[{"date_created":"2020-02-18T10:02:25Z","status":"public","day":"01","pmid":1,"volume":62,"isi":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1111/jipb.12905","open_access":"1"}],"doi":"10.1111/jipb.12905","publication":"Journal of Integrative Plant Biology","date_updated":"2023-08-18T06:44:16Z","issue":"9","oa":1,"month":"09","intvolume":"        62","date_published":"2020-09-01T00:00:00Z","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).","year":"2020","external_id":{"pmid":["31912615"],"isi":["000515803000001"]},"page":"1433-1451","_id":"7497","quality_controlled":"1","citation":{"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.","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.","ieee":"L. Han <i>et al.</i>, “Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid,” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9. Wiley, pp. 1433–1451, 2020.","ama":"Han L, Zhou X, Zhao Y, et al. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. <i>Journal of Integrative Plant Biology</i>. 2020;62(9):1433-1451. doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>","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.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>.","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. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>","mla":"Han, L., et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9, Wiley, 2020, pp. 1433–51, doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>."},"publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"type":"journal_article","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."}],"scopus_import":"1","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Han, L","first_name":"L","last_name":"Han"},{"first_name":"X","last_name":"Zhou","full_name":"Zhou, X"},{"last_name":"Zhao","first_name":"Y","full_name":"Zhao, Y"},{"first_name":"S","last_name":"Zhu","full_name":"Zhu, S"},{"last_name":"Wu","first_name":"L","full_name":"Wu, L"},{"full_name":"He, Y","last_name":"He","first_name":"Y"},{"full_name":"Ping, X","last_name":"Ping","first_name":"X"},{"first_name":"X","last_name":"Lu","full_name":"Lu, X"},{"last_name":"Huang","first_name":"W","full_name":"Huang, W"},{"full_name":"Qian, J","first_name":"J","last_name":"Qian"},{"full_name":"Zhang, L","first_name":"L","last_name":"Zhang"},{"first_name":"X","last_name":"Jiang","full_name":"Jiang, X"},{"first_name":"D","last_name":"Zhu","full_name":"Zhu, D"},{"first_name":"C","last_name":"Luo","full_name":"Luo, C"},{"full_name":"Li, S","first_name":"S","last_name":"Li"},{"last_name":"Dong","first_name":"Q","full_name":"Dong, Q"},{"first_name":"Q","last_name":"Fu","full_name":"Fu, Q"},{"last_name":"Deng","first_name":"K","full_name":"Deng, K"},{"last_name":"Wang","first_name":"X","full_name":"Wang, X"},{"full_name":"Wang, L","last_name":"Wang","first_name":"L"},{"first_name":"S","last_name":"Peng","full_name":"Peng, S"},{"full_name":"Wu, J","first_name":"J","last_name":"Wu"},{"last_name":"Li","first_name":"W","full_name":"Li, W"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Zhu, Y","last_name":"Zhu","first_name":"Y"},{"full_name":"He, X","first_name":"X","last_name":"He"},{"full_name":"Du, Y","last_name":"Du","first_name":"Y"}],"title":"Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid","publisher":"Wiley","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"JiFr"}]},{"publication":"New Phytologist","doi":"10.1111/nph.16446","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8822"}]},"oa_version":"Published Version","ec_funded":1,"isi":1,"volume":226,"pmid":1,"ddc":["580"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-02-18T10:03:47Z","day":"01","status":"public","external_id":{"isi":["000514939700001"],"pmid":["31971254"]},"page":"1375-1383","year":"2020","date_published":"2020-06-01T00:00:00Z","intvolume":"       226","month":"06","acknowledgement":"We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests.","date_updated":"2024-03-25T23:30:21Z","oa":1,"issue":"5","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development","_id":"2699E3D2-B435-11E9-9278-68D0E5697425","grant_number":"25239"}],"publication_status":"published","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"citation":{"mla":"Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” <i>New Phytologist</i>, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:<a href=\"https://doi.org/10.1111/nph.16446\">10.1111/nph.16446</a>.","apa":"Mazur, E., Kulik, I., Hajny, J., &#38; Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16446\">https://doi.org/10.1111/nph.16446</a>","chicago":"Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” <i>New Phytologist</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/nph.16446\">https://doi.org/10.1111/nph.16446</a>.","ama":"Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. <i>New Phytologist</i>. 2020;226(5):1375-1383. doi:<a href=\"https://doi.org/10.1111/nph.16446\">10.1111/nph.16446</a>","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383.","ista":"Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383.","ieee":"E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” <i>New Phytologist</i>, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020."},"abstract":[{"lang":"eng","text":"Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts."}],"file_date_updated":"2020-11-20T09:32:10Z","type":"journal_article","_id":"7500","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Mazur, E","last_name":"Mazur","first_name":"E"},{"first_name":"Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","last_name":"Kulik","full_name":"Kulik, Ivan"},{"orcid":"0000-0003-2140-7195","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","full_name":"Hajny, Jakub"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","file":[{"access_level":"open_access","checksum":"17de728b0205979feb95ce663ba918c2","relation":"main_file","content_type":"application/pdf","file_id":"8781","file_size":2106888,"creator":"dernst","date_created":"2020-11-20T09:32:10Z","date_updated":"2020-11-20T09:32:10Z","success":1,"file_name":"2020_NewPhytologist_Mazur.pdf"}]},{"month":"02","intvolume":"       325","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"date_published":"2020-02-24T00:00:00Z","acknowledgement":"We thank Christoph Lampert and Nikolaus Mayer for fruitful discussions. This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement No. 754411.","date_updated":"2023-08-18T06:38:16Z","oa":1,"external_id":{"isi":["000650971303002"],"arxiv":["1911.09032"]},"page":"2433-2440","conference":{"name":"ECAI: European Conference on Artificial Intelligence","end_date":"2020-09-08","start_date":"2020-08-29","location":"Santiago de Compostela, Spain"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","year":"2020","volume":325,"date_created":"2020-02-21T16:44:03Z","tmp":{"short":"CC BY-NC (4.0)","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"},"ddc":["000"],"status":"public","day":"24","doi":"10.3233/FAIA200375","publication":"24th European Conference on Artificial Intelligence","isi":1,"oa_version":"Published Version","ec_funded":1,"has_accepted_license":"1","publisher":"IOS Press","file":[{"file_id":"8540","content_type":"application/pdf","file_size":1692214,"creator":"dernst","access_level":"open_access","relation":"main_file","checksum":"80642fa0b6cd7da95dcd87d63789ad5e","success":1,"file_name":"2020_ECAI_Henzinger.pdf","date_updated":"2020-09-21T07:12:32Z","date_created":"2020-09-21T07:12:32Z"}],"author":[{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"last_name":"Lukina","first_name":"Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","full_name":"Lukina, Anna"},{"first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","last_name":"Schilling","full_name":"Schilling, Christian"}],"title":"Outside the box: Abstraction-based monitoring of neural networks","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"citation":{"mla":"Henzinger, Thomas A., et al. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” <i>24th European Conference on Artificial Intelligence</i>, vol. 325, IOS Press, 2020, pp. 2433–40, doi:<a href=\"https://doi.org/10.3233/FAIA200375\">10.3233/FAIA200375</a>.","apa":"Henzinger, T. A., Lukina, A., &#38; Schilling, C. (2020). Outside the box: Abstraction-based monitoring of neural networks. In <i>24th European Conference on Artificial Intelligence</i> (Vol. 325, pp. 2433–2440). Santiago de Compostela, Spain: IOS Press. <a href=\"https://doi.org/10.3233/FAIA200375\">https://doi.org/10.3233/FAIA200375</a>","chicago":"Henzinger, Thomas A, Anna Lukina, and Christian Schilling. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” In <i>24th European Conference on Artificial Intelligence</i>, 325:2433–40. IOS Press, 2020. <a href=\"https://doi.org/10.3233/FAIA200375\">https://doi.org/10.3233/FAIA200375</a>.","ama":"Henzinger TA, Lukina A, Schilling C. Outside the box: Abstraction-based monitoring of neural networks. In: <i>24th European Conference on Artificial Intelligence</i>. Vol 325. IOS Press; 2020:2433-2440. doi:<a href=\"https://doi.org/10.3233/FAIA200375\">10.3233/FAIA200375</a>","ieee":"T. A. Henzinger, A. Lukina, and C. Schilling, “Outside the box: Abstraction-based monitoring of neural networks,” in <i>24th European Conference on Artificial Intelligence</i>, Santiago de Compostela, Spain, 2020, vol. 325, pp. 2433–2440.","short":"T.A. Henzinger, A. Lukina, C. Schilling, in:, 24th European Conference on Artificial Intelligence, IOS Press, 2020, pp. 2433–2440.","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."},"type":"conference","file_date_updated":"2020-09-21T07:12:32Z","abstract":[{"lang":"eng","text":"Neural networks have demonstrated unmatched performance in a range of classification tasks. Despite numerous efforts of the research community, novelty detection remains one of the significant limitations of neural networks. The ability to identify previously unseen inputs as novel is crucial for our understanding of the decisions made by neural networks. At runtime, inputs not falling into any of the categories learned during training cannot be classified correctly by the neural network. Existing approaches treat the neural network as a black box and try to detect novel inputs based on the confidence of the output predictions. However, neural networks are not trained to reduce their confidence for novel inputs, which limits the effectiveness of these approaches. We propose a framework to monitor a neural network by observing the hidden layers. We employ a common abstraction from program analysis - boxes - to identify novel behaviors in the monitored layers, i.e., inputs that cause behaviors outside the box. For each neuron, the boxes range over the values seen in training. The framework is efficient and flexible to achieve a desired trade-off between raising false warnings and detecting novel inputs. We illustrate the performance and the robustness to variability in the unknown classes on popular image-classification benchmarks."}],"arxiv":1,"_id":"7505","quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"publication_status":"published"},{"department":[{"_id":"RoSe"}],"article_processing_charge":"Yes (via OA deal)","article_type":"original","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","title":"Higher order corrections to the mean-field description of the dynamics of interacting bosons","author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","last_name":"Bossmann","orcid":"0000-0002-6854-1343","full_name":"Bossmann, Lea"},{"first_name":"Nataša","last_name":"Pavlović","full_name":"Pavlović, Nataša"},{"last_name":"Pickl","first_name":"Peter","full_name":"Pickl, Peter"},{"last_name":"Soffer","first_name":"Avy","full_name":"Soffer, Avy"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2020_JournStatPhysics_Bossmann.pdf","success":1,"date_updated":"2020-11-20T09:26:46Z","date_created":"2020-11-20T09:26:46Z","creator":"dernst","file_size":576726,"file_id":"8780","content_type":"application/pdf","access_level":"open_access","checksum":"643e230bf147e64d9cdb3f6cc573679d","relation":"main_file"}],"publication_status":"published","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"scopus_import":"1","abstract":[{"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.","lang":"eng"}],"arxiv":1,"file_date_updated":"2020-11-20T09:26:46Z","type":"journal_article","citation":{"apa":"Bossmann, L., Pavlović, N., Pickl, P., &#38; Soffer, A. (2020). Higher order corrections to the mean-field description of the dynamics of interacting bosons. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-020-02500-8\">https://doi.org/10.1007/s10955-020-02500-8</a>","mla":"Bossmann, Lea, et al. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” <i>Journal of Statistical Physics</i>, vol. 178, Springer Nature, 2020, pp. 1362–96, doi:<a href=\"https://doi.org/10.1007/s10955-020-02500-8\">10.1007/s10955-020-02500-8</a>.","short":"L. Bossmann, N. Pavlović, P. Pickl, A. Soffer, Journal of Statistical Physics 178 (2020) 1362–1396.","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.","ieee":"L. Bossmann, N. Pavlović, P. Pickl, and A. Soffer, “Higher order corrections to the mean-field description of the dynamics of interacting bosons,” <i>Journal of Statistical Physics</i>, vol. 178. Springer Nature, pp. 1362–1396, 2020.","ama":"Bossmann L, Pavlović N, Pickl P, Soffer A. Higher order corrections to the mean-field description of the dynamics of interacting bosons. <i>Journal of Statistical Physics</i>. 2020;178:1362-1396. doi:<a href=\"https://doi.org/10.1007/s10955-020-02500-8\">10.1007/s10955-020-02500-8</a>","chicago":"Bossmann, Lea, Nataša Pavlović, Peter Pickl, and Avy Soffer. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” <i>Journal of Statistical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10955-020-02500-8\">https://doi.org/10.1007/s10955-020-02500-8</a>."},"publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"quality_controlled":"1","_id":"7508","page":"1362-1396","external_id":{"isi":["000516342200001"],"arxiv":["1905.06164"]},"year":"2020","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.","date_published":"2020-02-21T00:00:00Z","month":"02","intvolume":"       178","oa":1,"date_updated":"2023-08-18T06:37:46Z","publication":"Journal of Statistical Physics","doi":"10.1007/s10955-020-02500-8","oa_version":"Published Version","ec_funded":1,"isi":1,"volume":178,"status":"public","day":"21","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_created":"2020-02-23T09:45:51Z"},{"year":"2020","external_id":{"isi":["000522798000001"],"arxiv":["1811.01205"]},"oa":1,"date_updated":"2023-08-18T06:37:09Z","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.","article_number":"107053","date_published":"2020-05-13T00:00:00Z","intvolume":"       365","month":"05","oa_version":"Preprint","ec_funded":1,"isi":1,"publication":"Advances in Mathematics","doi":"10.1016/j.aim.2020.107053","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01205"}],"day":"13","status":"public","date_created":"2020-02-23T21:43:50Z","ddc":["515"],"volume":365,"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"article_processing_charge":"No","author":[{"full_name":"Zhang, Haonan","last_name":"Zhang","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"title":"From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","_id":"7509","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<p<1 which was first proved by Epstein using complex analysis. The key is to reduce the problem to the joint convexity/concavity of the trace functions Ψp,1−p,1(A,B)=TrK∗ApKB1−p,  −1≤p≤1, using a variational method. "}],"arxiv":1,"type":"journal_article","citation":{"ista":"Zhang H. 2020. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. 