[{"file_date_updated":"2020-07-14T12:47:46Z","date_updated":"2023-08-17T14:01:16Z","date_created":"2019-10-17T13:38:20Z","volume":128,"author":[{"full_name":"Henderson, Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","orcid":"0000-0002-5198-7445","first_name":"Paul M","last_name":"Henderson"},{"full_name":"Ferrari, Vittorio","last_name":"Ferrari","first_name":"Vittorio"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ChLa"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","year":"2020","month":"04","publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]},"language":[{"iso":"eng"}],"doi":"10.1007/s11263-019-01219-8","quality_controlled":"1","isi":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491042100002"],"arxiv":["1901.06447"]},"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."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2019_CompVision_Henderson.pdf","file_size":2243134,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6973","checksum":"a0f05dd4f5f64e4f713d8d9d4b5b1e3f","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-10-25T10:28:29Z"}],"oa_version":"Published Version","ddc":["004"],"status":"public","title":"Learning single-image 3D reconstruction by generative modelling of shape, pose and shading","intvolume":" 128","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6952","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2020-04-01T00:00:00Z","article_type":"original","page":"835-854","publication":"International Journal of Computer Vision","citation":{"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.","short":"P.M. Henderson, V. Ferrari, International Journal of Computer Vision 128 (2020) 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.","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","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.","ieee":"P. M. Henderson and V. Ferrari, “Learning single-image 3D reconstruction by generative modelling of shape, pose and shading,” International Journal of Computer Vision, vol. 128. Springer Nature, pp. 835–854, 2020.","apa":"Henderson, P. M., & Ferrari, V. (2020). Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01219-8"}},{"date_published":"2020-02-01T00:00:00Z","article_type":"original","page":"1070–1084","publication":"Molecular Neurobiology","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.","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.","apa":"Donahue, R., Maes, M. E., Grosser, J., & Nickells, R. (2020). BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. Springer Nature. https://doi.org/10.1007/s12035-019-01783-7","ama":"Donahue R, Maes ME, Grosser J, Nickells R. BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. 2020;57(2):1070–1084. doi:10.1007/s12035-019-01783-7","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.","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.","short":"R. Donahue, M.E. Maes, J. Grosser, R. Nickells, Molecular Neurobiology 57 (2020) 1070–1084."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","title":"BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage","status":"public","intvolume":" 57","_id":"7033","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality."}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s12035-019-01783-7","quality_controlled":"1","isi":1,"oa":1,"external_id":{"pmid":["31673950"],"isi":["000493754200001"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035206/"}],"month":"02","publication_identifier":{"issn":["0893-7648"],"eissn":["1559-1182"]},"date_updated":"2023-08-17T14:05:48Z","date_created":"2019-11-18T14:18:39Z","volume":57,"author":[{"full_name":"Donahue, RJ","first_name":"RJ","last_name":"Donahue"},{"full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","first_name":"Margaret E","last_name":"Maes"},{"last_name":"Grosser","first_name":"JA","full_name":"Grosser, JA"},{"full_name":"Nickells, RW","last_name":"Nickells","first_name":"RW"}],"publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Springer Nature","year":"2020","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).","pmid":1},{"file":[{"date_updated":"2020-11-18T16:42:48Z","date_created":"2020-11-18T16:42:48Z","success":1,"checksum":"cd42ffdb381fd52812b9583d4d407139","file_id":"8772","relation":"main_file","creator":"dernst","file_size":717345,"content_type":"application/pdf","file_name":"2020_NewPhytologist_Zhang.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6997","title":"Auxin guides roots to avoid obstacles during gravitropic growth","status":"public","ddc":["580"],"intvolume":" 225","issue":"3","type":"journal_article","date_published":"2020-02-01T00:00:00Z","publication":"New Phytologist","citation":{"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.","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","ista":"Zhang Y, Friml J. 2020. Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. 225(3), 1049–1052.","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","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.","short":"Y. Zhang, J. Friml, New Phytologist 225 (2020) 1049–1052.","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."},"article_type":"original","page":"1049-1052","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","author":[{"first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"date_updated":"2023-08-17T14:01:49Z","date_created":"2019-11-12T11:41:32Z","volume":225,"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","file_date_updated":"2020-11-18T16:42:48Z","ec_funded":1,"doi":"10.1111/nph.16203","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000489638800001"],"pmid":["31603260"]},"quality_controlled":"1","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"month":"02","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]}},{"quality_controlled":"1","isi":1,"project":[{"grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1810.10402","open_access":"1"}],"external_id":{"arxiv":["1810.10402"],"isi":["000536255500004"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00220-019-03575-5","month":"06","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"TaHa"}],"year":"2020","date_updated":"2023-08-17T14:02:59Z","date_created":"2019-11-12T14:01:27Z","volume":376,"author":[{"last_name":"Rapcak","first_name":"Miroslav","full_name":"Rapcak, Miroslav"},{"full_name":"Soibelman, Yan","last_name":"Soibelman","first_name":"Yan"},{"full_name":"Yang, Yaping","first_name":"Yaping","last_name":"Yang"},{"id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang","last_name":"Zhao","full_name":"Zhao, Gufang"}],"ec_funded":1,"article_type":"original","page":"1803-1873","publication":"Communications in Mathematical Physics","citation":{"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.","short":"M. Rapcak, Y. Soibelman, Y. Yang, G. Zhao, Communications in Mathematical Physics 376 (2020) 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.","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","ista":"Rapcak M, Soibelman Y, Yang Y, Zhao G. 2020. Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. 376, 1803–1873.","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","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."},"date_published":"2020-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Cohomological Hall algebras, vertex algebras and instantons","intvolume":" 376","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7004","oa_version":"Preprint","type":"journal_article","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."}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7204","intvolume":" 7","title":"Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex","status":"public","ddc":["580"],"file":[{"access_level":"open_access","file_name":"2020_AdvScience_Li.pdf","content_type":"application/pdf","file_size":3586924,"creator":"dernst","relation":"main_file","file_id":"7519","checksum":"016eeab5860860af038e2da95ffe75c3","date_updated":"2020-07-14T12:47:53Z","date_created":"2020-02-24T14:29:54Z"}],"oa_version":"Published Version","type":"journal_article","issue":"3","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."}],"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).","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.","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","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.","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","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."},"publication":"Advanced Science","article_type":"original","date_published":"2020-02-05T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"05","pmid":1,"year":"2020","department":[{"_id":"JiFr"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Li, Yang","last_name":"Li","first_name":"Yang"},{"full_name":"Wang, Yaping","first_name":"Yaping","last_name":"Wang"},{"full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285"},{"first_name":"Zhen","last_name":"Li","full_name":"Li, Zhen"},{"last_name":"Yuan","first_name":"Zhi","full_name":"Yuan, Zhi"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous"},{"orcid":"0000-0003-2267-106X","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","last_name":"Domjan","first_name":"David","full_name":"Domjan, David"},{"full_name":"Wang, Kai","first_name":"Kai","last_name":"Wang"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"last_name":"Guo","first_name":"Yan","full_name":"Guo, Yan"},{"last_name":"Gong","first_name":"Zhizhong","full_name":"Gong, Zhizhong"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"volume":7,"date_created":"2019-12-22T23:00:43Z","date_updated":"2023-08-17T14:13:17Z","article_number":"1901455","file_date_updated":"2020-07-14T12:47:53Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000501912800001"],"pmid":["32042554"]},"isi":1,"quality_controlled":"1","doi":"10.1002/advs.201901455","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2198-3844"]},"month":"02"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.nanolett.9b04445"}],"external_id":{"pmid":["31797672"],"isi":["000507151600087"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1021/acs.nanolett.9b04445","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"American Chemical Society","author":[{"full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","first_name":"Mehmet C","last_name":"Ucar"},{"last_name":"Lipowsky","first_name":"Reinhard","full_name":"Lipowsky, Reinhard"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9726"},{"id":"9885","status":"public","relation":"research_data"}]},"date_updated":"2023-08-17T14:07:52Z","date_created":"2019-12-10T15:36:05Z","volume":20,"publication":"Nano Letters","citation":{"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.","short":"M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 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.","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","ista":"Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 20(1), 669–676.","ieee":"M. C. Ucar and R. Lipowsky, “Collective force generation by molecular motors is determined by strain-induced unbinding,” Nano Letters, vol. 20, no. 1. American Chemical Society, pp. 669–676, 2020.","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"},"article_type":"letter_note","page":"669-676","date_published":"2020-01-08T00:00:00Z","scopus_import":"1","day":"08","article_processing_charge":"No","_id":"7166","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Collective force generation by molecular motors is determined by strain-induced unbinding","status":"public","intvolume":" 20","oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"1"},{"author":[{"first_name":"Peyman","last_name":"Obeidy","full_name":"Obeidy, Peyman"},{"full_name":"Ju, Lining A.","last_name":"Ju","first_name":"Lining A."},{"last_name":"Oehlers","first_name":"Stefan H.","full_name":"Oehlers, Stefan H."},{"full_name":"Zulkhernain, Nursafwana S.","first_name":"Nursafwana S.","last_name":"Zulkhernain"},{"last_name":"Lee","first_name":"Quintin","full_name":"Lee, Quintin"},{"full_name":"Galeano Niño, Jorge L.","first_name":"Jorge L.","last_name":"Galeano Niño"},{"last_name":"Kwan","first_name":"Rain Y.Q.","full_name":"Kwan, Rain Y.Q."},{"full_name":"Tikoo, Shweta","last_name":"Tikoo","first_name":"Shweta"},{"first_name":"Lois L.","last_name":"Cavanagh","full_name":"Cavanagh, Lois L."},{"first_name":"Paulus","last_name":"Mrass","full_name":"Mrass, Paulus"},{"first_name":"Adam J.L.","last_name":"Cook","full_name":"Cook, Adam J.L."},{"full_name":"Jackson, Shaun P.","first_name":"Shaun P.","last_name":"Jackson"},{"full_name":"Biro, Maté","last_name":"Biro","first_name":"Maté"},{"first_name":"Ben","last_name":"Roediger","full_name":"Roediger, Ben"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"first_name":"Wolfgang","last_name":"Weninger","full_name":"Weninger, Wolfgang"}],"date_created":"2020-01-05T23:00:48Z","date_updated":"2023-08-17T14:21:12Z","volume":98,"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Wiley","file_date_updated":"2020-11-19T11:22:33Z","doi":"10.1111/imcb.12304","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000503885600001"],"pmid":["31698518"]},"isi":1,"quality_controlled":"1","month":"02","publication_identifier":{"eissn":["14401711"],"issn":["08189641"]},"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8775","date_updated":"2020-11-19T11:22:33Z","date_created":"2020-11-19T11:22:33Z","checksum":"c389477b4b52172ef76afff8a06c6775","success":1,"file_name":"2020_ImmunologyCellBio_Obeidy.pdf","access_level":"open_access","content_type":"application/pdf","file_size":8569945,"creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7234","status":"public","ddc":["570"],"title":"Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes","intvolume":" 98","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"}],"issue":"2","type":"journal_article","date_published":"2020-02-01T00:00:00Z","publication":"Immunology and Cell Biology","citation":{"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","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.","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.","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.","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.","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."