{"last_name":"Jiang","full_name":"Jiang, X","first_name":"X"},{"full_name":"Zhu, D","last_name":"Zhu","first_name":"D"},{"last_name":"Luo","full_name":"Luo, C","first_name":"C"},{"last_name":"Li","full_name":"Li, S","first_name":"S"},{"first_name":"Q","full_name":"Dong, Q","last_name":"Dong"},{"first_name":"Q","full_name":"Fu, Q","last_name":"Fu"},{"first_name":"K","full_name":"Deng, K","last_name":"Deng"},{"full_name":"Wang, X","last_name":"Wang","first_name":"X"},{"last_name":"Wang","full_name":"Wang, L","first_name":"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"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhu, Y","last_name":"Zhu","first_name":"Y"},{"full_name":"He, X","last_name":"He","first_name":"X"},{"first_name":"Y","full_name":"Du, Y","last_name":"Du"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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","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."},"intvolume":" 62","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.12905"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"volume":62,"issue":"9","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"status":"public","article_type":"original","type":"journal_article","_id":"7497","department":[{"_id":"JiFr"}],"date_updated":"2023-08-18T06:44:16Z"},{"_id":"7534","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-18T06:44:46Z","department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1912.09270","open_access":"1"}],"scopus_import":"1","intvolume":" 5","month":"02","publication_status":"published","publication_identifier":{"issn":["2469-990X"]},"language":[{"iso":"eng"}],"volume":5,"issue":"2","article_number":"023903","citation":{"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.","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.","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.","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","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","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)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["1912.09270"],"isi":["000515065100001"]},"author":[{"last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"first_name":"Elena","last_name":"Marensi","full_name":"Marensi, Elena"},{"full_name":"Willis, Ashley P.","last_name":"Willis","first_name":"Ashley P."},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"title":"Upper edge of chaos and the energetics of transition in pipe flow","oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2020","isi":1,"publication":"Physical Review Fluids","day":"21","date_created":"2020-02-27T10:26:57Z","doi":"10.1103/physrevfluids.5.023903","date_published":"2020-02-21T00:00:00Z"},{"date_published":"2020-07-01T00:00:00Z","doi":"10.1016/j.jfa.2020.108507","date_created":"2020-02-23T23:00:36Z","isi":1,"year":"2020","day":"01","publication":"Journal of Functional Analysis","publisher":"Elsevier","quality_controlled":"1","oa":1,"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","author":[{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"},{"full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","last_name":"Nemish","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","first_name":"Yuriy"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.11340"],"isi":["000522798900001"]},"title":"Local laws for polynomials of Wigner matrices","citation":{"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.","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).","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","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","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.","ista":"Erdös L, Krüger TH, Nemish Y. 2020. Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. 278(12), 108507."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"article_number":"108507","issue":"12","volume":278,"ec_funded":1,"publication_identifier":{"eissn":["10960783"],"issn":["00221236"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11340"}],"month":"07","intvolume":" 278","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","department":[{"_id":"LaEr"}],"date_updated":"2023-08-18T06:36:10Z","type":"journal_article","article_type":"original","status":"public","_id":"7512"},{"author":[{"full_name":"Zhang, Haonan","last_name":"Zhang","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan"}],"external_id":{"arxiv":["1811.01205"],"isi":["000522798000001"]},"article_processing_charge":"No","title":"From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture","citation":{"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.","ista":"Zhang H. 2020. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. 365, 107053.","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.","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).","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"107053","date_published":"2020-05-13T00:00:00Z","doi":"10.1016/j.aim.2020.107053","date_created":"2020-02-23T21:43:50Z","isi":1,"year":"2020","day":"13","publication":"Advances in Mathematics","publisher":"Elsevier","quality_controlled":"1","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"}],"date_updated":"2023-08-18T06:37:09Z","ddc":["515"],"article_type":"original","type":"journal_article","status":"public","_id":"7509","volume":365,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1811.01205","open_access":"1"}],"month":"05","intvolume":" 365","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.","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.","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.","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","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."