365, 107053.","ieee":"H. Zhang, “From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture,” <i>Advances in Mathematics</i>, vol. 365. Elsevier, 2020.","short":"H. Zhang, Advances in Mathematics 365 (2020).","ama":"Zhang H. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. <i>Advances in Mathematics</i>. 2020;365. doi:<a href=\"https://doi.org/10.1016/j.aim.2020.107053\">10.1016/j.aim.2020.107053</a>","chicago":"Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” <i>Advances in Mathematics</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.aim.2020.107053\">https://doi.org/10.1016/j.aim.2020.107053</a>.","apa":"Zhang, H. (2020). From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2020.107053\">https://doi.org/10.1016/j.aim.2020.107053</a>","mla":"Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” <i>Advances in Mathematics</i>, vol. 365, 107053, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.aim.2020.107053\">10.1016/j.aim.2020.107053</a>."}},{"intvolume":"        11","month":"02","date_published":"2020-02-13T00:00:00Z","article_number":"876","date_updated":"2023-08-18T06:36:41Z","oa":1,"external_id":{"isi":["000514928000017"]},"year":"2020","volume":11,"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-02-23T23:00:35Z","day":"13","status":"public","doi":"10.1038/s41467-020-14535-2","publication":"Nature Communications","isi":1,"oa_version":"Published Version","has_accepted_license":"1","publisher":"Springer Nature","file":[{"file_name":"2020_NatureComm_Turonova.pdf","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-24T14:00:54Z","file_id":"7517","content_type":"application/pdf","creator":"dernst","file_size":2027529,"checksum":"2c8d10475e1b0d397500760e28bdf561","relation":"main_file","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Turoňová","first_name":"Beata","full_name":"Turoňová, Beata"},{"full_name":"Hagen, Wim J.H.","last_name":"Hagen","first_name":"Wim J.H."},{"orcid":"0000-0003-1756-6564","last_name":"Obr","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin"},{"last_name":"Mosalaganti","first_name":"Shyamal","full_name":"Mosalaganti, Shyamal"},{"first_name":"J. Wouter","last_name":"Beugelink","full_name":"Beugelink, J. Wouter"},{"first_name":"Christian E.","last_name":"Zimmerli","full_name":"Zimmerli, Christian E."},{"last_name":"Kräusslich","first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg"},{"first_name":"Martin","last_name":"Beck","full_name":"Beck, Martin"}],"title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","article_processing_charge":"No","department":[{"_id":"FlSc"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"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.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>.","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.","short":"B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020).","ieee":"B. Turoňová <i>et al.</i>, “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ama":"Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>","mla":"Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>, vol. 11, 876, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>"},"publication_identifier":{"eissn":["20411723"]},"type":"journal_article","file_date_updated":"2020-07-14T12:47:59Z","scopus_import":"1","abstract":[{"text":"Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.","lang":"eng"}],"_id":"7511","quality_controlled":"1","publication_status":"published"},{"isi":1,"ec_funded":1,"oa_version":"Preprint","doi":"10.1016/j.jfa.2020.108507","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11340"}],"publication":"Journal of Functional Analysis","status":"public","day":"01","date_created":"2020-02-23T23:00:36Z","volume":278,"year":"2020","external_id":{"isi":["000522798900001"],"arxiv":["1804.11340"]},"issue":"12","oa":1,"date_updated":"2023-08-18T06:36:10Z","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","article_number":"108507","month":"07","intvolume":"       278","date_published":"2020-07-01T00:00:00Z","publication_status":"published","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7"}],"quality_controlled":"1","_id":"7512","type":"journal_article","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."}],"scopus_import":"1","arxiv":1,"publication_identifier":{"eissn":["10960783"],"issn":["00221236"]},"citation":{"chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Local Laws for Polynomials of Wigner Matrices.” <i>Journal of Functional Analysis</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jfa.2020.108507\">https://doi.org/10.1016/j.jfa.2020.108507</a>.","ista":"Erdös L, Krüger TH, Nemish Y. 2020. Local laws for polynomials of Wigner matrices. Journal of Functional Analysis. 278(12), 108507.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Journal of Functional Analysis 278 (2020).","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Local laws for polynomials of Wigner matrices,” <i>Journal of Functional Analysis</i>, vol. 278, no. 12. Elsevier, 2020.","ama":"Erdös L, Krüger TH, Nemish Y. Local laws for polynomials of Wigner matrices. <i>Journal of Functional Analysis</i>. 2020;278(12). doi:<a href=\"https://doi.org/10.1016/j.jfa.2020.108507\">10.1016/j.jfa.2020.108507</a>","mla":"Erdös, László, et al. “Local Laws for Polynomials of Wigner Matrices.” <i>Journal of Functional Analysis</i>, vol. 278, no. 12, 108507, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jfa.2020.108507\">10.1016/j.jfa.2020.108507</a>.","apa":"Erdös, L., Krüger, T. H., &#38; Nemish, Y. (2020). Local laws for polynomials of Wigner matrices. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2020.108507\">https://doi.org/10.1016/j.jfa.2020.108507</a>"},"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"article_processing_charge":"No","title":"Local laws for polynomials of Wigner matrices","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"orcid":"0000-0002-4821-3297","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","full_name":"Krüger, Torben H"},{"last_name":"Nemish","orcid":"0000-0002-7327-856X","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","first_name":"Yuriy","full_name":"Nemish, Yuriy"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier"},{"supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"day":"24","status":"public","date_created":"2020-02-24T09:17:27Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"id":"7524","status":"public","relation":"part_of_dissertation"}]},"doi":"10.15479/AT:ISTA:7514","degree_awarded":"PhD","oa":1,"date_updated":"2023-09-07T13:12:42Z","month":"02","alternative_title":["ISTA Thesis"],"date_published":"2020-02-24T00:00:00Z","year":"2020","page":"148","_id":"7514","file_date_updated":"2020-07-14T12:47:59Z","type":"dissertation","abstract":[{"text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"apa":"Mayer, S. (2020). <i>The free energy of a dilute two-dimensional Bose gas</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7514\">https://doi.org/10.15479/AT:ISTA:7514</a>","mla":"Mayer, Simon. <i>The Free Energy of a Dilute Two-Dimensional Bose Gas</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7514\">10.15479/AT:ISTA:7514</a>.","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7514\">10.15479/AT:ISTA:7514</a>","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7514\">https://doi.org/10.15479/AT:ISTA:7514</a>."