},"article_type":"original","page":"93-113","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"has_accepted_license":"1","article_processing_charge":"No","day":"10","scopus_import":"1","date_published":"2020-01-10T00:00:00Z","citation":{"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.","short":"S. Laukoter, R.J. Beattie, F. Pauler, N. Amberg, K.I. Nakayama, S. Hippenmeyer, Nature Communications 11 (2020).","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.","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.","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.","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"},"publication":"Nature Communications","article_type":"original","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2020_NatureComm_Laukoter.pdf","access_level":"open_access","creator":"dernst","file_size":8063333,"content_type":"application/pdf","file_id":"7261","relation":"main_file","date_created":"2020-01-13T07:42:31Z","date_updated":"2020-07-14T12:47:54Z","checksum":"ebf1ed522f4e0be8d94c939c1806a709"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7253","intvolume":" 11","ddc":["570"],"status":"public","title":"Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development","publication_identifier":{"issn":["2041-1723"]},"month":"01","doi":"10.1038/s41467-019-14077-2","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000551459000005"]},"project":[{"_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:47:54Z","article_number":"195","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-function-for-potential-tumour-suppressor-in-brain-development/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","first_name":"Susanne","last_name":"Laukoter"},{"full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","first_name":"Robert J","last_name":"Beattie"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole"},{"full_name":"Nakayama, Keiichi I.","first_name":"Keiichi I.","last_name":"Nakayama"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"volume":11,"date_updated":"2023-08-17T14:23:41Z","date_created":"2020-01-11T10:42:48Z","year":"2020","publisher":"Springer Nature","department":[{"_id":"SiHi"}],"publication_status":"published"},{"has_accepted_license":"1","article_processing_charge":"No","day":"02","scopus_import":"1","date_published":"2020-01-02T00:00:00Z","page":"131-142","article_type":"original","citation":{"short":"L. Piriya Ananda Babu, H.Y. Wang, K. Eguchi, L. Guillaud, T. Takahashi, Journal of Neuroscience 40 (2020) 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.","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.","ama":"Piriya Ananda Babu L, Wang HY, Eguchi K, Guillaud L, Takahashi T. Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. Journal of neuroscience. 2020;40(1):131-142. doi:10.1523/JNEUROSCI.1571-19.2019","apa":"Piriya Ananda Babu, L., Wang, H. Y., Eguchi, K., Guillaud, L., & Takahashi, T. (2020). Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1571-19.2019","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.","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."},"publication":"Journal of neuroscience","issue":"1","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."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2020_JourNeuroscience_Piriya.pdf","creator":"dernst","file_size":4460781,"content_type":"application/pdf","file_id":"7345","relation":"main_file","checksum":"92f5e8a47f454fc131fb94cd7f106e60","date_created":"2020-01-20T14:44:10Z","date_updated":"2020-07-14T12:47:56Z"}],"oa_version":"Published Version","intvolume":" 40","title":"Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission","ddc":["570"],"status":"public","_id":"7339","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["15292401"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.1571-19.2019","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000505167600013"],"pmid":["31767677"]},"file_date_updated":"2020-07-14T12:47:56Z","volume":40,"date_updated":"2023-08-17T14:25:23Z","date_created":"2020-01-19T23:00:38Z","author":[{"full_name":"Piriya Ananda Babu, Lashmi","last_name":"Piriya Ananda Babu","first_name":"Lashmi"},{"full_name":"Wang, Han Ying","first_name":"Han Ying","last_name":"Wang"},{"full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546"},{"first_name":"Laurent","last_name":"Guillaud","full_name":"Guillaud, Laurent"},{"last_name":"Takahashi","first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki"}],"department":[{"_id":"RySh"}],"publisher":"Society for Neuroscience","publication_status":"published","pmid":1,"year":"2020"},{"citation":{"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.","short":"C. Nibau, M. Gallemi, D. Dadarou, J.H. Doonan, N. Cavallari, Frontiers in Plant Science 10 (2020).","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.","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","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.","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.","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"},"publication":"Frontiers in Plant Science","article_type":"original","date_published":"2020-01-22T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"22","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7350","intvolume":" 10","ddc":["580"],"status":"public","title":"Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_FrontiersPlantScience_Nibau.pdf","creator":"dernst","file_size":1951438,"content_type":"application/pdf","file_id":"7366","relation":"main_file","checksum":"d1f92e60a713fbd15097ce895e5c7ccb","date_updated":"2020-07-14T12:47:56Z","date_created":"2020-01-27T09:07:02Z"}],"type":"journal_article","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"}],"external_id":{"isi":["000511376000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.3389/fpls.2019.01680","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1664-462X"]},"month":"01","year":"2020","publisher":"Frontiers Media","department":[{"_id":"EvBe"}],"publication_status":"published","author":[{"first_name":"Candida","last_name":"Nibau","full_name":"Nibau, Candida"},{"full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi","first_name":"Marçal"},{"full_name":"Dadarou, Despoina","first_name":"Despoina","last_name":"Dadarou"},{"full_name":"Doonan, John H.","first_name":"John H.","last_name":"Doonan"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","first_name":"Nicola","full_name":"Cavallari, Nicola"}],"volume":10,"date_created":"2020-01-22T15:23:57Z","date_updated":"2023-08-17T14:21:45Z","article_number":"1680","file_date_updated":"2020-07-14T12:47:56Z"},{"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.","year":"2020","publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Springer Nature","author":[{"full_name":"Cubero, Ryan J","first_name":"Ryan J","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867"},{"full_name":"Marsili, Matteo","first_name":"Matteo","last_name":"Marsili"},{"first_name":"Yasser","last_name":"Roudi","full_name":"Roudi, Yasser"}],"date_created":"2020-01-28T10:34:00Z","date_updated":"2023-08-17T14:35:22Z","volume":48,"file_date_updated":"2020-07-14T12:47:56Z","ec_funded":1,"external_id":{"isi":["000515321800006"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"doi":"10.1007/s10827-020-00740-x","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["0929-5313"],"eissn":["1573-6873"]},"_id":"7369","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Multiscale relevance and informative encoding in neuronal spike trains","status":"public","ddc":["004","519","570"],"intvolume":" 48","file":[{"file_id":"7380","relation":"supplementary_material","date_updated":"2020-07-14T12:47:56Z","date_created":"2020-01-28T09:31:09Z","checksum":"036e9451d6cd0c190ad25791bf82393b","file_name":"10827_2020_740_MOESM1_ESM.pdf","access_level":"open_access","creator":"rcubero","file_size":1941355,"content_type":"application/pdf"},{"creator":"rcubero","content_type":"application/pdf","file_size":3257880,"file_name":"Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:56Z","date_created":"2020-01-28T09:31:09Z","checksum":"4dd8b1fd4b54486f79d82ac7b2a412b2","file_id":"7381","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","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"}],"publication":"Journal of Computational Neuroscience","citation":{"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","ista":"Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 48, 85–102.","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.","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","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.","short":"R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience 48 (2020) 85–102.","chicago":"Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” Journal of Computational Neuroscience. Springer Nature, 2020. https://doi.org/10.1007/s10827-020-00740-x."},"article_type":"original","page":"85-102","date_published":"2020-02-01T00:00:00Z","scopus_import":"1","keyword":["Time series analysis","Multiple time scale analysis","Spike train data","Information theory","Bayesian decoding"],"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"date_updated":"2023-08-17T14:29:59Z","date_created":"2020-01-26T23:00:35Z","volume":11,"author":[{"full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","first_name":"Jose M"},{"first_name":"Daniel","last_name":"Feldmann","full_name":"Feldmann, Daniel"},{"last_name":"Rampp","first_name":"Markus","full_name":"Rampp, Markus"},{"first_name":"Alberto","last_name":"Vela-Martín","full_name":"Vela-Martín, Alberto"},{"full_name":"Shi, Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","last_name":"Shi","first_name":"Liang"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"BjHo"}],"year":"2020","file_date_updated":"2020-07-14T12:47:56Z","article_number":"100395","language":[{"iso":"eng"}],"doi":"10.1016/j.softx.2019.100395","isi":1,"quality_controlled":"1","external_id":{"arxiv":["1908.00587"],"isi":["000552271200011"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"01","publication_identifier":{"eissn":["23527110"]},"oa_version":"Published Version","file":[{"file_name":"2020_SoftwareX_Lopez.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":679707,"file_id":"7365","relation":"main_file","date_updated":"2020-07-14T12:47:56Z","date_created":"2020-01-27T07:32:46Z","checksum":"2af1a1a3cc33557b345145276f221668"}],"status":"public","title":"nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow","ddc":["000"],"intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7364","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."}],"type":"journal_article","date_published":"2020-01-17T00:00:00Z","article_type":"original","publication":"SoftwareX","citation":{"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.","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","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.","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.","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."},"day":"17","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"doi":"10.1098/rsif.2019.0623","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1903.10693","open_access":"1"}],"external_id":{"arxiv":["1903.10693"],"pmid":["31964273"],"isi":["000538369800002"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["17425662"]},"month":"01","author":[{"full_name":"Kolchinsky, Artemy","last_name":"Kolchinsky","first_name":"Artemy"},{"last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat"}],"volume":17,"date_created":"2020-02-02T23:01:03Z","date_updated":"2023-08-17T14:31:28Z","pmid":1,"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. ","year":"2020","publisher":"The Royal Society","department":[{"_id":"EdHa"}],"publication_status":"published","article_number":"0623","date_published":"2020-01-29T00:00:00Z","citation":{"short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","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.","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.","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","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.","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","ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623."