},"volume":105,"issue":"1","file":[{"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","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"799bfd297a008753a688b30d3958fa48","file_id":"7558"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","month":"01","intvolume":" 105","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:00Z","department":[{"_id":"MaDe"}],"ddc":["570"],"date_updated":"2023-08-18T06:46:23Z","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":"7546"},{"date_published":"2020-03-03T00:00:00Z","doi":"10.1063/1.5122969","date_created":"2020-03-04T08:06:25Z","day":"03","publication":"Chaos","isi":1,"year":"2020","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"title":"Inferring symbolic dynamics of chaotic flows from persistence","author":[{"last_name":"Yalniz","full_name":"Yalniz, Gökhan","orcid":"0000-0002-8490-9312","first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425"},{"orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1910.04584"],"isi":["000519254800002"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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).","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","ama":"Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 2020;30(3). doi:10.1063/1.5122969"},"article_number":"033109","issue":"3","volume":30,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"publication_status":"published","month":"03","intvolume":" 30","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1063/1.5122969","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"department":[{"_id":"BjHo"}],"date_updated":"2023-08-18T06:47:16Z","status":"public","type":"journal_article","article_type":"original","_id":"7563"},{"department":[{"_id":"HeEd"}],"date_updated":"2023-08-18T06:45:48Z","type":"journal_article","article_type":"original","status":"public","_id":"7554","ec_funded":1,"issue":"4","volume":64,"publication_status":"published","publication_identifier":{"eissn":["10957219"],"issn":["0040585X"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1705.08735","open_access":"1"}],"scopus_import":"1","intvolume":" 64","month":"02","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","external_id":{"isi":["000551393100007"],"arxiv":["1705.08735"]},"article_processing_charge":"No","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201"}],"title":"Weighted Poisson–Delaunay mosaics","citation":{"ista":"Edelsbrunner H, Nikitenko A. 2020. Weighted Poisson–Delaunay mosaics. Theory of Probability and its Applications. 64(4), 595–614.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.” Theory of Probability and Its Applications. SIAM, 2020. https://doi.org/10.1137/S0040585X97T989726.","short":"H. Edelsbrunner, A. Nikitenko, Theory of Probability and Its Applications 64 (2020) 595–614.","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.","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"page":"595-614","date_created":"2020-03-01T23:00:39Z","doi":"10.1137/S0040585X97T989726","date_published":"2020-02-13T00:00:00Z","year":"2020","isi":1,"publication":"Theory of Probability and its Applications","day":"13","oa":1,"publisher":"SIAM","quality_controlled":"1"},{"status":"public","article_type":"original","type":"journal_article","_id":"7540","department":[{"_id":"JiFr"}],"date_updated":"2023-08-18T06:45:15Z","intvolume":" 67","month":"02","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":" In vitro propagation of the ornamentally interesting species Wikstroemia gemmata is limited by the recalcitrance to form adventitious roots. In this article, two strategies to improve the rooting capacity of in vitro microcuttings are presented. Firstly, the effect of exogenous auxin was evaluated in both light and dark cultivated stem segments and also the sucrose-content of the medium was varied in order to determine better rooting conditions. Secondly, different spectral lights were evaluated and the effect on shoot growth and root induction demonstrated that the exact spectral composition of light is important for successful in vitro growth and development of Wikstroemia gemmata. We show that exogenous auxin cannot compensate for the poor rooting under unfavorable light conditions. Adapting the culture conditions is therefore paramount for successful industrial propagation of Wikstroemia gemmata. "}],"issue":"1-2","volume":67,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2223-8980"],"issn":["0792-9978"]},"title":"In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality","article_processing_charge":"No","external_id":{"isi":["000525343300004"]},"author":[{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten"},{"first_name":"H.","last_name":"Buyle","full_name":"Buyle, H."},{"last_name":"Werbrouck","full_name":"Werbrouck, S.","first_name":"S."},{"first_name":"M.C.","last_name":"Van Labeke","full_name":"Van Labeke, M.C."},{"first_name":"D.","full_name":"Geelen, D.","last_name":"Geelen"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Verstraeten I, Buyle H, Werbrouck S, Van Labeke MC, Geelen D. 2020. In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality. Israel Journal of Plant Sciences. 67(1–2), 16–26.","chicago":"Verstraeten, Inge, H. Buyle, S. Werbrouck, M.C. Van Labeke, and D. Geelen. “In Vitro Shoot Growth and Adventitious Rooting of Wikstroemia Gemmata Depends on Light Quality.” Israel Journal of Plant Sciences. Brill, 2020. https://doi.org/10.1163/22238980-20191110.","short":"I. Verstraeten, H. Buyle, S. Werbrouck, M.C. Van Labeke, D. Geelen, Israel Journal of Plant Sciences 67 (2020) 16–26.","ieee":"I. Verstraeten, H. Buyle, S. Werbrouck, M. C. Van Labeke, and D. Geelen, “In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality,” Israel Journal of Plant Sciences, vol. 67, no. 1–2. Brill, pp. 16–26, 2020.","apa":"Verstraeten, I., Buyle, H., Werbrouck, S., Van Labeke, M. C., & Geelen, D. (2020). In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality. Israel Journal of Plant Sciences. Brill. https://doi.org/10.1163/22238980-20191110","ama":"Verstraeten I, Buyle H, Werbrouck S, Van Labeke MC, Geelen D. In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality. Israel Journal of Plant Sciences. 2020;67(1-2):16-26. doi:10.1163/22238980-20191110","mla":"Verstraeten, Inge, et al. “In Vitro Shoot Growth and Adventitious Rooting of Wikstroemia Gemmata Depends on Light Quality.” Israel Journal of Plant Sciences, vol. 67, no. 1–2, Brill, 2020, pp. 16–26, doi:10.1163/22238980-20191110."