},"publication_status":"published","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"}],"file":[{"date_created":"2020-02-24T09:15:06Z","date_updated":"2020-07-14T12:47:59Z","file_name":"thesis.pdf","access_level":"open_access","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","relation":"main_file","creator":"dernst","file_size":1563429,"content_type":"application/pdf","file_id":"7515"},{"date_created":"2020-02-24T09:15:16Z","date_updated":"2020-07-14T12:47:59Z","file_name":"thesis_source.zip","checksum":"ad7425867b52d7d9e72296e87bc9cb67","relation":"source_file","access_level":"closed","file_id":"7516","content_type":"application/x-zip-compressed","file_size":2028038,"creator":"dernst"}],"title":"The free energy of a dilute two-dimensional Bose gas","author":[{"full_name":"Mayer, Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Mayer"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"},{"_id":"GradSch"}],"article_processing_charge":"No"},{"date_created":"2020-02-26T10:56:37Z","ddc":["570"],"supervisor":[{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"day":"28","status":"public","oa_version":"Published Version","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7525","date_updated":"2023-09-07T13:20:03Z","keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"02","alternative_title":["ISTA Thesis"],"date_published":"2020-02-28T00:00:00Z","year":"2020","page":"79","_id":"7525","citation":{"ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7525\">10.15479/AT:ISTA:7525</a>","short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020.","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria.","ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020.","chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7525\">https://doi.org/10.15479/AT:ISTA:7525</a>.","apa":"Bhandari, P. (2020). <i>Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7525\">https://doi.org/10.15479/AT:ISTA:7525</a>","mla":"Bhandari, Pradeep. <i>Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7525\">10.15479/AT:ISTA:7525</a>."},"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2021-03-01T23:30:04Z","type":"dissertation","abstract":[{"text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n","lang":"eng"}],"publication_status":"published","file":[{"file_name":"Pradeep Bhandari Thesis.pdf","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","date_updated":"2021-03-01T23:30:04Z","date_created":"2020-02-28T08:37:53Z","file_id":"7538","content_type":"application/pdf","file_size":9646346,"creator":"pbhandari","checksum":"4589234fdb12b4ad72273b311723a7b4","access_level":"open_access","relation":"main_file","embargo":"2021-02-28"},{"creator":"pbhandari","file_size":35252164,"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"7539","access_level":"closed","checksum":"aa79490553ca0a5c9b6fbcd152e93928","relation":"source_file","file_name":"Pradeep Bhandari Thesis.docx","date_created":"2020-02-28T08:47:14Z","date_updated":"2021-03-01T23:30:04Z","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","author":[{"full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep","orcid":"0000-0003-0863-4481","last_name":"Bhandari"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"RySh"}]},{"publisher":"American Physical Society","author":[{"first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","last_name":"Budanur","full_name":"Budanur, Nazmi B"},{"last_name":"Marensi","first_name":"Elena","full_name":"Marensi, Elena"},{"first_name":"Ashley P.","last_name":"Willis","full_name":"Willis, Ashley P."},{"orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn"}],"title":"Upper edge of chaos and the energetics of transition in pipe flow","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"apa":"Budanur, N. B., Marensi, E., Willis, A. P., &#38; Hof, B. (2020). Upper edge of chaos and the energetics of transition in pipe flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevfluids.5.023903\">https://doi.org/10.1103/physrevfluids.5.023903</a>","mla":"Budanur, Nazmi B., et al. “Upper Edge of Chaos and the Energetics of Transition in Pipe Flow.” <i>Physical Review Fluids</i>, vol. 5, no. 2, 023903, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevfluids.5.023903\">10.1103/physrevfluids.5.023903</a>.","short":"N.B. Budanur, E. Marensi, A.P. Willis, B. Hof, Physical Review Fluids 5 (2020).","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.","ieee":"N. B. Budanur, E. Marensi, A. P. Willis, and B. Hof, “Upper edge of chaos and the energetics of transition in pipe flow,” <i>Physical Review Fluids</i>, vol. 5, no. 2. American Physical Society, 2020.","ama":"Budanur NB, Marensi E, Willis AP, Hof B. Upper edge of chaos and the energetics of transition in pipe flow. <i>Physical Review Fluids</i>. 2020;5(2). doi:<a href=\"https://doi.org/10.1103/physrevfluids.5.023903\">10.1103/physrevfluids.5.023903</a>","chicago":"Budanur, Nazmi B, Elena Marensi, Ashley P. Willis, and Björn Hof. “Upper Edge of Chaos and the Energetics of Transition in Pipe Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevfluids.5.023903\">https://doi.org/10.1103/physrevfluids.5.023903</a>."},"publication_identifier":{"issn":["2469-990X"]},"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."}],"arxiv":1,"scopus_import":"1","type":"journal_article","_id":"7534","quality_controlled":"1","publication_status":"published","date_published":"2020-02-21T00:00:00Z","intvolume":"         5","month":"02","article_number":"023903","date_updated":"2023-08-18T06:44:46Z","oa":1,"issue":"2","external_id":{"isi":["000515065100001"],"arxiv":["1912.09270"]},"year":"2020","volume":5,"date_created":"2020-02-27T10:26:57Z","status":"public","day":"21","publication":"Physical Review Fluids","doi":"10.1103/physrevfluids.5.023903","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.09270"}],"oa_version":"Preprint","isi":1},{"issue":"1-2","date_updated":"2023-08-18T06:45:15Z","date_published":"2020-02-01T00:00:00Z","intvolume":"        67","month":"02","year":"2020","external_id":{"isi":["000525343300004"]},"page":"16-26","day":"01","status":"public","date_created":"2020-02-28T09:18:01Z","volume":67,"oa_version":"None","isi":1,"publication":"Israel Journal of Plant Sciences","doi":"10.1163/22238980-20191110","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"full_name":"Buyle, H.","last_name":"Buyle","first_name":"H."},{"first_name":"S.","last_name":"Werbrouck","full_name":"Werbrouck, S."},{"first_name":"M.C.","last_name":"Van Labeke","full_name":"Van Labeke, M.C."},{"full_name":"Geelen, D.","first_name":"D.","last_name":"Geelen"}],"title":"In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality","publisher":"Brill","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"article_processing_charge":"No","quality_controlled":"1","_id":"7540","scopus_import":"1","abstract":[{"lang":"eng","text":" In vitro propagation of the ornamentally interesting species Wikstroemia gemmata is limited by the recalcitrance to form adventitious roots. In this article, two strategies to improve the rooting capacity of in vitro microcuttings are presented. Firstly, the effect of exogenous auxin was evaluated in both light and dark cultivated stem segments and also the sucrose-content of the medium was varied in order to determine better rooting conditions. Secondly, different spectral lights were evaluated and the effect on shoot growth and root induction demonstrated that the exact spectral composition of light is important for successful in vitro growth and development of Wikstroemia gemmata. We show that exogenous auxin cannot compensate for the poor rooting under unfavorable light conditions. Adapting the culture conditions is therefore paramount for successful industrial propagation of Wikstroemia gemmata. "}],"type":"journal_article","citation":{"chicago":"Verstraeten, Inge, H. Buyle, S. Werbrouck, M.C. Van Labeke, and D. Geelen. “In Vitro Shoot Growth and Adventitious Rooting of Wikstroemia Gemmata Depends on Light Quality.” <i>Israel Journal of Plant Sciences</i>. Brill, 2020. <a href=\"https://doi.org/10.1163/22238980-20191110\">https://doi.org/10.1163/22238980-20191110</a>.","ama":"Verstraeten I, Buyle H, Werbrouck S, Van Labeke MC, Geelen D. In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality. <i>Israel Journal of Plant Sciences</i>. 2020;67(1-2):16-26. doi:<a href=\"https://doi.org/10.1163/22238980-20191110\">10.1163/22238980-20191110</a>","ista":"Verstraeten I, Buyle H, Werbrouck S, Van Labeke MC, Geelen D. 2020. In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality. Israel Journal of Plant Sciences. 