},"publication":"Journal of the Royal Society Interface","article_type":"original","article_processing_charge":"No","day":"29","scopus_import":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7431","intvolume":" 17","status":"public","title":"Decomposing information into copying versus transformation","issue":"162","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"month":"08","publication_identifier":{"eissn":["10886850"],"issn":["00029947"]},"external_id":{"isi":["000551418100018"],"arxiv":["2002.00859"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.00859"}],"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Geometric study of Wasserstein spaces and free probability","_id":"26A455A6-B435-11E9-9278-68D0E5697425","grant_number":"846294"}],"doi":"10.1090/tran/8113","language":[{"iso":"eng"}],"ec_funded":1,"year":"2020","publication_status":"published","publisher":"American Mathematical Society","department":[{"_id":"LaEr"}],"author":[{"full_name":"Geher, Gyorgy Pal","first_name":"Gyorgy Pal","last_name":"Geher"},{"first_name":"Tamas","last_name":"Titkos","full_name":"Titkos, Tamas"},{"full_name":"Virosztek, Daniel","first_name":"Daniel","last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511"}],"date_updated":"2023-08-17T14:31:03Z","date_created":"2020-01-29T10:20:46Z","volume":373,"keyword":["Wasserstein space","isometric embeddings","isometric rigidity","exotic isometry flow"],"day":"01","article_processing_charge":"No","publication":"Transactions of the American Mathematical Society","citation":{"short":"G.P. Geher, T. Titkos, D. Virosztek, Transactions of the American Mathematical Society 373 (2020) 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.","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.","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.","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."},"article_type":"original","page":"5855-5883","date_published":"2020-08-01T00:00:00Z","type":"journal_article","abstract":[{"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)).","lang":"eng"}],"issue":"8","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7389","title":"Isometric study of Wasserstein spaces - the real line","status":"public","ddc":["515"],"intvolume":" 373","oa_version":"Preprint"},{"external_id":{"isi":["000526598300012"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.1021/acsaem.9b02137","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["2574-0962"]},"year":"2020","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.","publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","author":[{"full_name":"Cadavid, Doris","last_name":"Cadavid","first_name":"Doris"},{"full_name":"Ortega, Silvia","first_name":"Silvia","last_name":"Ortega"},{"first_name":"Sergio","last_name":"Illera","full_name":"Illera, Sergio"},{"first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"last_name":"Shavel","first_name":"Alexey","full_name":"Shavel, Alexey"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"full_name":"López, Antonio M.","last_name":"López","first_name":"Antonio M."},{"first_name":"Germán","last_name":"Noriega","full_name":"Noriega, Germán"},{"full_name":"Durá, Oscar Juan","last_name":"Durá","first_name":"Oscar Juan"},{"full_name":"López De La Torre, M. A.","last_name":"López De La Torre","first_name":"M. A."},{"full_name":"Prades, Joan Daniel","first_name":"Joan Daniel","last_name":"Prades"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"date_updated":"2023-08-17T14:36:16Z","date_created":"2020-02-09T23:00:52Z","volume":3,"file_date_updated":"2022-08-23T08:34:17Z","ec_funded":1,"publication":"ACS Applied Energy Materials","citation":{"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.","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.","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.","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"},"article_type":"original","page":"2120-2129","date_published":"2020-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7467","status":"public","title":"Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials","ddc":["540"],"intvolume":" 3","file":[{"file_id":"11942","relation":"main_file","success":1,"checksum":"f23be731a766a480c77c962c1380315c","date_updated":"2022-08-23T08:34:17Z","date_created":"2022-08-23T08:34:17Z","access_level":"open_access","file_name":"2020_ACSAppliedEnergyMat_Cadavid.pdf","creator":"dernst","content_type":"application/pdf","file_size":6423548}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"3"},{"type":"journal_article","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"}],"issue":"4","status":"public","title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","ddc":["580"],"intvolume":" 293","_id":"7465","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2020_PlantScience_Mazur.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3499069,"creator":"dernst","relation":"main_file","file_id":"7471","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-10T08:59:36Z","checksum":"f7f27c6a8fea985ceb9279be2204461c"}],"oa_version":"Published Version","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Plant Science","citation":{"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.","short":"E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020).","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.","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.","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","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.","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"},"date_published":"2020-04-01T00:00:00Z","article_number":"110414","file_date_updated":"2020-07-14T12:47:59Z","ec_funded":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JiFr"}],"year":"2020","date_updated":"2023-08-17T14:37:32Z","date_created":"2020-02-09T23:00:50Z","volume":293,"author":[{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C"},{"full_name":"Adamowski, Maciek","last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han"},{"full_name":"Robert, Hélène S.","last_name":"Robert","first_name":"Hélène S."},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"related_material":{"record":[{"id":"11626","status":"public","relation":"dissertation_contains"}]},"month":"04","publication_identifier":{"issn":["01689452"],"eissn":["18732259"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000520609800009"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.plantsci.2020.110414"},{"author":[{"first_name":"Katrin","last_name":"Kierdorf","full_name":"Kierdorf, Katrin"},{"full_name":"Hersperger, Fabian","last_name":"Hersperger","first_name":"Fabian"},{"first_name":"Jessica","last_name":"Sharrock","full_name":"Sharrock, Jessica"},{"full_name":"Vincent, Crystal M.","first_name":"Crystal M.","last_name":"Vincent"},{"first_name":"Pinar","last_name":"Ustaoglu","full_name":"Ustaoglu, Pinar"},{"full_name":"Dou, Jiawen","first_name":"Jiawen","last_name":"Dou"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","first_name":"Attila","last_name":"György","full_name":"György, Attila"},{"full_name":"Groß, Olaf","first_name":"Olaf","last_name":"Groß"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"},{"full_name":"Dionne, Marc S.","last_name":"Dionne","first_name":"Marc S."}],"volume":9,"date_updated":"2023-08-17T14:36:39Z","date_created":"2020-02-09T23:00:51Z","year":"2020","publisher":"eLife Sciences Publications","department":[{"_id":"DaSi"}],"publication_status":"published","file_date_updated":"2020-07-14T12:47:59Z","article_number":"e51595","doi":"10.7554/eLife.51595","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000512304800001"]},"project":[{"grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["2050084X"]},"month":"01","file":[{"relation":"main_file","file_id":"7470","checksum":"3a072be843f416c7a7d532a51dc0addb","date_created":"2020-02-10T08:53:16Z","date_updated":"2020-07-14T12:47:59Z","access_level":"open_access","file_name":"2020_eLife_Kierdorf.pdf","content_type":"application/pdf","file_size":4959933,"creator":"dernst"}],"oa_version":"Published Version","_id":"7466","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 9","status":"public","title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","ddc":["570"],"abstract":[{"text":"Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis.","lang":"eng"}],"type":"journal_article","date_published":"2020-01-20T00:00:00Z","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.","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.","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","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.","ieee":"K. Kierdorf et al., “Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila,” eLife, vol. 9. eLife Sciences Publications, 2020.","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"},"publication":"eLife","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"20","scopus_import":"1"},{"day":"08","article_processing_charge":"No","scopus_import":"1","date_published":"2020-04-08T00:00:00Z","publication":"Neuron","citation":{"short":"K. Käfer, M. Nardin, K. Blahna, J.L. Csicsvari, Neuron 106 (2020) 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.","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.","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","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","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."},"article_type":"original","page":"P154-165.e6","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"}],"issue":"1","type":"journal_article","oa_version":"Published Version","_id":"7472","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Replay of behavioral sequences in the medial prefrontal cortex during rule switching","intvolume":" 106","month":"04","publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2020.01.015","acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2020.01.015"}],"external_id":{"pmid":["32032512"],"isi":["000525319300016"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Inter-and intracellular signalling in schizophrenia","grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"author":[{"first_name":"Karola","last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola"},{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","first_name":"Michele"},{"id":"3EA859AE-F248-11E8-B48F-1D18A9856A87","first_name":"Karel","last_name":"Blahna","full_name":"Blahna, Karel"},{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/this-brain-area-helps-us-decide/","relation":"press_release","description":"News on IST Homepage"}]},"date_updated":"2023-08-17T14:38:02Z","date_created":"2020-02-10T15:45:48Z","volume":106,"year":"2020","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 ).","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JoCs"}]},{"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"663-682","publication":"Annales de l'Institut Henri Poincaré C, Analyse non linéaire","citation":{"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.","mla":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire, vol. 37, no. 3, Elsevier, 2020, pp. 663–82, doi:10.1016/j.anihpc.2020.01.003.","short":"M. Gerencser, Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire 37 (2020) 663–682.","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.","ieee":"M. Gerencser, “Nondivergence form quasilinear heat equations driven by space-time white noise,” Annales de l’Institut Henri Poincaré C, Analyse non linéaire, vol. 37, no. 3. Elsevier, pp. 663–682, 2020.","apa":"Gerencser, M. (2020). Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire. Elsevier. https://doi.org/10.1016/j.anihpc.2020.01.003","ama":"Gerencser M. Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse non linéaire. 2020;37(3):663-682. doi:10.1016/j.anihpc.2020.01.003"},"date_published":"2020-05-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"3","title":"Nondivergence form quasilinear heat equations driven by space-time white noise","status":"public","intvolume":" 37","_id":"7388","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"05","publication_identifier":{"issn":["0294-1449"]},"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000531049800007"],"arxiv":["1902.07635"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07635"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.anihpc.2020.01.003","publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"Elsevier","year":"2020","date_updated":"2023-08-17T14:35:46Z","date_created":"2020-01-29T09:39:41Z","volume":37,"author":[{"full_name":"Gerencser, Mate","first_name":"Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"}]},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaBe"}],"year":"2020","pmid":1,"date_updated":"2023-08-18T06:35:13Z","date_created":"2020-02-16T23:00:49Z","volume":10,"author":[{"last_name":"López De La Oliva","first_name":"Amada R.","full_name":"López De La Oliva, Amada R."},{"full_name":"Campos-Sandoval, José A.","last_name":"Campos-Sandoval","first_name":"José A."},{"full_name":"Gómez-García, María C.","first_name":"María C.","last_name":"Gómez-García"},{"last_name":"Cardona","first_name":"Carolina","full_name":"Cardona, Carolina"},{"full_name":"Martín-Rufián, Mercedes","last_name":"Martín-Rufián","first_name":"Mercedes"},{"first_name":"Fernando J.","last_name":"Sialana","full_name":"Sialana, Fernando J."},{"full_name":"Castilla, Laura","last_name":"Castilla","first_name":"Laura"},{"first_name":"Narkhyun","last_name":"Bae","id":"3A5F7CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Bae, Narkhyun"},{"last_name":"Lobo","first_name":"Carolina","full_name":"Lobo, Carolina"},{"full_name":"Peñalver, Ana","last_name":"Peñalver","first_name":"Ana"},{"full_name":"García-Frutos, Marina","last_name":"García-Frutos","first_name":"Marina"},{"full_name":"Carro, David","last_name":"Carro","first_name":"David"},{"first_name":"Victoria","last_name":"Enrique","full_name":"Enrique, Victoria"},{"full_name":"Paz, José C.","first_name":"José C.","last_name":"Paz"},{"last_name":"Mirmira","first_name":"Raghavendra G.","full_name":"Mirmira, Raghavendra G."