},"publisher":"Brill","quality_controlled":"1","date_created":"2020-02-28T09:18:01Z","date_published":"2020-02-01T00:00:00Z","doi":"10.1163/22238980-20191110","page":"16-26","publication":"Israel Journal of Plant Sciences","day":"01","year":"2020","isi":1},{"publisher":"Public Library of Science","month":"02","oa_version":"Published Version","date_created":"2021-08-06T07:24:37Z","related_material":{"record":[{"id":"7569","status":"public","relation":"research_data"}]},"date_published":"2020-02-25T00:00:00Z","doi":"10.1371/journal.pcbi.1007642.s003","year":"2020","day":"25","type":"research_data_reference","status":"public","_id":"9779","article_processing_charge":"No","author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","last_name":"Grah"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"department":[{"_id":"GaTk"}],"title":"Distribution of crosstalk values","citation":{"ama":"Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003","apa":"Grah, R., & Friedlander, T. (2020). Distribution of crosstalk values. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s003","ieee":"R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020.","short":"R. Grah, T. Friedlander, (2020).","mla":"Grah, Rok, and Tamar Friedlander. Distribution of Crosstalk Values. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s003.","ista":"Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library of Science, 10.1371/journal.pcbi.1007642.s003.","chicago":"Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s003."},"date_updated":"2023-08-18T06:47:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Grah R, Friedlander T. 2020. Supporting information, Public Library of Science, 10.1371/journal.pcbi.1007642.s001.","chicago":"Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s001.","ama":"Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001","apa":"Grah, R., & Friedlander, T. (2020). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s001","short":"R. Grah, T. Friedlander, (2020).","ieee":"R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020.","mla":"Grah, Rok, and Tamar Friedlander. Supporting Information. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s001."},"date_updated":"2023-08-18T06:47:47Z","title":"Supporting information","department":[{"_id":"GaTk"}],"author":[{"orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"article_processing_charge":"No","_id":"9776","status":"public","type":"research_data_reference","day":"25","year":"2020","date_published":"2020-02-25T00:00:00Z","doi":"10.1371/journal.pcbi.1007642.s001","related_material":{"record":[{"relation":"used_in_publication","id":"7569","status":"public"}]},"date_created":"2021-08-06T07:15:04Z","oa_version":"Published Version","month":"02","publisher":"Public Library of Science"},{"oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2020-03-08T18:02:01Z","doi":"10.1103/physrevx.10.011055","date_published":"2020-03-04T00:00:00Z","publication":"Physical Review X","day":"04","year":"2020","isi":1,"has_accepted_license":"1","article_number":"011055","title":"Slow quantum thermalization and many-body revivals from mixed phase space","article_processing_charge":"No","external_id":{"arxiv":["1905.08564"],"isi":["000517969300001"]},"author":[{"last_name":"Michailidis","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"C. J.","last_name":"Turner","full_name":"Turner, C. J."},{"first_name":"Z.","last_name":"Papić","full_name":"Papić, Z."},{"last_name":"Abanin","full_name":"Abanin, D. A.","first_name":"D. A."},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"A. Michailidis, C.J. Turner, Z. Papić, D.A. Abanin, M. Serbyn, Physical Review X 10 (2020).","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.","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.","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.","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."},"intvolume":" 10","month":"03","scopus_import":"1","oa_version":"Published Version","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."}],"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"}]},"language":[{"iso":"eng"}],"file":[{"file_id":"7581","checksum":"4b3f2c13873d35230173c73d0e11c408","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PhysicalReviewX_Michailidis.pdf","date_created":"2020-03-12T12:13:07Z","creator":"dernst","file_size":17828638,"date_updated":"2020-07-14T12:48:00Z"}],"publication_status":"published","publication_identifier":{"issn":["2160-3308"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"7570","file_date_updated":"2020-07-14T12:48:00Z","department":[{"_id":"MaSe"}],"ddc":["530"],"date_updated":"2023-08-18T07:01:07Z"},{"date_updated":"2023-08-18T07:07:08Z","ddc":["580"],"file_date_updated":"2020-07-14T12:48:00Z","department":[{"_id":"JiFr"}],"_id":"7582","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":["22237747"]},"publication_status":"published","file":[{"date_created":"2020-03-23T13:37:00Z","file_name":"2020_Plants_Moturu.pdf","date_updated":"2020-07-14T12:48:00Z","file_size":2373484,"creator":"dernst","checksum":"6d5af3e17266a48996b4af4e67e88a85","file_id":"7614","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":9,"issue":"3","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 9","citation":{"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.","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).