67(1–2), 16–26.","ieee":"I. Verstraeten, H. Buyle, S. Werbrouck, M. C. Van Labeke, and D. Geelen, “In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality,” <i>Israel Journal of Plant Sciences</i>, vol. 67, no. 1–2. Brill, pp. 16–26, 2020.","short":"I. Verstraeten, H. Buyle, S. Werbrouck, M.C. Van Labeke, D. Geelen, Israel Journal of Plant Sciences 67 (2020) 16–26.","mla":"Verstraeten, Inge, et al. “In Vitro Shoot Growth and Adventitious Rooting of Wikstroemia Gemmata Depends on Light Quality.” <i>Israel Journal of Plant Sciences</i>, vol. 67, no. 1–2, Brill, 2020, pp. 16–26, doi:<a href=\"https://doi.org/10.1163/22238980-20191110\">10.1163/22238980-20191110</a>.","apa":"Verstraeten, I., Buyle, H., Werbrouck, S., Van Labeke, M. C., &#38; Geelen, D. (2020). In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality. <i>Israel Journal of Plant Sciences</i>. Brill. <a href=\"https://doi.org/10.1163/22238980-20191110\">https://doi.org/10.1163/22238980-20191110</a>"},"publication_identifier":{"eissn":["2223-8980"],"issn":["0792-9978"]},"publication_status":"published"},{"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"GeKa"}],"article_processing_charge":"Yes (via OA deal)","file":[{"file_name":"2020_AdvancedMaterials_Gao.pdf","success":1,"date_updated":"2020-11-20T10:11:35Z","date_created":"2020-11-20T10:11:35Z","file_size":5242880,"creator":"dernst","file_id":"8782","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c622737dc295972065782558337124a2"}],"title":"Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling","author":[{"full_name":"Gao, Fei","last_name":"Gao","first_name":"Fei"},{"last_name":"Wang","first_name":"Jian-Huan","full_name":"Wang, Jian-Huan"},{"full_name":"Watzinger, Hannes","last_name":"Watzinger","first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hu, Hao","last_name":"Hu","first_name":"Hao"},{"full_name":"Rančić, Marko J.","last_name":"Rančić","first_name":"Marko J."},{"last_name":"Zhang","first_name":"Jie-Yin","full_name":"Zhang, Jie-Yin"},{"full_name":"Wang, Ting","first_name":"Ting","last_name":"Wang"},{"full_name":"Yao, Yuan","first_name":"Yuan","last_name":"Yao"},{"first_name":"Gui-Lei","last_name":"Wang","full_name":"Wang, Gui-Lei"},{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","full_name":"Kukucka, Josip"},{"id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","last_name":"Vukušić","orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada"},{"last_name":"Kloeffel","first_name":"Christoph","full_name":"Kloeffel, Christoph"},{"last_name":"Loss","first_name":"Daniel","full_name":"Loss, Daniel"},{"first_name":"Feng","last_name":"Liu","full_name":"Liu, Feng"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","has_accepted_license":"1","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires"},{"grant_number":"P32235","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","call_identifier":"H2020"}],"quality_controlled":"1","_id":"7541","file_date_updated":"2020-11-20T10:11:35Z","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon."}],"citation":{"chicago":"Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” <i>Advanced Materials</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/adma.201906523\">https://doi.org/10.1002/adma.201906523</a>.","ieee":"F. Gao <i>et al.</i>, “Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling,” <i>Advanced Materials</i>, vol. 32, no. 16. Wiley, 2020.","short":"F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang, Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros, J.-J. Zhang, Advanced Materials 32 (2020).","ista":"Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 32(16), 1906523.","ama":"Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. <i>Advanced Materials</i>. 2020;32(16). doi:<a href=\"https://doi.org/10.1002/adma.201906523\">10.1002/adma.201906523</a>","mla":"Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” <i>Advanced Materials</i>, vol. 32, no. 16, 1906523, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/adma.201906523\">10.1002/adma.201906523</a>.","apa":"Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., … Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.201906523\">https://doi.org/10.1002/adma.201906523</a>"},"publication_identifier":{"issn":["0935-9648"]},"year":"2020","external_id":{"isi":["000516660900001"]},"issue":"16","oa":1,"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_updated":"2024-02-21T12:42:12Z","article_number":"1906523","acknowledgement":"This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010, and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000), the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union's Horizon 2020 research and innovation program under Grant Agreement #862046. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding from Xi'an Jiaotong University.","intvolume":"        32","month":"04","date_published":"2020-04-23T00:00:00Z","isi":1,"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7996"},{"status":"public","relation":"research_data","id":"9222"}]},"doi":"10.1002/adma.201906523","publication":"Advanced Materials","day":"23","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_created":"2020-02-28T09:47:00Z","volume":32},{"intvolume":"       105","month":"01","date_published":"2020-01-08T00:00:00Z","date_updated":"2023-08-18T06:46:23Z","issue":"1","oa":1,"page":"106-121.e10","external_id":{"pmid":["31757604"],"isi":["000507341300012"]},"year":"2020","pmid":1,"volume":105,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2020-02-28T10:43:39Z","day":"08","status":"public","doi":"10.1016/j.neuron.2019.10.001","publication":"Neuron","isi":1,"oa_version":"Published Version","has_accepted_license":"1","publisher":"Cell Press","file":[{"date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-02T15:43:57Z","file_name":"2020_Neuron_Beets.pdf","checksum":"799bfd297a008753a688b30d3958fa48","relation":"main_file","access_level":"open_access","file_id":"7558","content_type":"application/pdf","creator":"dernst","file_size":3294066}],"title":"Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Beets, Isabel","first_name":"Isabel","last_name":"Beets"},{"full_name":"Zhang, Gaotian","last_name":"Zhang","first_name":"Gaotian"},{"full_name":"Fenk, Lorenz A.","last_name":"Fenk","first_name":"Lorenz A."},{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"},{"full_name":"Nelson, Geoffrey M.","last_name":"Nelson","first_name":"Geoffrey M."},{"full_name":"Félix, Marie-Anne","last_name":"Félix","first_name":"Marie-Anne"},{"orcid":"0000-0001-8347-0443","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"de Bono, Mario"}],"article_processing_charge":"No","department":[{"_id":"MaDe"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"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.” <i>Neuron</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2019.10.001\">https://doi.org/10.1016/j.neuron.2019.10.001</a>.","ama":"Beets I, Zhang G, Fenk LA, et al. Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. <i>Neuron</i>. 2020;105(1):106-121.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.10.001\">10.1016/j.neuron.2019.10.001</a>","ieee":"I. Beets <i>et al.</i>, “Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression,” <i>Neuron</i>, vol. 105, no. 1. Cell Press, p. 106–121.e10, 2020.","short":"I. Beets, G. Zhang, L.A. Fenk, C. Chen, G.M. Nelson, M.-A. Félix, M. de Bono, Neuron 105 (2020) 106–121.e10.","ista":"Beets I, Zhang G, Fenk LA, Chen C, Nelson GM, Félix M-A, de Bono M. 2020. Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. Neuron. 105(1), 106–121.e10.","mla":"Beets, Isabel, et al. “Natural Variation in a Dendritic Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide Expression.” <i>Neuron</i>, vol. 105, no. 1, Cell Press, 2020, p. 106–121.