},{"last_name":"Gutiérrez","first_name":"Antonia","full_name":"Gutiérrez, Antonia"},{"first_name":"Francisco J.","last_name":"Alonso","full_name":"Alonso, Francisco J."},{"last_name":"Segura","first_name":"Juan A.","full_name":"Segura, Juan A."},{"full_name":"Matés, José M.","last_name":"Matés","first_name":"José M."},{"last_name":"Lubec","first_name":"Gert","full_name":"Lubec, Gert"},{"last_name":"Márquez","first_name":"Javier","full_name":"Márquez, Javier"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-020-80651-0"}]},"article_number":"2259","file_date_updated":"2020-07-14T12:47:59Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000560694800012"],"pmid":["32042057"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-020-58264-4","month":"02","publication_identifier":{"eissn":["20452322"]},"ddc":["570"],"status":"public","title":"Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation","intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7487","file":[{"file_id":"7495","relation":"main_file","checksum":"c780bd87476a9c9e12668ff66de3dc96","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-18T07:43:21Z","access_level":"open_access","file_name":"2020_ScientificReport_Lopez.pdf","creator":"dernst","file_size":4703751,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","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."}],"issue":"1","article_type":"original","publication":"Scientific reports","citation":{"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.","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.","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).","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.","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"},"date_published":"2020-02-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"No","has_accepted_license":"1"},{"citation":{"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.","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.","short":"M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020).","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.","apa":"Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas Perez, B. E., & Friml, J. (2020). Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.52067","ieee":"M. Narasimhan et al., “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences Publications, 2020.","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"},"publication":"eLife","article_type":"original","date_published":"2020-01-23T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"23","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7490","intvolume":" 9","title":"Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants","status":"public","ddc":["570","580"],"oa_version":"Published Version","file":[{"date_created":"2020-02-18T07:21:16Z","date_updated":"2020-07-14T12:47:59Z","checksum":"2052daa4be5019534f3a42f200a09f32","file_id":"7494","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":7247468,"file_name":"2020_eLife_Narasimhan.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"text":"In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31971511"],"isi":["000514104100001"]},"oa":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"quality_controlled":"1","isi":1,"doi":"10.7554/eLife.52067","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_identifier":{"eissn":["2050-084X"]},"month":"01","pmid":1,"year":"2020","publisher":"eLife Sciences Publications","department":[{"_id":"JiFr"},{"_id":"GaTk"},{"_id":"EM-Fac"},{"_id":"SyCr"}],"publication_status":"published","author":[{"full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","first_name":"Madhumitha"},{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","last_name":"Casillas Perez"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"volume":9,"date_created":"2020-02-16T23:00:50Z","date_updated":"2023-08-18T06:33:07Z","article_number":"e52067","ec_funded":1,"file_date_updated":"2020-07-14T12:47:59Z"},{"abstract":[{"lang":"eng","text":"Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS."}],"issue":"3","type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4271234,"file_name":"2020_IntMolecSciences_Latorre.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-18T07:49:22Z","checksum":"0e6658c4fe329d55d4d9bef01c5b15d0","file_id":"7496","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7488","title":"Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes","status":"public","ddc":["570"],"intvolume":" 21","day":"04","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-02-04T00:00:00Z","publication":"International Journal of Molecular Sciences","citation":{"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.","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.","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).","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.","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.","apa":"Latorre-Pellicer, A., Ascaso, Á., Trujillano, L., Gil-Salvador, M., Arnedo, M., Lucia-Campos, C., … Pié, J. (2020). Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21031042","ama":"Latorre-Pellicer A, Ascaso Á, Trujillano L, et al. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. 2020;21(3). doi:10.3390/ijms21031042"},"article_type":"original","file_date_updated":"2020-07-14T12:47:59Z","article_number":"1042","author":[{"full_name":"Latorre-Pellicer, Ana","last_name":"Latorre-Pellicer","first_name":"Ana"},{"last_name":"Ascaso","first_name":"Ángela","full_name":"Ascaso, Ángela"},{"full_name":"Trujillano, Laura","first_name":"Laura","last_name":"Trujillano"},{"first_name":"Marta","last_name":"Gil-Salvador","full_name":"Gil-Salvador, Marta"},{"full_name":"Arnedo, Maria","first_name":"Maria","last_name":"Arnedo"},{"last_name":"Lucia-Campos","first_name":"Cristina","full_name":"Lucia-Campos, Cristina"},{"full_name":"Antoñanzas-Pérez, Rebeca","last_name":"Antoñanzas-Pérez","first_name":"Rebeca"},{"last_name":"Marcos-Alcalde","first_name":"Iñigo","full_name":"Marcos-Alcalde, Iñigo"},{"full_name":"Parenti, Ilaria","first_name":"Ilaria","last_name":"Parenti","id":"D93538B0-5B71-11E9-AC62-02EBE5697425"},{"first_name":"Gloria","last_name":"Bueno-Lozano","full_name":"Bueno-Lozano, Gloria"},{"full_name":"Musio, Antonio","last_name":"Musio","first_name":"Antonio"},{"full_name":"Puisac, Beatriz","first_name":"Beatriz","last_name":"Puisac"},{"first_name":"Frank J.","last_name":"Kaiser","full_name":"Kaiser, Frank J."},{"full_name":"Ramos, Feliciano J.","first_name":"Feliciano J.","last_name":"Ramos"},{"full_name":"Gómez-Puertas, Paulino","last_name":"Gómez-Puertas","first_name":"Paulino"},{"full_name":"Pié, Juan","first_name":"Juan","last_name":"Pié"}],"date_created":"2020-02-16T23:00:49Z","date_updated":"2023-08-18T06:35:41Z","volume":21,"year":"2020","publication_status":"published","department":[{"_id":"GaNo"}],"publisher":"MDPI","month":"02","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"doi":"10.3390/ijms21031042","language":[{"iso":"eng"}],"external_id":{"isi":["000522551606028"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1},{"author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","first_name":"Anna","last_name":"Lukina","full_name":"Lukina, Anna"},{"orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian"}],"date_updated":"2023-08-18T06:38:16Z","date_created":"2020-02-21T16:44:03Z","volume":325,"year":"2020","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.","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IOS Press","file_date_updated":"2020-09-21T07:12:32Z","ec_funded":1,"conference":{"name":"ECAI: European Conference on Artificial Intelligence","start_date":"2020-08-29","location":"Santiago de Compostela, Spain","end_date":"2020-09-08"},"doi":"10.3233/FAIA200375","language":[{"iso":"eng"}],"external_id":{"arxiv":["1911.09032"],"isi":["000650971303002"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"month":"02","file":[{"file_name":"2020_ECAI_Henzinger.pdf","access_level":"open_access","creator":"dernst","file_size":1692214,"content_type":"application/pdf","file_id":"8540","relation":"main_file","date_updated":"2020-09-21T07:12:32Z","date_created":"2020-09-21T07:12:32Z","success":1,"checksum":"80642fa0b6cd7da95dcd87d63789ad5e"}],"oa_version":"Published Version","_id":"7505","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Outside the box: Abstraction-based monitoring of neural networks","status":"public","ddc":["000"],"intvolume":" 325","abstract":[{"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.","lang":"eng"}],"type":"conference","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"date_published":"2020-02-24T00:00:00Z","publication":"24th European Conference on Artificial Intelligence","citation":{"mla":"Henzinger, Thomas A., et al. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” 24th European Conference on Artificial Intelligence, vol. 325, IOS Press, 2020, pp. 2433–40, doi:10.3233/FAIA200375.","short":"T.A. Henzinger, A. Lukina, C. Schilling, in:, 24th European Conference on Artificial Intelligence, IOS Press, 2020, pp. 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.","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","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.","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.","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"},"page":"2433-2440","day":"24","article_processing_charge":"No","has_accepted_license":"1"},{"author":[{"full_name":"Bossmann, Lea","last_name":"Bossmann","first_name":"Lea","orcid":"0000-0002-6854-1343","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425"},{"first_name":"Nataša","last_name":"Pavlović","full_name":"Pavlović, Nataša"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"},{"last_name":"Soffer","first_name":"Avy","full_name":"Soffer, Avy"}],"date_created":"2020-02-23T09:45:51Z","date_updated":"2023-08-18T06:37:46Z","volume":178,"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.","year":"2020","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","file_date_updated":"2020-11-20T09:26:46Z","ec_funded":1,"doi":"10.1007/s10955-020-02500-8","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000516342200001"],"arxiv":["1905.06164"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"month":"02","publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"oa_version":"Published Version","file":[{"success":1,"checksum":"643e230bf147e64d9cdb3f6cc573679d","date_updated":"2020-11-20T09:26:46Z","date_created":"2020-11-20T09:26:46Z","file_id":"8780","relation":"main_file","creator":"dernst","file_size":576726,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_JournStatPhysics_Bossmann.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7508","status":"public","ddc":["510"],"title":"Higher order corrections to the mean-field description of the dynamics of interacting bosons","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."}],"type":"journal_article","date_published":"2020-02-21T00:00:00Z","publication":"Journal of Statistical Physics","citation":{"short":"L. Bossmann, N. Pavlović, P. Pickl, A. Soffer, Journal of Statistical Physics 178 (2020) 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.","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.","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","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","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."},"article_type":"original","page":"1362-1396","day":"21","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-14535-2","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000514928000017"]},"publication_identifier":{"eissn":["20411723"]},"month":"02","volume":11,"date_created":"2020-02-23T23:00:35Z","date_updated":"2023-08-18T06:36:41Z","author":[{"full_name":"Turoňová, Beata","first_name":"Beata","last_name":"Turoňová"},{"last_name":"Hagen","first_name":"Wim J.H.","full_name":"Hagen, Wim J.H."},{"first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin"},{"full_name":"Mosalaganti, Shyamal","first_name":"Shyamal","last_name":"Mosalaganti"},{"first_name":"J. Wouter","last_name":"Beugelink","full_name":"Beugelink, J. Wouter"},{"first_name":"Christian E.","last_name":"Zimmerli","full_name":"Zimmerli, Christian E."},{"full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg","last_name":"Kräusslich"},{"first_name":"Martin","last_name":"Beck","full_name":"Beck, Martin"}],"department":[{"_id":"FlSc"}],"publisher":"Springer Nature","publication_status":"published","year":"2020","file_date_updated":"2020-07-14T12:47:59Z","article_number":"876","date_published":"2020-02-13T00:00:00Z","article_type":"original","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","ieee":"B. Turoňová et al., “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” Nature Communications, vol. 11. Springer Nature, 2020.","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.","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","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.","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).","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."},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"13","scopus_import":"1","oa_version":"Published Version","file":[{"date_created":"2020-02-24T14:00:54Z","date_updated":"2020-07-14T12:47:59Z","checksum":"2c8d10475e1b0d397500760e28bdf561","relation":"main_file","file_id":"7517","file_size":2027529,"content_type":"application/pdf","creator":"dernst","file_name":"2020_NatureComm_Turonova.pdf","access_level":"open_access"}],"intvolume":" 11","status":"public","ddc":["570"],"title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","_id":"7511","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","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."