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Taraka Ramji","last_name":"Moturu","full_name":"Moturu, Taraka Ramji"},{"first_name":"Sansrity","last_name":"Sinha","full_name":"Sinha, Sansrity"},{"first_name":"Hymavathi","last_name":"Salava","full_name":"Salava, Hymavathi"},{"first_name":"Sravankumar","last_name":"Thula","full_name":"Thula, Sravankumar"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","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","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Simon","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"}],"article_processing_charge":"No","external_id":{"isi":["000525315000035"],"pmid":["32121542"]},"title":"Molecular evolution and diversification of proteins involved in miRNA maturation pathway","article_number":"299","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Plants","date_published":"2020-03-01T00:00:00Z","doi":"10.3390/plants9030299","date_created":"2020-03-15T23:00:52Z","publisher":"MDPI","quality_controlled":"1","oa":1},{"volume":9,"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","file":[{"creator":"dernst","file_size":15089438,"date_updated":"2020-09-24T07:03:20Z","file_name":"2020_elife_Moon.pdf","date_created":"2020-09-24T07:03:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8567","checksum":"396ceb2dd10b102ef4e699666b9342c3"}],"language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/751958"}],"month":"03","intvolume":" 9","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"SiHi"}],"file_date_updated":"2020-09-24T07:03:20Z","date_updated":"2023-08-18T07:06:31Z","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":"7593","date_published":"2020-03-11T00:00:00Z","doi":"10.7554/elife.51512","date_created":"2020-03-20T13:16:41Z","isi":1,"has_accepted_license":"1","year":"2020","day":"11","publication":"eLife","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"author":[{"first_name":"Hyang Mi","last_name":"Moon","full_name":"Moon, Hyang Mi"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"},{"last_name":"Wynshaw-Boris","full_name":"Wynshaw-Boris, Anthony","first_name":"Anthony"}],"article_processing_charge":"No","external_id":{"isi":["000522835800001"],"pmid":["32159512"]},"title":"LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility","citation":{"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.","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","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","short":"H.M. Moon, S. Hippenmeyer, L. Luo, A. Wynshaw-Boris, ELife 9 (2020).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"51512"},{"title":"The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis","external_id":{"isi":["000531787500006"],"pmid":["32393881"]},"article_processing_charge":"No","author":[{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","last_name":"Zhang","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"last_name":"Kong","full_name":"Kong, Wei","first_name":"Wei"},{"last_name":"Yang","full_name":"Yang, Xiao-Li","first_name":"Xiao-Li"},{"full_name":"Molnar, Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely"},{"full_name":"Vondráková, Zuzana","last_name":"Vondráková","first_name":"Zuzana"},{"full_name":"Filepová, Roberta","last_name":"Filepová","first_name":"Roberta"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xue, Hong-Wei","last_name":"Xue","first_name":"Hong-Wei"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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.","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."},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"name":"Long Term Fellowship","grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-03-21T16:34:16Z","date_published":"2020-05-01T00:00:00Z","doi":"10.1038/s41477-020-0648-9","page":"556-569","publication":"Nature Plants","day":"01","year":"2020","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","department":[{"_id":"JiFr"}],"date_updated":"2023-08-18T07:05:57Z","status":"public","type":"journal_article","article_type":"original","_id":"7600","ec_funded":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41477-020-0719-y","relation":"erratum"}]},"volume":6,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["20550278"]},"intvolume":" 6","month":"05","main_file_link":[{"url":"https://doi.org/10.1101/755504","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Preprint","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","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."}]},{"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:48:01Z","date_updated":"2023-08-18T07:05:18Z","ddc":["580"],"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":"7603","volume":11,"publication_status":"published","publication_identifier":{"eissn":["1664462X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"57c37209f7b6712ced86c0f11b2be74e","file_id":"7607","date_updated":"2020-07-14T12:48:01Z","file_size":507414,"creator":"dernst","date_created":"2020-03-23T09:03:40Z","file_name":"2020_FrontiersPlants_Nimeth.pdf"}],"scopus_import":"1","intvolume":" 11","month":"02","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."}],"oa_version":"Published Version","external_id":{"isi":["000518903600001"]},"article_processing_charge":"No","author":[{"full_name":"Nimeth, Barbara Anna","last_name":"Nimeth","first_name":"Barbara Anna"},{"first_name":"Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","last_name":"Riegler","orcid":"0000-0003-3413-1343","full_name":"Riegler, Stefan"},{"full_name":"Kalyna, Maria","last_name":"Kalyna","first_name":"Maria"}],"title":"Alternative splicing and DNA damage response in plants","citation":{"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).","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","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","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.","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"91","date_created":"2020-03-22T23:00:46Z","doi":"10.3389/fpls.2020.00091","date_published":"2020-02-19T00:00:00Z","year":"2020","has_accepted_license":"1","isi":1,"publication":"Frontiers in Plant Science","day":"19","oa":1,"quality_controlled":"1","publisher":"Frontiers"},{"has_accepted_license":"1","isi":1,"year":"2020","day":"02","publication":"EMBO Journal","doi":"10.15252/embj.2019103358","date_published":"2020-03-02T00:00:00Z","date_created":"2020-03-15T23:00:55Z","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.","publisher":"EMBO Press","quality_controlled":"1","oa":1,"citation":{"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.","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.","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Stefanie","full_name":"Weinert, Stefanie","last_name":"Weinert"},{"first_name":"Niclas","full_name":"Gimber, Niclas","last_name":"Gimber"},{"first_name":"Dorothea","last_name":"Deuschel","full_name":"Deuschel, Dorothea"},{"last_name":"Stuhlmann","full_name":"Stuhlmann, Till","first_name":"Till"},{"first_name":"Dmytro","full_name":"Puchkov, Dmytro","last_name":"Puchkov"},{"full_name":"Farsi, Zohreh","last_name":"Farsi","first_name":"Zohreh"},{"first_name":"Carmen F.","full_name":"Ludwig, Carmen F.","last_name":"Ludwig"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"López-Cayuqueo","full_name":"López-Cayuqueo, Karen I.","first_name":"Karen I."