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.10.001\">10.1016/j.neuron.2019.10.001</a>.","apa":"Beets, I., Zhang, G., Fenk, L. A., Chen, C., Nelson, G. M., Félix, M.-A., &#38; de Bono, M. (2020). Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2019.10.001\">https://doi.org/10.1016/j.neuron.2019.10.001</a>"},"publication_identifier":{"issn":["0896-6273"]},"file_date_updated":"2020-07-14T12:48:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The extent to which behavior is shaped by experience varies between individuals. Genetic differences contribute to this variation, but the neural mechanisms are not understood. Here, we dissect natural variation in the behavioral flexibility of two Caenorhabditis elegans wild strains. In one strain, a memory of exposure to 21% O2 suppresses CO2-evoked locomotory arousal; in the other, CO2 evokes arousal regardless of previous O2 experience. We map that variation to a polymorphic dendritic scaffold protein, ARCP-1, expressed in sensory neurons. ARCP-1 binds the Ca2+-dependent phosphodiesterase PDE-1 and co-localizes PDE-1 with molecular sensors for CO2 at dendritic ends. Reducing ARCP-1 or PDE-1 activity promotes CO2 escape by altering neuropeptide expression in the BAG CO2 sensors. Variation in ARCP-1 alters behavioral plasticity in multiple paradigms. Our findings are reminiscent of genetic accommodation, an evolutionary process by which phenotypic flexibility in response to environmental variation is reset by genetic change."}],"_id":"7546","quality_controlled":"1","publication_status":"published"},{"status":"public","day":"13","date_created":"2020-03-01T23:00:39Z","volume":64,"isi":1,"ec_funded":1,"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.08735"}],"doi":"10.1137/S0040585X97T989726","publication":"Theory of Probability and its Applications","issue":"4","oa":1,"date_updated":"2023-08-18T06:45:48Z","month":"02","intvolume":"        64","date_published":"2020-02-13T00:00:00Z","year":"2020","page":"595-614","external_id":{"arxiv":["1705.08735"],"isi":["000551393100007"]},"quality_controlled":"1","_id":"7554","type":"journal_article","scopus_import":"1","arxiv":1,"abstract":[{"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 ${R}^n$.","lang":"eng"}],"citation":{"ama":"Edelsbrunner H, Nikitenko A. Weighted Poisson–Delaunay mosaics. <i>Theory of Probability and its Applications</i>. 2020;64(4):595-614. doi:<a href=\"https://doi.org/10.1137/S0040585X97T989726\">10.1137/S0040585X97T989726</a>","ista":"Edelsbrunner H, Nikitenko A. 2020. Weighted Poisson–Delaunay mosaics. Theory of Probability and its Applications. 64(4), 595–614.","ieee":"H. Edelsbrunner and A. Nikitenko, “Weighted Poisson–Delaunay mosaics,” <i>Theory of Probability and its Applications</i>, vol. 64, no. 4. SIAM, pp. 595–614, 2020.","short":"H. Edelsbrunner, A. Nikitenko, Theory of Probability and Its Applications 64 (2020) 595–614.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.” <i>Theory of Probability and Its Applications</i>. SIAM, 2020. <a href=\"https://doi.org/10.1137/S0040585X97T989726\">https://doi.org/10.1137/S0040585X97T989726</a>.","apa":"Edelsbrunner, H., &#38; Nikitenko, A. (2020). Weighted Poisson–Delaunay mosaics. <i>Theory of Probability and Its Applications</i>. SIAM. <a href=\"https://doi.org/10.1137/S0040585X97T989726\">https://doi.org/10.1137/S0040585X97T989726</a>","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.” <i>Theory of Probability and Its Applications</i>, vol. 64, no. 4, SIAM, 2020, pp. 595–614, doi:<a href=\"https://doi.org/10.1137/S0040585X97T989726\">10.1137/S0040585X97T989726</a>."},"publication_identifier":{"issn":["0040585X"],"eissn":["10957219"]},"publication_status":"published","project":[{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Weighted Poisson–Delaunay mosaics","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"full_name":"Nikitenko, Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton","orcid":"0000-0002-0659-3201","last_name":"Nikitenko"}],"publisher":"SIAM","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"article_processing_charge":"No"},{"publication":"Chaos","doi":"10.1063/1.5122969","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/1.5122969"}],"oa_version":"Published Version","isi":1,"volume":30,"date_created":"2020-03-04T08:06:25Z","day":"03","status":"public","external_id":{"arxiv":["1910.04584"],"isi":["000519254800002"]},"year":"2020","date_published":"2020-03-03T00:00:00Z","month":"03","intvolume":"        30","article_number":"033109","date_updated":"2023-08-18T06:47:16Z","oa":1,"issue":"3","publication_status":"published","citation":{"ama":"Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. 2020;30(3). doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>","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,” <i>Chaos</i>, vol. 30, no. 3. AIP Publishing, 2020.","chicago":"Yalniz, Gökhan, and Nazmi B Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>.","apa":"Yalniz, G., &#38; Budanur, N. B. (2020). Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>","mla":"Yalniz, Gökhan, and Nazmi B. Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>, vol. 30, no. 3, 033109, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>."},"publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"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."}],"scopus_import":"1","arxiv":1,"type":"journal_article","_id":"7563","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"article_type":"original","publisher":"AIP Publishing","author":[{"last_name":"Yalniz","orcid":"0000-0002-8490-9312","first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan"},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Inferring symbolic dynamics of chaotic flows from persistence"},{"file_date_updated":"2020-11-20T10:18:02Z","type":"journal_article","abstract":[{"text":"Coxeter triangulations are triangulations of Euclidean space based on a single simplex. By this we mean that given an individual simplex we can recover the entire triangulation of Euclidean space by inductively reflecting in the faces of the simplex. In this paper we establish that the quality of the simplices in all Coxeter triangulations is O(1/d−−√) of the quality of regular simplex. We further investigate the Delaunay property for these triangulations. Moreover, we consider an extension of the Delaunay property, namely protection, which is a measure of non-degeneracy of a Delaunay triangulation. In particular, one family of Coxeter triangulations achieves the protection O(1/d2). We conjecture that both bounds are optimal for triangulations in Euclidean space.","lang":"eng"}],"scopus_import":"1","citation":{"ista":"Choudhary A, Kachanovich S, Wintraecken M. 2020. Coxeter triangulations have good quality. Mathematics in Computer Science. 14, 141–176.","short":"A. Choudhary, S. Kachanovich, M. Wintraecken, Mathematics in Computer Science 14 (2020) 141–176.","ieee":"A. Choudhary, S. Kachanovich, and M. Wintraecken, “Coxeter triangulations have good quality,” <i>Mathematics in Computer Science</i>, vol. 14. Springer Nature, pp. 141–176, 2020.","ama":"Choudhary A, Kachanovich S, Wintraecken M. Coxeter triangulations have good quality. <i>Mathematics in Computer Science</i>. 2020;14:141-176. doi:<a href=\"https://doi.org/10.1007/s11786-020-00461-5\">10.1007/s11786-020-00461-5</a>","chicago":"Choudhary, Aruni, Siargey Kachanovich, and Mathijs Wintraecken. “Coxeter Triangulations Have Good Quality.” <i>Mathematics in Computer Science</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11786-020-00461-5\">https://doi.org/10.1007/s11786-020-00461-5</a>.","apa":"Choudhary, A., Kachanovich, S., &#38; Wintraecken, M. (2020). Coxeter triangulations have good quality. <i>Mathematics in Computer Science</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11786-020-00461-5\">https://doi.org/10.1007/s11786-020-00461-5</a>","mla":"Choudhary, Aruni, et al. “Coxeter Triangulations Have Good Quality.” <i>Mathematics in Computer Science</i>, vol. 14, Springer Nature, 2020, pp. 141–76, doi:<a href=\"https://doi.org/10.1007/s11786-020-00461-5\">10.1007/s11786-020-00461-5</a>."