}],"type":"journal_article"},{"intvolume":" 62","status":"public","title":"Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7497","oa_version":"Published Version","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover, the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross‐talk between JA signalling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants."}],"page":"1433-1451","article_type":"original","citation":{"ama":"Han L, Zhou X, Zhao Y, et al. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. 2020;62(9):1433-1451. doi:10.1111/jipb.12905","apa":"Han, L., Zhou, X., Zhao, Y., Zhu, S., Wu, L., He, Y., … Du, Y. (2020). Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.12905","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.","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.","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.","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.","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."},"publication":"Journal of Integrative Plant Biology","date_published":"2020-09-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","department":[{"_id":"JiFr"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2020","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).","volume":62,"date_updated":"2023-08-18T06:44:16Z","date_created":"2020-02-18T10:02:25Z","author":[{"first_name":"L","last_name":"Han","full_name":"Han, L"},{"full_name":"Zhou, X","first_name":"X","last_name":"Zhou"},{"first_name":"Y","last_name":"Zhao","full_name":"Zhao, Y"},{"first_name":"S","last_name":"Zhu","full_name":"Zhu, S"},{"full_name":"Wu, L","first_name":"L","last_name":"Wu"},{"last_name":"He","first_name":"Y","full_name":"He, Y"},{"first_name":"X","last_name":"Ping","full_name":"Ping, X"},{"first_name":"X","last_name":"Lu","full_name":"Lu, X"},{"full_name":"Huang, W","last_name":"Huang","first_name":"W"},{"full_name":"Qian, J","first_name":"J","last_name":"Qian"},{"first_name":"L","last_name":"Zhang","full_name":"Zhang, L"},{"first_name":"X","last_name":"Jiang","full_name":"Jiang, X"},{"full_name":"Zhu, D","last_name":"Zhu","first_name":"D"},{"full_name":"Luo, C","last_name":"Luo","first_name":"C"},{"last_name":"Li","first_name":"S","full_name":"Li, S"},{"last_name":"Dong","first_name":"Q","full_name":"Dong, Q"},{"full_name":"Fu, Q","last_name":"Fu","first_name":"Q"},{"full_name":"Deng, K","first_name":"K","last_name":"Deng"},{"first_name":"X","last_name":"Wang","full_name":"Wang, X"},{"full_name":"Wang, L","last_name":"Wang","first_name":"L"},{"full_name":"Peng, S","last_name":"Peng","first_name":"S"},{"last_name":"Wu","first_name":"J","full_name":"Wu, J"},{"full_name":"Li, W","last_name":"Li","first_name":"W"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Zhu, Y","first_name":"Y","last_name":"Zhu"},{"full_name":"He, X","first_name":"X","last_name":"He"},{"full_name":"Du, Y","first_name":"Y","last_name":"Du"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1111/jipb.12905","open_access":"1"}],"external_id":{"pmid":["31912615"],"isi":["000515803000001"]},"language":[{"iso":"eng"}],"doi":"10.1111/jipb.12905","publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"month":"09"},{"article_number":"023903","date_updated":"2023-08-18T06:44:46Z","date_created":"2020-02-27T10:26:57Z","volume":5,"author":[{"orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B","full_name":"Budanur, Nazmi B"},{"last_name":"Marensi","first_name":"Elena","full_name":"Marensi, Elena"},{"full_name":"Willis, Ashley P.","first_name":"Ashley P.","last_name":"Willis"},{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","year":"2020","month":"02","publication_identifier":{"issn":["2469-990X"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevfluids.5.023903","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.09270"}],"external_id":{"arxiv":["1912.09270"],"isi":["000515065100001"]},"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."}],"issue":"2","type":"journal_article","oa_version":"Preprint","status":"public","title":"Upper edge of chaos and the energetics of transition in pipe flow","intvolume":" 5","_id":"7534","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"21","article_processing_charge":"No","scopus_import":"1","date_published":"2020-02-21T00:00:00Z","article_type":"original","publication":"Physical Review Fluids","citation":{"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.","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","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.","short":"N.B. Budanur, E. Marensi, A.P. Willis, B. Hof, Physical Review Fluids 5 (2020).","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.","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."}},{"language":[{"iso":"eng"}],"doi":"10.1016/j.jfa.2020.108507","isi":1,"quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11340"}],"external_id":{"arxiv":["1804.11340"],"isi":["000522798900001"]},"oa":1,"month":"07","publication_identifier":{"eissn":["10960783"],"issn":["00221236"]},"date_updated":"2023-08-18T06:36:10Z","date_created":"2020-02-23T23:00:36Z","volume":278,"author":[{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H"},{"first_name":"Yuriy","last_name":"Nemish","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7327-856X","full_name":"Nemish, Yuriy"}],"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Elsevier","year":"2020","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","ec_funded":1,"article_number":"108507","date_published":"2020-07-01T00:00:00Z","article_type":"original","publication":"Journal of Functional Analysis","citation":{"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.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Journal of Functional Analysis 278 (2020).","mla":"Erdös, László, et al. “Local Laws for Polynomials of Wigner Matrices.” Journal of Functional Analysis, vol. 278, no. 12, 108507, Elsevier, 2020, doi:10.1016/j.jfa.2020.108507.","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","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.","ista":"Erdös L, Krüger TH, Nemish Y. 2020. Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. 278(12), 108507.","ama":"Erdös L, Krüger TH, Nemish Y. Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. 2020;278(12). doi:10.1016/j.jfa.2020.108507"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"Local laws for polynomials of Wigner matrices","intvolume":" 278","_id":"7512","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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."}],"issue":"12","type":"journal_article"},{"month":"05","language":[{"iso":"eng"}],"doi":"10.1016/j.aim.2020.107053","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1811.01205","open_access":"1"}],"external_id":{"arxiv":["1811.01205"],"isi":["000522798000001"]},"ec_funded":1,"article_number":"107053","date_updated":"2023-08-18T06:37:09Z","date_created":"2020-02-23T21:43:50Z","volume":365,"author":[{"full_name":"Zhang, Haonan","first_name":"Haonan","last_name":"Zhang","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"Elsevier","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.","year":"2020","day":"13","article_processing_charge":"No","date_published":"2020-05-13T00:00:00Z","article_type":"original","publication":"Advances in Mathematics","citation":{"ista":"Zhang H. 2020. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. 365, 107053.","apa":"Zhang, H. (2020). From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2020.107053","ieee":"H. Zhang, “From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture,” Advances in Mathematics, vol. 365. Elsevier, 2020.","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","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.","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.","short":"H. Zhang, Advances in Mathematics 365 (2020)."},"abstract":[{"lang":"eng","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. 2020;105(1):106-121.e10. doi:10.1016/j.neuron.2019.10.001","ieee":"I. Beets et al., “Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression,” Neuron, vol. 105, no. 1. Cell Press, p. 106–121.e10, 2020.","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","ista":"Beets I, Zhang G, Fenk LA, Chen C, Nelson GM, Félix M-A, de Bono M. 2020. Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. Neuron. 105(1), 106–121.e10.","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.","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.","chicago":"Beets, Isabel, Gaotian Zhang, Lorenz A. Fenk, Changchun Chen, Geoffrey M. Nelson, Marie-Anne Félix, and Mario de Bono. “Natural Variation in a Dendritic Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide Expression.” Neuron. Cell Press, 2020. https://doi.org/10.1016/j.neuron.2019.10.001."},"publication":"Neuron","page":"106-121.e10","article_type":"original","date_published":"2020-01-08T00:00:00Z"},{"article_processing_charge":"No","day":"03","scopus_import":"1","date_published":"2020-03-03T00:00:00Z","article_type":"original","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.","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.","short":"G. Yalniz, N.B. Budanur, Chaos 30 (2020).","ista":"Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 30(3), 033109.","ieee":"G. Yalniz and N. B. Budanur, “Inferring symbolic dynamics of chaotic flows from persistence,” Chaos, vol. 30, no. 3. AIP Publishing, 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"},"publication":"Chaos","issue":"3","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."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 30","title":"Inferring symbolic dynamics of chaotic flows from persistence","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7563","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1063/1.5122969","isi":1,"quality_controlled":"1","external_id":{"isi":["000519254800002"],"arxiv":["1910.04584"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1063/1.5122969","open_access":"1"}],"article_number":"033109","volume":30,"date_updated":"2023-08-18T06:47:16Z","date_created":"2020-03-04T08:06:25Z","author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312","first_name":"Gökhan","last_name":"Yalniz","full_name":"Yalniz, Gökhan"},{"full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BjHo"}],"publisher":"AIP Publishing","publication_status":"published","year":"2020"},{"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"full_name":"Nikitenko, Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201","first_name":"Anton","last_name":"Nikitenko"}],"date_created":"2020-03-01T23:00:39Z","date_updated":"2023-08-18T06:45:48Z","volume":64,"year":"2020","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"SIAM","ec_funded":1,"doi":"10.1137/S0040585X97T989726","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.08735"}],"external_id":{"arxiv":["1705.08735"],"isi":["000551393100007"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"month":"02","publication_identifier":{"eissn":["10957219"],"issn":["0040585X"]},"oa_version":"Preprint","_id":"7554","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Weighted Poisson–Delaunay mosaics","intvolume":" 64","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 ${R}^n$."}],"issue":"4","type":"journal_article","date_published":"2020-02-13T00:00:00Z","publication":"Theory of Probability and its Applications","citation":{"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.","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.","apa":"Edelsbrunner, H., & Nikitenko, A. (2020). Weighted Poisson–Delaunay mosaics. Theory of Probability and Its Applications. SIAM. https://doi.org/10.1137/S0040585X97T989726","ieee":"H. Edelsbrunner and A. Nikitenko, “Weighted Poisson–Delaunay mosaics,” Theory of Probability and its Applications, vol. 64, no. 4. SIAM, pp. 595–614, 2020.","ista":"Edelsbrunner H, Nikitenko A. 2020. Weighted Poisson–Delaunay mosaics. Theory of Probability and its Applications. 64(4), 595–614.","ama":"Edelsbrunner H, Nikitenko A. Weighted Poisson–Delaunay mosaics. Theory of Probability and its Applications. 2020;64(4):595-614. doi:10.1137/S0040585X97T989726"},"article_type":"original","page":"595-614","day":"13","article_processing_charge":"No","scopus_import":"1"},{"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000517969300001"],"arxiv":["1905.08564"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevx.10.011055","month":"03","publication_identifier":{"issn":["2160-3308"]},"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"year":"2020","date_updated":"2023-08-18T07:01:07Z","date_created":"2020-03-08T18:02:01Z","volume":10,"author":[{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","first_name":"Alexios","last_name":"Michailidis","full_name":"Michailidis, Alexios"},{"last_name":"Turner","first_name":"C. J.","full_name":"Turner, C. J."},{"last_name":"Papić","first_name":"Z.","full_name":"Papić, Z."},{"full_name":"Abanin, D. A.","last_name":"Abanin","first_name":"D. A."},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/classical-physics-helps-predict-fate-of-interacting-quantum-systems/","relation":"press_release","description":"News on IST Homepage"}]},"article_number":"011055","file_date_updated":"2020-07-14T12:48:00Z","article_type":"original","publication":"Physical Review X","citation":{"mla":"Michailidis, Alexios, et al. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” Physical Review X, vol. 10, no. 1, 011055, American Physical Society, 2020, doi:10.1103/physrevx.10.011055.","short":"A. Michailidis, C.J. Turner, Z. Papić, D.A. Abanin, M. Serbyn, Physical Review X 10 (2020).","chicago":"Michailidis, Alexios, C. J. Turner, Z. Papić, D. A. Abanin, and Maksym Serbyn. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” Physical Review X. American Physical Society, 2020. https://doi.org/10.1103/physrevx.10.011055.","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","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.","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.","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"},"date_published":"2020-03-04T00:00:00Z","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"No","title":"Slow quantum thermalization and many-body revivals from mixed phase space","status":"public","ddc":["530"],"intvolume":" 10","_id":"7570","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"4b3f2c13873d35230173c73d0e11c408","date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-12T12:13:07Z","file_id":"7581","relation":"main_file","creator":"dernst","file_size":17828638,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_PhysicalReviewX_Michailidis.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"1"},{"month":"03","publication_identifier":{"eissn":["22237747"]},"language":[{"iso":"eng"}],"doi":"10.3390/plants9030299","isi":1,"quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000525315000035"],"pmid":["32121542"]},"file_date_updated":"2020-07-14T12:48:00Z","ec_funded":1,"article_number":"299","date_created":"2020-03-15T23:00:52Z","date_updated":"2023-08-18T07:07:08Z","volume":9,"author":[{"full_name":"Moturu, Taraka Ramji","last_name":"Moturu","first_name":"Taraka Ramji"},{"last_name":"Sinha","first_name":"Sansrity","full_name":"Sinha, Sansrity"},{"last_name":"Salava","first_name":"Hymavathi","full_name":"Salava, Hymavathi"},{"first_name":"Sravankumar","last_name":"Thula","full_name":"Thula, Sravankumar"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"full_name":"Vařeková, Radka Svobodová","first_name":"Radka Svobodová","last_name":"Vařeková"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu"}],"publication_status":"published","publisher":"MDPI","department":[{"_id":"JiFr"}],"year":"2020","pmid":1,"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-03-01T00:00:00Z","article_type":"original","publication":"Plants","citation":{"ieee":"T. R. Moturu et al., “Molecular evolution and diversification of proteins involved in miRNA maturation pathway,” Plants, vol. 9, no. 3. MDPI, 2020.","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","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.","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","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.","short":"T.R. Moturu, S. Sinha, H. Salava, S. Thula, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Plants 9 (2020).","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” Plants, vol. 9, no. 3, 299, MDPI, 2020, doi:10.3390/plants9030299."},"abstract":[{"lang":"eng","text":"Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes."}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"7614","relation":"main_file","checksum":"6d5af3e17266a48996b4af4e67e88a85","date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-23T13:37:00Z","access_level":"open_access","file_name":"2020_Plants_Moturu.pdf","creator":"dernst","file_size":2373484,"content_type":"application/pdf"}],"title":"Molecular evolution and diversification of proteins involved in miRNA maturation pathway","ddc":["580"],"status":"public","intvolume":" 9","_id":"7582","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Heterozygous loss of human PAFAH1B1 (coding for LIS1) results in the disruption of neurogenesis and neuronal migration via dysregulation of microtubule (MT) stability and dynein motor function/localization that alters mitotic spindle orientation, chromosomal segregation, and nuclear migration. Recently, human induced pluripotent stem cell (iPSC) models revealed an important role for LIS1 in controlling the length of terminal cell divisions of outer radial glial (oRG) progenitors, suggesting cellular functions of LIS1 in regulating neural progenitor cell (NPC) daughter cell separation. Here we examined the late mitotic stages NPCs in vivo and mouse embryonic fibroblasts (MEFs) in vitro from Pafah1b1-deficient mutants. Pafah1b1-deficient neocortical NPCs and MEFs similarly exhibited cleavage plane displacement with mislocalization of furrow-associated markers, associated with actomyosin dysfunction and cell membrane hyper-contractility. Thus, it suggests LIS1 acts as a key molecular link connecting MTs/dynein and actomyosin, ensuring that cell membrane contractility is tightly controlled to execute proper daughter cell separation."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7593","intvolume":" 9","status":"public","title":"LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility","ddc":["570"],"file":[{"creator":"dernst","content_type":"application/pdf","file_size":15089438,"access_level":"open_access","file_name":"2020_elife_Moon.pdf","success":1,"checksum":"396ceb2dd10b102ef4e699666b9342c3","date_created":"2020-09-24T07:03:20Z","date_updated":"2020-09-24T07:03:20Z","file_id":"8567","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"11","citation":{"chicago":"Moon, Hyang Mi, Simon Hippenmeyer, Liqun Luo, and Anthony Wynshaw-Boris. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.51512.","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.","short":"H.M. Moon, S. Hippenmeyer, L. Luo, A. Wynshaw-Boris, ELife 9 (2020).","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.","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.","apa":"Moon, H. M., Hippenmeyer, S., Luo, L., & Wynshaw-Boris, A. (2020). LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.51512","ama":"Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. eLife. 2020;9. doi:10.7554/elife.51512"},"publication":"eLife","article_type":"original","date_published":"2020-03-11T00:00:00Z","article_number":"51512","file_date_updated":"2020-09-24T07:03:20Z","pmid":1,"year":"2020","department":[{"_id":"SiHi"}],"publisher":"eLife Sciences Publications","publication_status":"published","author":[{"full_name":"Moon, Hyang Mi","last_name":"Moon","first_name":"Hyang Mi"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"},{"full_name":"Wynshaw-Boris, Anthony","first_name":"Anthony","last_name":"Wynshaw-Boris"}],"volume":9,"date_updated":"2023-08-18T07:06:31Z","date_created":"2020-03-20T13:16:41Z","publication_identifier":{"issn":["2050-084X"]},"month":"03","external_id":{"pmid":["32159512"],"isi":["000522835800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.1101/751958","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","doi":"10.7554/elife.51512","language":[{"iso":"eng"}]},{"oa_version":"Preprint","intvolume":" 6","title":"The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis","status":"public","_id":"7600","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Directional intercellular transport of the phytohormone auxin mediated by PIN FORMED (PIN) efflux carriers plays essential roles in both coordinating patterning processes and integrating multiple external cues by rapidly redirecting auxin fluxes. Multilevel regulations of PIN activity under internal and external cues are complicated; however, the underlying molecular mechanism remains elusive. Here we demonstrate that 3’-Phosphoinositide-Dependent Protein Kinase1 (PDK1), which is conserved in plants and mammals, functions as a molecular hub integrating the upstream lipid signalling and the downstream substrate activity through phosphorylation. Genetic analysis uncovers that loss-of-function Arabidopsis mutant pdk1.1 pdk1.2 exhibits a plethora of abnormalities in organogenesis and growth, due to the defective PIN-dependent auxin transport. Further cellular and biochemical analyses reveal that PDK1 phosphorylates D6 Protein Kinase to facilitate its activity towards PIN proteins. Our studies establish a lipid-dependent phosphorylation cascade connecting membrane composition-based cellular signalling with plant growth and patterning by regulating morphogenetic auxin fluxes.","lang":"eng"}],"type":"journal_article","date_published":"2020-05-01T00:00:00Z","page":"556-569","article_type":"original","citation":{"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.","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","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.","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","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."},"publication":"Nature Plants","article_processing_charge":"No","day":"01","scopus_import":"1","volume":6,"date_created":"2020-03-21T16:34:16Z","date_updated":"2023-08-18T07:05:57Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41477-020-0719-y"}]},"author":[{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang"},{"first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"first_name":"Wei","last_name":"Kong","full_name":"Kong, Wei"},{"full_name":"Yang, Xiao-Li","first_name":"Xiao-Li","last_name":"Yang"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely"},{"last_name":"Vondráková","first_name":"Zuzana","full_name":"Vondráková, Zuzana"},{"first_name":"Roberta","last_name":"Filepová","full_name":"Filepová, Roberta"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Xue, Hong-Wei","last_name":"Xue","first_name":"Hong-Wei"}],"department":[{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2020","ec_funded":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1038/s41477-020-0648-9","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Long Term Fellowship"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"pmid":["32393881"],"isi":["000531787500006"]},"main_file_link":[{"url":"https://doi.org/10.1101/755504","open_access":"1"}],"publication_identifier":{"eissn":["20550278"]},"month":"05"},{"volume":11,"date_created":"2020-03-22T23:00:46Z","date_updated":"2023-08-18T07:05:18Z","author":[{"last_name":"Nimeth","first_name":"Barbara Anna","full_name":"Nimeth, Barbara Anna"},{"orcid":"0000-0003-3413-1343","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","last_name":"Riegler","first_name":"Stefan","full_name":"Riegler, Stefan"},{"first_name":"Maria","last_name":"Kalyna","full_name":"Kalyna, Maria"}],"publisher":"Frontiers","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2020","file_date_updated":"2020-07-14T12:48:01Z","article_number":"91","language":[{"iso":"eng"}],"doi":"10.3389/fpls.2020.00091","isi":1,"quality_controlled":"1","external_id":{"isi":["000518903600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["1664462X"]},"month":"02","file":[{"date_updated":"2020-07-14T12:48:01Z","date_created":"2020-03-23T09:03:40Z","checksum":"57c37209f7b6712ced86c0f11b2be74e","relation":"main_file","file_id":"7607","content_type":"application/pdf","file_size":507414,"creator":"dernst","file_name":"2020_FrontiersPlants_Nimeth.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 11","title":"Alternative splicing and DNA damage response in plants","status":"public","ddc":["580"],"_id":"7603","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_published":"2020-02-19T00:00:00Z","article_type":"original","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.","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","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91.","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","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.","short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","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."},"publication":"Frontiers in Plant Science","article_processing_charge":"No","has_accepted_license":"1","day":"19","scopus_import":"1"},{"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.","year":"2020","pmid":1,"publication_status":"published","publisher":"EMBO Press","department":[{"_id":"GaNo"}],"author":[{"full_name":"Weinert, Stefanie","first_name":"Stefanie","last_name":"Weinert"},{"last_name":"Gimber","first_name":"Niclas","full_name":"Gimber, Niclas"},{"first_name":"Dorothea","last_name":"Deuschel","full_name":"Deuschel, Dorothea"},{"last_name":"Stuhlmann","first_name":"Till","full_name":"Stuhlmann, Till"},{"full_name":"Puchkov, Dmytro","first_name":"Dmytro","last_name":"Puchkov"},{"last_name":"Farsi","first_name":"Zohreh","full_name":"Farsi, Zohreh"},{"last_name":"Ludwig","first_name":"Carmen F.","full_name":"Ludwig, Carmen F."},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"},{"first_name":"Karen I.","last_name":"López-Cayuqueo","full_name":"López-Cayuqueo, Karen I."},{"full_name":"Planells-Cases, Rosa","first_name":"Rosa","last_name":"Planells-Cases"},{"first_name":"Thomas J.","last_name":"Jentsch","full_name":"Jentsch, Thomas J."}],"date_created":"2020-03-15T23:00:55Z","date_updated":"2023-08-18T07:07:36Z","volume":39,"article_number":"e103358","file_date_updated":"2020-07-14T12:48:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000517335000001"],"pmid":["32118314"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.15252/embj.2019103358","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7586","title":"Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration","ddc":["570"],"status":"public","intvolume":" 39","oa_version":"Published Version","file":[{"date_created":"2020-03-23T13:51:11Z","date_updated":"2020-07-14T12:48:00Z","checksum":"82750a7a93e3740decbce8474004111a","relation":"main_file","file_id":"7615","file_size":12243278,"content_type":"application/pdf","creator":"dernst","file_name":"2020_EMBO_Weinert.