},{"last_name":"Planells-Cases","full_name":"Planells-Cases, Rosa","first_name":"Rosa"},{"first_name":"Thomas J.","last_name":"Jentsch","full_name":"Jentsch, Thomas J."}],"article_processing_charge":"No","external_id":{"isi":["000517335000001"],"pmid":["32118314"]},"title":"Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration","article_number":"e103358","publication_identifier":{"issn":["02614189"],"eissn":["14602075"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"82750a7a93e3740decbce8474004111a","file_id":"7615","date_updated":"2020-07-14T12:48:00Z","file_size":12243278,"creator":"dernst","date_created":"2020-03-23T13:51:11Z","file_name":"2020_EMBO_Weinert.pdf"}],"language":[{"iso":"eng"}],"volume":39,"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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 39","date_updated":"2023-08-18T07:07:36Z","ddc":["570"],"department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:48:00Z","_id":"7586","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public"},{"date_updated":"2023-08-18T10:17:26Z","department":[{"_id":"LaEr"}],"_id":"7618","status":"public","type":"journal_article","article_type":"original","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"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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."},"title":"Quantum Hellinger distances revisited","author":[{"first_name":"Jozsef","last_name":"Pitrik","full_name":"Pitrik, Jozsef"},{"full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511","last_name":"Virosztek","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000551556000002"],"arxiv":["1903.10455"]},"article_processing_charge":"No","project":[{"_id":"26A455A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"846294","name":"Geometric study of Wasserstein spaces and free probability"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"day":"01","publication":"Letters in Mathematical Physics","isi":1,"year":"2020","doi":"10.1007/s11005-020-01282-0","date_published":"2020-08-01T00:00:00Z","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},{"_id":"7632","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"],"date_updated":"2023-08-18T10:25:13Z","department":[{"_id":"SaSi"}],"file_date_updated":"2020-07-14T12:48:01Z","oa_version":"Published Version","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"}],"month":"03","intvolume":" 10","scopus_import":"1","file":[{"checksum":"e6cfaaaf7986532132934400038b824a","file_id":"7644","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-04-06T10:44:23Z","file_name":"2020_ScientificReports_Tombaz.pdf","date_updated":"2020-07-14T12:48:01Z","file_size":2621249,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20452322"]},"publication_status":"published","issue":"1","volume":10,"article_number":"5559","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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."},"title":"Action representation in the mouse parieto-frontal network","author":[{"full_name":"Tombaz, Tuce","last_name":"Tombaz","first_name":"Tuce"},{"first_name":"Benjamin A.","last_name":"Dunn","full_name":"Dunn, Benjamin A."},{"last_name":"Hovde","full_name":"Hovde, Karoline","first_name":"Karoline"},{"last_name":"Cubero","full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J"},{"full_name":"Mimica, Bartul","last_name":"Mimica","first_name":"Bartul"},{"full_name":"Mamidanna, Pranav","last_name":"Mamidanna","first_name":"Pranav"},{"last_name":"Roudi","full_name":"Roudi, Yasser","first_name":"Yasser"},{"full_name":"Whitlock, Jonathan R.","last_name":"Whitlock","first_name":"Jonathan R."}],"external_id":{"isi":["000560406800007"]},"article_processing_charge":"No","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"27","publication":"Scientific reports","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1038/s41598-020-62089-6","date_published":"2020-03-27T00:00:00Z","date_created":"2020-04-05T22:00:47Z"},{"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)"},"article_type":"original","type":"journal_article","_id":"7622","volume":41,"issue":"3","language":[{"iso":"eng"}],"file":[{"file_id":"7641","checksum":"47dda164e33b6c0c6c3ed14aad298376","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_EuropJourPhysics_Plesch.pdf","date_created":"2020-04-06T08:53:53Z","file_size":1533672,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["13616404"],"issn":["01430807"]},"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."}],"title":"The IYPT and the 'Ring Oiler' problem","article_processing_charge":"No","external_id":{"isi":["000537425400001"],"arxiv":["1910.03290"]},"author":[{"first_name":"Martin","last_name":"Plesch","full_name":"Plesch, Martin"},{"first_name":"Samuel","last_name":"Plesník","full_name":"Plesník, Samuel"},{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","first_name":"Natalia","last_name":"Ruzickova","full_name":"Ruzickova, Natalia"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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).","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","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","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.","ista":"Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001."