},"publication_identifier":{"eissn":["1661-8289"],"issn":["1661-8270"]},"quality_controlled":"1","_id":"7567","publication_status":"published","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"publisher":"Springer Nature","has_accepted_license":"1","file":[{"date_updated":"2020-11-20T10:18:02Z","date_created":"2020-11-20T10:18:02Z","success":1,"file_name":"2020_MathCompScie_Choudhary.pdf","access_level":"open_access","checksum":"1d145f3ab50ccee735983cb89236e609","relation":"main_file","content_type":"application/pdf","file_id":"8783","file_size":872275,"creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Choudhary","first_name":"Aruni","full_name":"Choudhary, Aruni"},{"last_name":"Kachanovich","first_name":"Siargey","full_name":"Kachanovich, Siargey"},{"last_name":"Wintraecken","orcid":"0000-0002-7472-2220","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs"}],"title":"Coxeter triangulations have good quality","department":[{"_id":"HeEd"}],"article_processing_charge":"Yes (via OA deal)","article_type":"original","language":[{"iso":"eng"}],"volume":14,"day":"01","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_created":"2020-03-05T13:30:18Z","doi":"10.1007/s11786-020-00461-5","publication":"Mathematics in Computer Science","ec_funded":1,"oa_version":"Published Version","intvolume":"        14","month":"03","date_published":"2020-03-01T00:00:00Z","oa":1,"date_updated":"2021-01-12T08:14:13Z","page":"141-176","year":"2020"},{"external_id":{"isi":["000526725200019"]},"year":"2020","intvolume":"        16","month":"02","date_published":"2020-02-25T00:00:00Z","article_number":"e1007642","date_updated":"2023-09-12T11:02:24Z","issue":"2","oa":1,"doi":"10.1371/journal.pcbi.1007642","publication":"PLOS Computational Biology","related_material":{"record":[{"status":"deleted","relation":"research_data","id":"9716"},{"status":"public","relation":"research_data","id":"9776"},{"status":"public","relation":"used_in_publication","id":"9779"},{"status":"public","relation":"dissertation_contains","id":"8155"},{"id":"9777","relation":"research_data","status":"public"}]},"isi":1,"oa_version":"Published Version","volume":16,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-03-06T07:39:38Z","ddc":["000","570"],"status":"public","day":"25","article_processing_charge":"No","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Public Library of Science","file":[{"file_name":"2020_PlosCompBio_Grah.pdf","date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-09T15:12:21Z","content_type":"application/pdf","file_id":"7579","file_size":2209325,"creator":"dernst","checksum":"5239dd134dc6e1c71fe7b3ce2953da37","relation":"main_file","access_level":"open_access"}],"author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The relation between crosstalk and gene regulation form revisited","publication_status":"published","publication_identifier":{"issn":["1553-7358"]},"citation":{"mla":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” <i>PLOS Computational Biology</i>, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">10.1371/journal.pcbi.1007642</a>.","apa":"Grah, R., &#38; Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">https://doi.org/10.1371/journal.pcbi.1007642</a>","chicago":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">https://doi.org/10.1371/journal.pcbi.1007642</a>.","ama":"Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. <i>PLOS Computational Biology</i>. 2020;16(2). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">10.1371/journal.pcbi.1007642</a>","ieee":"R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” <i>PLOS Computational Biology</i>, vol. 16, no. 2. Public Library of Science, 2020.","short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).","ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642."},"file_date_updated":"2020-07-14T12:48:00Z","type":"journal_article","abstract":[{"text":"Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models.","lang":"eng"}],"scopus_import":"1","_id":"7569","quality_controlled":"1"},{"volume":10,"status":"public","day":"04","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-03-08T18:02:01Z","ddc":["530"],"publication":"Physical Review X","doi":"10.1103/physrevx.10.011055","oa_version":"Published Version","isi":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/classical-physics-helps-predict-fate-of-interacting-quantum-systems/","description":"News on IST Homepage"}]},"article_number":"011055","date_published":"2020-03-04T00:00:00Z","intvolume":"        10","month":"03","oa":1,"issue":"1","date_updated":"2023-08-18T07:01:07Z","external_id":{"isi":["000517969300001"],"arxiv":["1905.08564"]},"year":"2020","abstract":[{"lang":"eng","text":"The relaxation of few-body quantum systems can strongly depend on the initial state when the system’s semiclassical phase space is mixed; i.e., regions of chaotic motion coexist with regular islands. In recent years, there has been much effort to understand the process of thermalization in strongly interacting quantum systems that often lack an obvious semiclassical limit. The time-dependent variational principle (TDVP) allows one to systematically derive an effective classical (nonlinear) dynamical system by projecting unitary many-body dynamics onto a manifold of weakly entangled variational states. We demonstrate that such dynamical systems generally possess mixed phase space. When TDVP errors are small, the mixed phase space leaves a footprint on the exact dynamics of the quantum model. For example, when the system is initialized in a state belonging to a stable periodic orbit or the surrounding regular region, it exhibits persistent many-body quantum revivals. As a proof of principle, we identify new types of “quantum many-body scars,” i.e., initial states that lead to long-time oscillations in a model of interacting Rydberg atoms in one and two dimensions. Intriguingly, the initial states that give rise to most robust revivals are typically entangled states. On the other hand, even when TDVP errors are large, as in the thermalizing tilted-field Ising model, initializing the system in a regular region of phase space leads to a surprising slowdown of thermalization. Our work establishes TDVP as a method for identifying interacting quantum systems with anomalous dynamics in arbitrary dimensions. Moreover, the mixed phase space classical variational equations allow one to find slowly thermalizing initial conditions in interacting models. Our results shed light on a link between classical and quantum chaos, pointing toward possible extensions of the classical Kolmogorov-Arnold-Moser theorem to quantum systems."}],"arxiv":1,"scopus_import":"1","file_date_updated":"2020-07-14T12:48:00Z","type":"journal_article","citation":{"ama":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. Slow quantum thermalization and many-body revivals from mixed phase space. <i>Physical Review X</i>. 2020;10(1). doi:<a href=\"https://doi.org/10.1103/physrevx.10.011055\">10.1103/physrevx.10.011055</a>","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,” <i>Physical Review X</i>, vol. 10, no. 1. American Physical Society, 2020.","short":"A. Michailidis, C.J. Turner, Z. Papić, D.A. Abanin, M. Serbyn, Physical Review X 10 (2020).","ista":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. 2020. Slow quantum thermalization and many-body revivals from mixed phase space. Physical Review X. 10(1), 011055.","chicago":"Michailidis, Alexios, C. J. Turner, Z. Papić, D. A. Abanin, and Maksym Serbyn. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” <i>Physical Review X</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevx.10.011055\">https://doi.org/10.1103/physrevx.10.011055</a>.","apa":"Michailidis, A., Turner, C. J., Papić, Z., Abanin, D. A., &#38; Serbyn, M. (2020). Slow quantum thermalization and many-body revivals from mixed phase space. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.10.011055\">https://doi.org/10.1103/physrevx.10.011055</a>","mla":"Michailidis, Alexios, et al. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” <i>Physical Review X</i>, vol. 10, no. 1, 011055, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevx.10.011055\">10.1103/physrevx.10.011055</a>."},"publication_identifier":{"issn":["2160-3308"]},"quality_controlled":"1","_id":"7570","publication_status":"published","publisher":"American Physical Society","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Slow quantum thermalization and many-body revivals from mixed phase space","author":[{"full_name":"Michailidis, Alexios","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","last_name":"Michailidis"},{"full_name":"Turner, C. J.","last_name":"Turner","first_name":"C. J."},{"full_name":"Papić, Z.","first_name":"Z.","last_name":"Papić"},{"last_name":"Abanin","first_name":"D. A.","full_name":"Abanin, D. A."},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"file":[{"file_name":"2020_PhysicalReviewX_Michailidis.pdf","date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-12T12:13:07Z","creator":"dernst","file_size":17828638,"file_id":"7581","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"4b3f2c13873d35230173c73d0e11c408"}],"department":[{"_id":"MaSe"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}]},{"page":"145-161","external_id":{"isi":["000611826500008"]},"year":"2020","date_published":"2020-02-27T00:00:00Z","alternative_title":["Methods in Cell Biology"],"intvolume":"       158","month":"02","date_updated":"2023-10-04T09:50:24Z","oa":1,"publication":"Methods in Cell Biology","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"doi":"10.1016/bs.mcb.2020.01.006","related_material":{"record":[{"id":"8358","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Preprint","ec_funded":1,"isi":1,"volume":158,"date_created":"2020-03-08T23:00:47Z","day":"27","status":"public","article_processing_charge":"No","department":[{"_id":"MaLo"}],"language":[{"iso":"eng"}],"publisher":"Elsevier","title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","author":[{"full_name":"Dos Santos Caldas, Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461"},{"full_name":"Radler, Philipp","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","last_name":"Radler"},{"last_name":"Sommer","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"publication_status":"published","citation":{"apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., &#38; Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), <i>Methods in Cell Biology</i> (Vol. 158, pp. 145–161). Elsevier. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” <i>Methods in Cell Biology</i>, edited by Phong  Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>.","ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in <i>Methods in Cell Biology</i>, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.","ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.","short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161.","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. <i>Methods in Cell Biology</i>. Vol 158. Elsevier; 2020:145-161. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>","chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In <i>Methods in Cell Biology</i>, edited by Phong  Tran, 158:145–61. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>."},"publication_identifier":{"issn":["0091679X"]},"abstract":[{"lang":"eng","text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material."}],"scopus_import":"1","type":"book_chapter","_id":"7572","editor":[{"full_name":"Tran, Phong ","last_name":"Tran","first_name":"Phong "}],"quality_controlled":"1"},{"year":"2020","page":"204-234","external_id":{"isi":["000539439400008"],"arxiv":["1905.05757"]},"date_updated":"2023-09-07T13:31:05Z","oa":1,"issue":"7","date_published":"2020-07-01T00:00:00Z","intvolume":"       139","month":"07","acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 716117). J.M. and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 350398276.","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10030"}]},"oa_version":"Preprint","ec_funded":1,"isi":1,"publication":"Journal de Mathematiques Pures et Appliquees","main_file_link":[{"url":"https://arxiv.org/abs/1905.05757","open_access":"1"}],"doi":"10.1016/j.matpur.2020.02.008","date_created":"2020-03-08T23:00:47Z","status":"public","day":"01","volume":139,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"JaMa"}],"author":[{"last_name":"Gladbach","first_name":"Peter","full_name":"Gladbach, Peter"},{"last_name":"Kopfer","first_name":"Eva","full_name":"Kopfer, Eva"},{"last_name":"Maas","orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"},{"full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","last_name":"Portinale"}],"title":"Homogenisation of one-dimensional discrete optimal transport","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","project":[{"call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","grant_number":" F06504"},{"call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"}],"publication_status":"published","_id":"7573","quality_controlled":"1","citation":{"apa":"Gladbach, P., Kopfer, E., Maas, J., &#38; Portinale, L. (2020). Homogenisation of one-dimensional discrete optimal transport. <i>Journal de Mathematiques Pures et Appliquees</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">https://doi.org/10.1016/j.matpur.2020.02.008</a>","mla":"Gladbach, Peter, et al. “Homogenisation of One-Dimensional Discrete Optimal Transport.” <i>Journal de Mathematiques Pures et Appliquees</i>, vol. 139, no. 7, Elsevier, 2020, pp. 204–34, doi:<a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">10.1016/j.matpur.2020.02.008</a>.","ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional discrete optimal transport. <i>Journal de Mathematiques Pures et Appliquees</i>. 2020;139(7):204-234. doi:<a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">10.1016/j.matpur.2020.02.008</a>","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234.","ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2020. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 139(7), 204–234.","ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of one-dimensional discrete optimal transport,” <i>Journal de Mathematiques Pures et Appliquees</i>, vol. 139, no. 7. Elsevier, pp. 204–234, 2020.","chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of One-Dimensional Discrete Optimal Transport.” <i>Journal de Mathematiques Pures et Appliquees</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">https://doi.org/10.1016/j.matpur.2020.02.008</a>."},"publication_identifier":{"issn":["00217824"]},"scopus_import":"1","abstract":[{"text":"This paper deals with dynamical optimal transport metrics defined by spatial discretisation of the Benamou–Benamou formula for the Kantorovich metric . Such metrics appear naturally in discretisations of -gradient flow formulations for dissipative PDE. However, it has recently been shown that these metrics do not in general converge to , unless strong geometric constraints are imposed on the discrete mesh. In this paper we prove that, in a 1-dimensional periodic setting, discrete transport metrics converge to a limiting transport metric with a non-trivial effective mobility. This mobility depends sensitively on the geometry of the mesh and on the non-local mobility at the discrete level. Our result quantifies to what extent discrete transport can make use of microstructure in the mesh to reduce the cost of transport.","lang":"eng"}],"arxiv":1,"type":"journal_article"}]