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"publication":"EMBO Journal","citation":{"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","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.","ieee":"S. Weinert et al., “Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration,” EMBO Journal, vol. 39. EMBO Press, 2020.","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","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.","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).","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."},"article_type":"original","date_published":"2020-03-02T00:00:00Z","scopus_import":"1","day":"02","has_accepted_license":"1","article_processing_charge":"No"},{"month":"08","publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"doi":"10.1007/s11005-020-01282-0","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000551556000002"],"arxiv":["1903.10455"]},"main_file_link":[{"url":"https://arxiv.org/abs/1903.10455","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"_id":"26A455A6-B435-11E9-9278-68D0E5697425","grant_number":"846294","call_identifier":"H2020","name":"Geometric study of Wasserstein spaces and free probability"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"ec_funded":1,"author":[{"full_name":"Pitrik, Jozsef","first_name":"Jozsef","last_name":"Pitrik"},{"full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","first_name":"Daniel"}],"date_updated":"2023-08-18T10:17:26Z","date_created":"2020-03-25T15:57:48Z","volume":110,"year":"2020","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.","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Springer Nature","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2020-08-01T00:00:00Z","publication":"Letters in Mathematical Physics","citation":{"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","ista":"Pitrik J, Virosztek D. 2020. Quantum Hellinger distances revisited. Letters in Mathematical Physics. 110(8), 2039–2052.","ieee":"J. Pitrik and D. Virosztek, “Quantum Hellinger distances revisited,” Letters in Mathematical Physics, vol. 110, no. 8. Springer Nature, pp. 2039–2052, 2020.","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","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.","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."},"article_type":"original","page":"2039-2052","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. "}],"issue":"8","type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7618","status":"public","title":"Quantum Hellinger distances revisited","intvolume":" 110"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41598-020-62089-6","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000560406800007"]},"month":"03","publication_identifier":{"eissn":["20452322"]},"date_updated":"2023-08-18T10:25:13Z","date_created":"2020-04-05T22:00:47Z","volume":10,"author":[{"last_name":"Tombaz","first_name":"Tuce","full_name":"Tombaz, Tuce"},{"first_name":"Benjamin A.","last_name":"Dunn","full_name":"Dunn, Benjamin A."},{"full_name":"Hovde, Karoline","last_name":"Hovde","first_name":"Karoline"},{"first_name":"Ryan J","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J"},{"last_name":"Mimica","first_name":"Bartul","full_name":"Mimica, Bartul"},{"first_name":"Pranav","last_name":"Mamidanna","full_name":"Mamidanna, Pranav"},{"last_name":"Roudi","first_name":"Yasser","full_name":"Roudi, Yasser"},{"full_name":"Whitlock, Jonathan R.","last_name":"Whitlock","first_name":"Jonathan R."}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"SaSi"}],"year":"2020","file_date_updated":"2020-07-14T12:48:01Z","article_number":"5559","date_published":"2020-03-27T00:00:00Z","article_type":"original","publication":"Scientific reports","citation":{"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","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","ieee":"T. Tombaz et al., “Action representation in the mouse parieto-frontal network,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020.","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.","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.","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."},"day":"27","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"checksum":"e6cfaaaf7986532132934400038b824a","date_created":"2020-04-06T10:44:23Z","date_updated":"2020-07-14T12:48:01Z","relation":"main_file","file_id":"7644","content_type":"application/pdf","file_size":2621249,"creator":"dernst","access_level":"open_access","file_name":"2020_ScientificReports_Tombaz.pdf"}],"title":"Action representation in the mouse parieto-frontal network","status":"public","ddc":["570"],"intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7632","abstract":[{"lang":"eng","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."}],"issue":"1","type":"journal_article"},{"date_published":"2020-02-24T00:00:00Z","article_type":"original","citation":{"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.","short":"M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (2020).","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.","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","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.","ista":"Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001.","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"},"publication":"European Journal of Physics","article_processing_charge":"No","has_accepted_license":"1","day":"24","scopus_import":"1","oa_version":"Published Version","file":[{"checksum":"47dda164e33b6c0c6c3ed14aad298376","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-06T08:53:53Z","file_id":"7641","relation":"main_file","creator":"dernst","file_size":1533672,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_EuropJourPhysics_Plesch.pdf"}],"intvolume":" 41","ddc":["530"],"title":"The IYPT and the 'Ring Oiler' problem","status":"public","_id":"7622","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","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."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1088/1361-6404/ab6414","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000537425400001"],"arxiv":["1910.03290"]},"publication_identifier":{"issn":["01430807"],"eissn":["13616404"]},"month":"02","volume":41,"date_created":"2020-03-31T11:25:04Z","date_updated":"2023-08-18T10:18:29Z","author":[{"full_name":"Plesch, Martin","first_name":"Martin","last_name":"Plesch"},{"full_name":"Plesník, Samuel","first_name":"Samuel","last_name":"Plesník"},{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova","first_name":"Natalia","full_name":"Ruzickova, Natalia"}],"publisher":"IOP Publishing","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2020","file_date_updated":"2020-07-14T12:48:01Z","article_number":"034001"},{"publication_identifier":{"issn":["02182025"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1142/S021820252050013X","project":[{"name":"Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments","_id":"25AD6156-B435-11E9-9278-68D0E5697425","grant_number":"LS13-029"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.09426"}],"external_id":{"arxiv":["1903.09426"],"isi":["000525349900003"]},"volume":30,"date_created":"2020-03-31T11:25:05Z","date_updated":"2023-08-18T10:18:56Z","author":[{"last_name":"Jankowiak","first_name":"Gaspard","full_name":"Jankowiak, Gaspard"},{"first_name":"Diane","last_name":"Peurichard","full_name":"Peurichard, Diane"},{"last_name":"Reversat","first_name":"Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne"},{"last_name":"Schmeiser","first_name":"Christian","full_name":"Schmeiser, Christian"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publisher":"World Scientific","department":[{"_id":"MiSi"}],"publication_status":"published","year":"2020","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.","article_processing_charge":"No","day":"18","scopus_import":"1","date_published":"2020-03-18T00:00:00Z","page":"513-537","article_type":"original","citation":{"chicago":"Jankowiak, Gaspard, Diane Peurichard, Anne Reversat, Christian Schmeiser, and Michael K Sixt. “Modeling Adhesion-Independent Cell Migration.” Mathematical Models and Methods in Applied Sciences. World Scientific, 2020. https://doi.org/10.1142/S021820252050013X.","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.","short":"G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, M.K. Sixt, Mathematical Models and Methods in Applied Sciences 30 (2020) 513–537.","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.","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.","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","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"},"publication":"Mathematical Models and Methods in Applied Sciences","issue":"3","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"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 30","title":"Modeling adhesion-independent cell migration","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7623"},{"file_date_updated":"2020-10-06T07:41:35Z","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2020","volume":71,"date_updated":"2023-08-18T10:27:52Z","date_created":"2020-04-06T10:57:08Z","author":[{"full_name":"Lee, E","last_name":"Lee","first_name":"E"},{"full_name":"Vila Nova Santana, B","last_name":"Vila Nova Santana","first_name":"B"},{"full_name":"Samuels, E","first_name":"E","last_name":"Samuels"},{"first_name":"F","last_name":"Benitez-Fuente","full_name":"Benitez-Fuente, F"},{"full_name":"Corsi, E","first_name":"E","last_name":"Corsi"},{"full_name":"Botella, MA","last_name":"Botella","first_name":"MA"},{"last_name":"Perez-Sancho","first_name":"J","full_name":"Perez-Sancho, J"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Macho, A","first_name":"A","last_name":"Macho"},{"last_name":"Alves Azevedo","first_name":"A","full_name":"Alves Azevedo, A"},{"last_name":"Rosado","first_name":"A","full_name":"Rosado, A"}],"publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"month":"07","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000553125400007"],"pmid":["32179893"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/jxb/eraa138","type":"journal_article","issue":"14","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"}],"intvolume":" 71","title":"Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis","ddc":["580"],"status":"public","_id":"7646","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"b06aaaa93dc41896da805fe4b75cf3a1","date_updated":"2020-10-06T07:41:35Z","date_created":"2020-10-06T07:41:35Z","file_id":"8613","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1916031,"access_level":"open_access","file_name":"2020_JourExperimBotany_Lee.pdf"}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"06","page":"3986–3998","article_type":"original","citation":{"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.","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.","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.","ama":"Lee E, Vila Nova Santana B, Samuels E, et al. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. 2020;71(14):3986–3998. doi:10.1093/jxb/eraa138","apa":"Lee, E., Vila Nova Santana, B., Samuels, E., Benitez-Fuente, F., Corsi, E., Botella, M., … Rosado, A. (2020). Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa138","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.","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."},"publication":"Journal of Experimental Botany","date_published":"2020-07-06T00:00:00Z"},{"article_type":"original","citation":{"ama":"Berry MJ, Tkačik G. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020","ista":"Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 14, 20.","apa":"Berry, M. J., & Tkačik, G. (2020). Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. Frontiers. https://doi.org/10.3389/fncom.2020.00020","ieee":"M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle for population codes,” Frontiers in Computational Neuroscience, vol. 14. Frontiers, 2020.","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).","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."},"publication":"Frontiers in Computational Neuroscience","date_published":"2020-03-13T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"13","intvolume":" 14","ddc":["570"],"status":"public","title":"Clustering of neural activity: A design principle for population codes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7656","oa_version":"Published Version","file":[{"file_id":"7659","relation":"main_file","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-14T12:20:39Z","checksum":"2b1da23823eae9cedbb42d701945b61e","file_name":"2020_Frontiers_Berry.pdf","access_level":"open_access","creator":"dernst","file_size":4082937,"content_type":"application/pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement."}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["32231528"],"isi":["000525543200001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fncom.2020.00020","publication_identifier":{"eissn":["16625188"]},"month":"03","department":[{"_id":"GaTk"}],"publisher":"Frontiers","publication_status":"published","pmid":1,"year":"2020","volume":14,"date_updated":"2023-08-18T10:30:11Z","date_created":"2020-04-12T22:00:40Z","author":[{"last_name":"Berry","first_name":"Michael J.","full_name":"Berry, Michael J."