},"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,"quality_controlled":"1","publisher":"IOP Publishing"},{"issue":"3","volume":14,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1936-086X"]},"publication_status":"published","month":"03","intvolume":" 14","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Assemblies of colloidal semiconductor nanocrystals (NCs) in the form of thin solid films leverage the size-dependent quantum confinement properties and the wet chemical methods vital for the development of the emerging solution-processable electronics, photonics, and optoelectronics technologies. The ability to control the charge carrier transport in the colloidal NC assemblies is fundamental for altering their electronic and optical properties for the desired applications. Here we demonstrate a strategy to render the solids of narrow-bandgap NC assemblies exclusively electron-transporting by creating a type-II heterojunction via shelling. Electronic transport of molecularly cross-linked PbTe@PbS core@shell NC assemblies is measured using both a conventional solid gate transistor and an electric-double-layer transistor, as well as compared with those of core-only PbTe NCs. In contrast to the ambipolar characteristics demonstrated by many narrow-bandgap NCs, the core@shell NCs exhibit exclusive n-type transport, i.e., drastically suppressed contribution of holes to the overall transport. The PbS shell that forms a type-II heterojunction assists the selective carrier transport by heavy doping of electrons into the PbTe-core conduction level and simultaneously strongly localizes the holes within the NC core valence level. This strongly enhanced n-type transport makes these core@shell NCs suitable for applications where ambipolar characteristics should be actively suppressed, in particular, for thermoelectric and electron-transporting layers in photovoltaic devices."}],"department":[{"_id":"MaIb"}],"date_updated":"2023-08-18T10:25:40Z","status":"public","type":"journal_article","article_type":"original","_id":"7634","doi":"10.1021/acsnano.9b08687","date_published":"2020-03-24T00:00:00Z","date_created":"2020-04-05T22:00:48Z","page":"3242-3250","day":"24","publication":"ACS Nano","isi":1,"year":"2020","publisher":"American Chemical Society","quality_controlled":"1","acknowledgement":"This work is partly supported by Grants-in-Aid for Scientific Research by Young Scientist A (KAKENHI Wakate-A) No. JP17H04802, Grants-in-Aid for Scientific Research No. JP19H05602 from the Japan Society for the Promotion of Science, and RIKEN Incentive Research Grant (Shoreikadai) 2016. M.V.K. and M.I. acknowledge financial support from the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID, GA No. 306733) and ETH Zurich via ETH career seed grant (SEED-18 16-2). Support from Cambridge Display Technology, Ltd., and Sumitomo Chemical Company is also acknowledged. We thank Mrs. T. Kikitsu and Dr. D. Hashizume (RIKEN-CEMS) for access to the transmission electron microscope facility.","title":"Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies","author":[{"last_name":"Miranti","full_name":"Miranti, Retno","first_name":"Retno"},{"last_name":"Shin","full_name":"Shin, Daiki","first_name":"Daiki"},{"first_name":"Ricky Dwi","full_name":"Septianto, Ricky Dwi","last_name":"Septianto"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kovalenko","full_name":"Kovalenko, Maksym V.","first_name":"Maksym V."},{"full_name":"Matsushita, Nobuhiro","last_name":"Matsushita","first_name":"Nobuhiro"},{"last_name":"Iwasa","full_name":"Iwasa, Yoshihiro","first_name":"Yoshihiro"},{"full_name":"Bisri, Satria Zulkarnaen","last_name":"Bisri","first_name":"Satria Zulkarnaen"}],"external_id":{"pmid":["32073817"],"isi":["000526301400057"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Miranti, R., Shin, D., Septianto, R. D., Ibáñez, M., Kovalenko, M. V., Matsushita, N., … Bisri, S. Z. (2020). Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.9b08687","ama":"Miranti R, Shin D, Septianto RD, et al. Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies. ACS Nano. 2020;14(3):3242-3250. doi:10.1021/acsnano.9b08687","short":"R. Miranti, D. Shin, R.D. Septianto, M. Ibáñez, M.V. Kovalenko, N. Matsushita, Y. Iwasa, S.Z. Bisri, ACS Nano 14 (2020) 3242–3250.","ieee":"R. Miranti et al., “Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies,” ACS Nano, vol. 14, no. 3. American Chemical Society, pp. 3242–3250, 2020.","mla":"Miranti, Retno, et al. “Exclusive Electron Transport in Core@Shell PbTe@PbS Colloidal Semiconductor Nanocrystal Assemblies.” ACS Nano, vol. 14, no. 3, American Chemical Society, 2020, pp. 3242–50, doi:10.1021/acsnano.9b08687.","ista":"Miranti R, Shin D, Septianto RD, Ibáñez M, Kovalenko MV, Matsushita N, Iwasa Y, Bisri SZ. 2020. Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies. ACS Nano. 14(3), 3242–3250.","chicago":"Miranti, Retno, Daiki Shin, Ricky Dwi Septianto, Maria Ibáñez, Maksym V. Kovalenko, Nobuhiro Matsushita, Yoshihiro Iwasa, and Satria Zulkarnaen Bisri. “Exclusive Electron Transport in Core@Shell PbTe@PbS Colloidal Semiconductor Nanocrystal Assemblies.” ACS Nano. American Chemical Society, 2020. https://doi.org/10.1021/acsnano.9b08687."}},{"_id":"7623","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-18T10:18:56Z","department":[{"_id":"MiSi"}],"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"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.09426"}],"month":"03","intvolume":" 30","publication_identifier":{"issn":["02182025"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":30,"issue":"3","project":[{"_id":"25AD6156-B435-11E9-9278-68D0E5697425","name":"Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments","grant_number":"LS13-029"}],"citation":{"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.","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.","short":"G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, M.K. Sixt, Mathematical Models and Methods in Applied Sciences 30 (2020) 513–537.","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Jankowiak, Gaspard","last_name":"Jankowiak","first_name":"Gaspard"},{"full_name":"Peurichard, Diane","last_name":"Peurichard","first_name":"Diane"},{"first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne"},{"last_name":"Schmeiser","full_name":"Schmeiser, Christian","first_name":"Christian"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"external_id":{"isi":["000525349900003"],"arxiv":["1903.09426"]},"article_processing_charge":"No","title":"Modeling adhesion-independent cell migration","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,"isi":1,"year":"2020","day":"18","publication":"Mathematical Models and Methods in Applied Sciences","page":"513-537","doi":"10.1142/S021820252050013X","date_published":"2020-03-18T00:00:00Z","date_created":"2020-03-31T11:25:05Z"},{"volume":71,"issue":"14","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-10-06T07:41:35Z","file_size":1916031,"date_created":"2020-10-06T07:41:35Z","file_name":"2020_JourExperimBotany_Lee.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"b06aaaa93dc41896da805fe4b75cf3a1","file_id":"8613","success":1}],"language":[{"iso":"eng"}],"month":"07","intvolume":" 71","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2020-10-06T07:41:35Z","department":[{"_id":"JiFr"}],"date_updated":"2023-08-18T10:27:52Z","ddc":["580"],"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":"7646","page":"3986–3998","doi":"10.1093/jxb/eraa138","date_published":"2020-07-06T00:00:00Z","date_created":"2020-04-06T10:57:08Z","has_accepted_license":"1","isi":1,"year":"2020","day":"06","publication":"Journal of Experimental Botany","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"author":[{"first_name":"E","full_name":"Lee, E","last_name":"Lee"},{"last_name":"Vila Nova Santana","full_name":"Vila Nova Santana, B","first_name":"B"},{"last_name":"Samuels","full_name":"Samuels, E","first_name":"E"},{"first_name":"F","full_name":"Benitez-Fuente, F","last_name":"Benitez-Fuente"},{"first_name":"E","full_name":"Corsi, E","last_name":"Corsi"},{"first_name":"MA","last_name":"Botella","full_name":"Botella, MA"},{"last_name":"Perez-Sancho","full_name":"Perez-Sancho, J","first_name":"J"},{"first_name":"S","full_name":"Vanneste, S","last_name":"Vanneste"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"A","full_name":"Macho, A","last_name":"Macho"},{"first_name":"A","full_name":"Alves Azevedo, A","last_name":"Alves Azevedo"},{"first_name":"A","full_name":"Rosado, A","last_name":"Rosado"}],"external_id":{"pmid":["32179893"],"isi":["000553125400007"]},"article_processing_charge":"No","title":"Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis","citation":{"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.","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.","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_number":"20","citation":{"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.","short":"M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).","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.","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","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.","ista":"Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 14, 20."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000525543200001"],"pmid":["32231528"]},"article_processing_charge":"No","author":[{"first_name":"Michael J.","full_name":"Berry, Michael J.","last_name":"Berry"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"title":"Clustering of neural activity: A design principle for population codes","oa":1,"publisher":"Frontiers","quality_controlled":"1","year":"2020","has_accepted_license":"1","isi":1,"publication":"Frontiers in Computational Neuroscience","day":"13","date_created":"2020-04-12T22:00:40Z","doi":"10.3389/fncom.2020.00020","date_published":"2020-03-13T00:00:00Z","_id":"7656","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":"2023-08-18T10:30:11Z","ddc":["570"],"file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"GaTk"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 14","month":"03","publication_status":"published","publication_identifier":{"eissn":["16625188"]},"language":[{"iso":"eng"}],"file":[{"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","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"2b1da23823eae9cedbb42d701945b61e","file_id":"7659"}],"volume":14},{"publication":"Journal of Statistical Mechanics: Theory and Experiment","day":"22","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-04-05T22:00:50Z","doi":"10.1088/1742-5468/ab6093","date_published":"2020-01-22T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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.","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.","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."},"title":"Non-equilibrium quantum spin dynamics from classical stochastic processes","external_id":{"arxiv":["1909.13142"],"isi":["000520187500001"]},"article_processing_charge":"No","author":[{"last_name":"De Nicola","full_name":"De Nicola, Stefano","orcid":"0000-0002-4842-6671","first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Doyon","full_name":"Doyon, B.","first_name":"B."},{"first_name":"M. J.","last_name":"Bhaseen","full_name":"Bhaseen, M. J."}],"article_number":"013106","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7648","checksum":"4030e683c15d30b7b4794ec7dc1b6537","file_size":3159026,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_name":"2020_JournStatisticalMech_DeNicola.pdf","date_created":"2020-04-06T13:15:49Z"}],"publication_status":"published","publication_identifier":{"eissn":["17425468"]},"ec_funded":1,"issue":"1","volume":2020,"oa_version":"Published Version","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."