},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"article_number":"20","file_date_updated":"2020-07-14T12:48:01Z"},{"article_number":"013106","ec_funded":1,"file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"MaSe"}],"publisher":"IOP Publishing","publication_status":"published","year":"2020","volume":2020,"date_updated":"2023-08-18T10:27:15Z","date_created":"2020-04-05T22:00:50Z","author":[{"full_name":"De Nicola, Stefano","first_name":"Stefano","last_name":"De Nicola","id":"42832B76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4842-6671"},{"full_name":"Doyon, B.","last_name":"Doyon","first_name":"B."},{"full_name":"Bhaseen, M. J.","last_name":"Bhaseen","first_name":"M. J."}],"publication_identifier":{"eissn":["17425468"]},"month":"01","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000520187500001"],"arxiv":["1909.13142"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1088/1742-5468/ab6093","type":"journal_article","issue":"1","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","title":"Non-equilibrium quantum spin dynamics from classical stochastic processes","ddc":["530"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7638","oa_version":"Published Version","file":[{"file_id":"7648","relation":"main_file","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-06T13:15:49Z","checksum":"4030e683c15d30b7b4794ec7dc1b6537","file_name":"2020_JournStatisticalMech_DeNicola.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3159026}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"22","article_type":"original","citation":{"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","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.","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.","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","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.","short":"S. De Nicola, B. Doyon, M.J. Bhaseen, Journal of Statistical Mechanics: Theory and Experiment 2020 (2020).","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."},"publication":"Journal of Statistical Mechanics: Theory and Experiment","date_published":"2020-01-22T00:00:00Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7637","intvolume":" 33","title":"From weakly interacting particles to a regularised Dean-Kawasaki model","status":"public","oa_version":"Preprint","type":"journal_article","issue":"2","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."}],"citation":{"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.","short":"F. Cornalba, T. Shardlow, J. Zimmer, Nonlinearity 33 (2020) 864–891.","chicago":"Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab5174.","ama":"Cornalba F, Shardlow T, Zimmer J. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 2020;33(2):864-891. doi:10.1088/1361-6544/ab5174","ista":"Cornalba F, Shardlow T, Zimmer J. 2020. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 33(2), 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.","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"},"publication":"Nonlinearity","page":"864-891","article_type":"original","date_published":"2020-01-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"10","year":"2020","department":[{"_id":"JuFi"}],"publisher":"IOP Publishing","publication_status":"published","author":[{"full_name":"Cornalba, Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425","orcid":"0000-0002-6269-5149","first_name":"Federico","last_name":"Cornalba"},{"last_name":"Shardlow","first_name":"Tony","full_name":"Shardlow, Tony"},{"full_name":"Zimmer, Johannes","first_name":"Johannes","last_name":"Zimmer"}],"volume":33,"date_updated":"2023-08-18T10:26:07Z","date_created":"2020-04-05T22:00:49Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.06448"}],"oa":1,"external_id":{"isi":["000508175400001"],"arxiv":["1811.06448"]},"isi":1,"quality_controlled":"1","doi":"10.1088/1361-6544/ab5174","language":[{"iso":"eng"}],"publication_identifier":{"issn":["09517715"],"eissn":["13616544"]},"month":"01"},{"article_number":"2459","file_date_updated":"2020-07-14T12:48:01Z","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"MDPI","year":"2020","pmid":1,"date_updated":"2023-08-21T06:13:19Z","date_created":"2020-04-19T22:00:55Z","volume":21,"author":[{"full_name":"Martín-Belmonte, Alejandro","last_name":"Martín-Belmonte","first_name":"Alejandro"},{"last_name":"Aguado","first_name":"Carolina","full_name":"Aguado, Carolina"},{"first_name":"Rocío","last_name":"Alfaro-Ruíz","full_name":"Alfaro-Ruíz, Rocío"},{"full_name":"Moreno-Martínez, Ana Esther","last_name":"Moreno-Martínez","first_name":"Ana Esther"},{"first_name":"Luis","last_name":"De La Ossa","full_name":"De La Ossa, Luis"},{"full_name":"Martínez-Hernández, José","first_name":"José","last_name":"Martínez-Hernández"},{"last_name":"Buisson","first_name":"Alain","full_name":"Buisson, Alain"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"last_name":"Luján","first_name":"Rafael","full_name":"Luján, Rafael"}],"month":"04","publication_identifier":{"eissn":["14220067"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["32252271"],"isi":["000535574200201"]},"language":[{"iso":"eng"}],"doi":"10.3390/ijms21072459","type":"journal_article","abstract":[{"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","lang":"eng"}],"issue":"7","status":"public","title":"Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease","ddc":["570"],"intvolume":" 21","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7664","file":[{"relation":"main_file","file_id":"7669","checksum":"b9d2f1657d8c4a74b01a62b474d009b0","date_created":"2020-04-20T11:43:18Z","date_updated":"2020-07-14T12:48:01Z","access_level":"open_access","file_name":"2020_JournMolecSciences_Martin_Belmonte.pdf","content_type":"application/pdf","file_size":2941197,"creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","day":"02","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"International journal of molecular sciences","citation":{"chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, Ryuichi Shigemoto, Yugo Fukazawa, and Rafael Luján. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21072459.","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).","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.","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.","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.","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"},"date_published":"2020-04-02T00:00:00Z"},{"article_number":"63","ec_funded":1,"file_date_updated":"2020-07-14T12:48:01Z","publisher":"Frontiers Media","department":[{"_id":"JoDa"},{"_id":"RySh"}],"publication_status":"published","year":"2020","volume":14,"date_created":"2020-04-19T22:00:55Z","date_updated":"2023-08-21T06:12:48Z","author":[{"orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","last_name":"Eguchi","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku"},{"last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp"},{"first_name":"Elena","last_name":"Hollergschwandtner","id":"3C054040-F248-11E8-B48F-1D18A9856A87","full_name":"Hollergschwandtner, Elena"},{"full_name":"Itakura, Makoto","first_name":"Makoto","last_name":"Itakura"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["16625102"]},"month":"03","project":[{"call_identifier":"H2020","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","_id":"2659CC84-B435-11E9-9278-68D0E5697425","grant_number":"793482"},{"grant_number":"694539","_id":"25CA28EA-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"},{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000525582200001"]},"language":[{"iso":"eng"}],"doi":"10.3389/fncel.2020.00063","type":"journal_article","abstract":[{"lang":"eng","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."}],"intvolume":" 14","status":"public","title":"Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions","ddc":["570"],"_id":"7665","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":9227283,"creator":"dernst","access_level":"open_access","file_name":"2020_FrontiersCellularNeurosc_Eguchi.pdf","checksum":"1c145123c6f8dc3e2e4bd5a66a1ad60e","date_created":"2020-04-20T10:59:49Z","date_updated":"2020-07-14T12:48:01Z","relation":"main_file","file_id":"7668"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"19","article_type":"original","citation":{"short":"K. Eguchi, P. Velicky, E. Saeckl, M. Itakura, Y. Fukazawa, J.G. Danzl, R. Shigemoto, Frontiers in Cellular Neuroscience 14 (2020).","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.","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.","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","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.","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."},"publication":"Frontiers in Cellular Neuroscience","date_published":"2020-03-19T00:00:00Z"},{"file_date_updated":"2020-07-14T12:48:01Z","author":[{"first_name":"Martin","last_name":"Felhofer","full_name":"Felhofer, Martin"},{"full_name":"Bock, Peter","last_name":"Bock","first_name":"Peter"},{"full_name":"Singh, Adya","last_name":"Singh","first_name":"Adya"},{"full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze","last_name":"Prats Mateu"},{"first_name":"Ronald","last_name":"Zirbs","full_name":"Zirbs, Ronald"},{"last_name":"Gierlinger","first_name":"Notburga","full_name":"Gierlinger, Notburga"}],"volume":20,"date_updated":"2023-08-21T06:12:09Z","date_created":"2020-04-19T22:00:54Z","pmid":1,"year":"2020","department":[{"_id":"MaLo"}],"publisher":"American Chemical Society","publication_status":"published","publication_identifier":{"eissn":["15306992"]},"month":"04","doi":"10.1021/acs.nanolett.0c00205","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32196350"],"isi":["000526413400055"]},"isi":1,"quality_controlled":"1","issue":"4","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":7108014,"creator":"dernst","file_name":"2020_NanoLetters_Felhofer.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-20T10:43:36Z","checksum":"fe46146a9c4c620592a1932a8599069e","relation":"main_file","file_id":"7667"}],"_id":"7663","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 20","status":"public","title":"Wood deformation leads to rearrangement of molecules at the nanoscale","ddc":["530"],"article_processing_charge":"No","has_accepted_license":"1","day":"08","scopus_import":"1","date_published":"2020-04-08T00:00:00Z","citation":{"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.","short":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger, Nano Letters 20 (2020) 2647–2653.","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.","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","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.","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.","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"},"publication":"Nano Letters","page":"2647-2653","article_type":"original"},{"file":[{"success":1,"checksum":"f8cc96e497f00c38340b5dafe0cb91d7","date_created":"2020-11-20T13:22:21Z","date_updated":"2020-11-20T13:22:21Z","file_id":"8786","relation":"main_file","creator":"dernst","file_size":701673,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_DiscreteCompGeo_Edelsbrunner.pdf"}],"oa_version":"Published Version","_id":"7666","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 64","ddc":["510"],"title":"Tri-partitions and bases of an ordered complex","status":"public","abstract":[{"lang":"eng","text":"Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral complex, K, and every dimension, p, there is a partition of the set of p-cells into a maximal p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition is unique, and it can be computed by a matrix reduction algorithm that also constructs canonical bases of cycle and boundary groups."}],"type":"journal_article","date_published":"2020-03-20T00:00:00Z","citation":{"short":"H. Edelsbrunner, K. Ölsböck, Discrete and Computational Geometry 64 (2020) 759–775.","mla":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 759–75, doi:10.1007/s00454-020-00188-x.","chicago":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00188-x.","ama":"Edelsbrunner H, Ölsböck K. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 2020;64:759-775. doi:10.1007/s00454-020-00188-x","apa":"Edelsbrunner, H., & Ölsböck, K. (2020). Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00188-x","ieee":"H. Edelsbrunner and K. Ölsböck, “Tri-partitions and bases of an ordered complex,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 759–775, 2020.","ista":"Edelsbrunner H, Ölsböck K. 2020. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 64, 759–775."},"publication":"Discrete and Computational Geometry","page":"759-775","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"20","scopus_import":"1","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"orcid":"0000-0002-4672-8297","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","last_name":"Ölsböck","first_name":"Katharina","full_name":"Ölsböck, Katharina"}],"volume":64,"date_updated":"2023-08-21T06:13:48Z","date_created":"2020-04-19T22:00:56Z","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF).","year":"2020","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"file_date_updated":"2020-11-20T13:22:21Z","doi":"10.1007/s00454-020-00188-x","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000520918800001"]},"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"month":"03"}]