}],"intvolume":" 2020","month":"01","scopus_import":"1","ddc":["530"],"date_updated":"2023-08-18T10:27:15Z","file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"MaSe"}],"_id":"7638","status":"public","type":"journal_article","article_type":"original"},{"external_id":{"arxiv":["1811.06448"],"isi":["000508175400001"]},"article_processing_charge":"No","author":[{"full_name":"Cornalba, Federico","orcid":"0000-0002-6269-5149","last_name":"Cornalba","id":"2CEB641C-A400-11E9-A717-D712E6697425","first_name":"Federico"},{"last_name":"Shardlow","full_name":"Shardlow, Tony","first_name":"Tony"},{"full_name":"Zimmer, Johannes","last_name":"Zimmer","first_name":"Johannes"}],"title":"From weakly interacting particles to a regularised Dean-Kawasaki model","citation":{"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.","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","page":"864-891","date_created":"2020-04-05T22:00:49Z","date_published":"2020-01-10T00:00:00Z","doi":"10.1088/1361-6544/ab5174","year":"2020","isi":1,"publication":"Nonlinearity","day":"10","type":"journal_article","article_type":"original","status":"public","_id":"7637","department":[{"_id":"JuFi"}],"date_updated":"2023-08-18T10:26:07Z","main_file_link":[{"url":"https://arxiv.org/abs/1811.06448","open_access":"1"}],"scopus_import":"1","intvolume":" 33","month":"01","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","issue":"2","volume":33,"publication_status":"published","publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"language":[{"iso":"eng"}]},{"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,"volume":21,"issue":"7","publication_identifier":{"eissn":["14220067"]},"publication_status":"published","file":[{"file_id":"7669","checksum":"b9d2f1657d8c4a74b01a62b474d009b0","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_JournMolecSciences_Martin_Belmonte.pdf","date_created":"2020-04-20T11:43:18Z","file_size":2941197,"date_updated":"2020-07-14T12:48:01Z","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":"7664","file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"RySh"}],"date_updated":"2023-08-21T06:13:19Z","ddc":["570"],"quality_controlled":"1","publisher":"MDPI","oa":1,"date_published":"2020-04-02T00:00:00Z","doi":"10.3390/ijms21072459","date_created":"2020-04-19T22:00:55Z","has_accepted_license":"1","isi":1,"year":"2020","day":"02","publication":"International journal of molecular sciences","article_number":"2459","author":[{"first_name":"Alejandro","last_name":"Martín-Belmonte","full_name":"Martín-Belmonte, Alejandro"},{"first_name":"Carolina","last_name":"Aguado","full_name":"Aguado, Carolina"},{"full_name":"Alfaro-Ruíz, Rocío","last_name":"Alfaro-Ruíz","first_name":"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","full_name":"Martínez-Hernández, José","last_name":"Martínez-Hernández"},{"full_name":"Buisson, Alain","last_name":"Buisson","first_name":"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":{"pmid":["32252271"],"isi":["000535574200201"]},"title":"Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease","citation":{"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.","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","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).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa":1,"quality_controlled":"1","publisher":"Frontiers Media","publication":"Frontiers in Cellular Neuroscience","day":"19","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-04-19T22:00:55Z","date_published":"2020-03-19T00:00:00Z","doi":"10.3389/fncel.2020.00063","article_number":"63","project":[{"name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","grant_number":"793482","_id":"2659CC84-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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","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","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.","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.","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."},"title":"Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions","external_id":{"isi":["000525582200001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Eguchi","orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velicky","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"first_name":"Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87","last_name":"Hollergschwandtner","full_name":"Hollergschwandtner, Elena"},{"last_name":"Itakura","full_name":"Itakura, Makoto","first_name":"Makoto"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"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"}],"intvolume":" 14","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:01Z","file_size":9227283,"date_created":"2020-04-20T10:59:49Z","file_name":"2020_FrontiersCellularNeurosc_Eguchi.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1c145123c6f8dc3e2e4bd5a66a1ad60e","file_id":"7668"}],"publication_status":"published","publication_identifier":{"issn":["16625102"]},"ec_funded":1,"volume":14,"_id":"7665","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":"2023-08-21T06:12:48Z","department":[{"_id":"JoDa"},{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:48:01Z"},{"quality_controlled":"1","publisher":"American Chemical Society","oa":1,"doi":"10.1021/acs.nanolett.0c00205","date_published":"2020-04-08T00:00:00Z","date_created":"2020-04-19T22:00:54Z","page":"2647-2653","day":"08","publication":"Nano Letters","has_accepted_license":"1","isi":1,"year":"2020","title":"Wood deformation leads to rearrangement of molecules at the nanoscale","author":[{"last_name":"Felhofer","full_name":"Felhofer, Martin","first_name":"Martin"},{"last_name":"Bock","full_name":"Bock, Peter","first_name":"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","last_name":"Zirbs","full_name":"Zirbs, Ronald"},{"first_name":"Notburga","last_name":"Gierlinger","full_name":"Gierlinger, Notburga"}],"external_id":{"isi":["000526413400055"],"pmid":["32196350"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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.","short":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger, Nano Letters 20 (2020) 2647–2653.","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","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"},"month":"04","intvolume":" 20","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","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."}],"volume":20,"issue":"4","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"fe46146a9c4c620592a1932a8599069e","file_id":"7667","creator":"dernst","date_updated":"2020-07-14T12:48:01Z","file_size":7108014,"date_created":"2020-04-20T10:43:36Z","file_name":"2020_NanoLetters_Felhofer.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15306992"]},"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":"7663","department":[{"_id":"MaLo"}],"file_date_updated":"2020-07-14T12:48:01Z","ddc":["530"],"date_updated":"2023-08-21T06:12:09Z"}]