[{"article_processing_charge":"No","article_type":"original","scopus_import":"1","ddc":["570"],"publication":"Nature Communications","type":"journal_article","date_updated":"2025-06-12T07:01:22Z","doi":"10.1038/s41467-020-19372-x","publication_status":"published","file_date_updated":"2020-11-09T07:56:24Z","language":[{"iso":"eng"}],"article_number":"5569","abstract":[{"text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.","lang":"eng"}],"oa":1,"day":"04","year":"2020","title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","volume":11,"month":"11","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"department":[{"_id":"EM-Fac"}],"date_created":"2020-11-09T07:49:36Z","publisher":"Springer Nature","citation":{"ieee":"L. Schulte <i>et al.</i>, “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>","apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>.","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569.","short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>, vol. 11, 5569, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>."},"_id":"8744","intvolume":"        11","publication_identifier":{"issn":["2041-1723"]},"quality_controlled":"1","date_published":"2020-11-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","isi":1,"external_id":{"isi":["000592028600001"],"pmid":["33149120"]},"author":[{"first_name":"Linda","last_name":"Schulte","full_name":"Schulte, Linda"},{"last_name":"Mao","first_name":"Jiafei","full_name":"Mao, Jiafei"},{"last_name":"Reitz","first_name":"Julian","full_name":"Reitz, Julian"},{"full_name":"Sreeramulu, Sridhar","last_name":"Sreeramulu","first_name":"Sridhar"},{"full_name":"Kudlinzki, Denis","last_name":"Kudlinzki","first_name":"Denis"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"full_name":"Meier-Credo, Jakob","first_name":"Jakob","last_name":"Meier-Credo"},{"last_name":"Saxena","first_name":"Krishna","full_name":"Saxena, Krishna"},{"first_name":"Florian","last_name":"Buhr","full_name":"Buhr, Florian"},{"full_name":"Langer, Julian D.","last_name":"Langer","first_name":"Julian D."},{"full_name":"Blackledge, Martin","last_name":"Blackledge","first_name":"Martin"},{"full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S.","last_name":"Frangakis"},{"full_name":"Glaubitz, Clemens","first_name":"Clemens","last_name":"Glaubitz"},{"full_name":"Schwalbe, Harald","last_name":"Schwalbe","first_name":"Harald"}],"pmid":1,"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"file":[{"file_id":"8745","date_updated":"2020-11-09T07:56:24Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2020-11-09T07:56:24Z","file_name":"2020_NatureComm_Schulte.pdf","file_size":1670898,"success":1,"checksum":"b2688f0347e69e6629bba582077278c5"}],"has_accepted_license":"1","acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC."},{"abstract":[{"lang":"eng","text":"Research in the field of colloidal semiconductor nanocrystals (NCs) has progressed tremendously, mostly because of their exceptional optoelectronic properties. Core@shell NCs, in which one or more inorganic layers overcoat individual NCs, recently received significant attention due to their remarkable optical characteristics. Reduced Auger recombination, suppressed blinking, and enhanced carrier multiplication are among the merits of core@shell NCs. Despite their importance in device development, the influence of the shell and the surface modification of the core@shell NC assemblies on the charge carrier transport remains a pertinent research objective. Type-II PbTe@PbS core@shell NCs, in which exclusive electron transport was demonstrated, still exhibit instability of their electron \r\n ransport. Here, we demonstrate the enhancement of electron transport and stability in PbTe@PbS core@shell NC assemblies using iodide as a surface passivating ligand. The combination of the PbS shelling and the use of the iodide ligand contributes to the addition of one mobile electron for each core@shell NC. Furthermore, both electron mobility and on/off current modulation ratio values of the core@shell NC field-effect transistor are steady with the usage of iodide. Excellent stability in these exclusively electron-transporting core@shell NCs paves the way for their utilization in electronic devices. "}],"article_number":"173101","language":[{"iso":"eng"}],"volume":117,"title":"Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids","year":"2020","day":"26","oa":1,"publication_status":"published","doi":"10.1063/5.0025965","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/5.0025965"}],"scopus_import":"1","date_updated":"2023-09-05T11:57:23Z","type":"journal_article","publication":"Applied Physics Letters","article_type":"original","article_processing_charge":"No","acknowledgement":"This work was partly supported by Grants-in-Aid for Scientific Research by Young Scientist A (KAKENHI Wakate-A) No.\r\nJP17H04802, Grants-in-Aid for Scientific Research No. JP19H05602 from the Japan Society for the Promotion of Science, and RIKEN Incentive Research Grant (Shoreikadai) 2016. M.V.K. and M.I. acknowledge financial support from the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID, GA No. 306733) and ETH Zurich via ETH career seed grant (No. SEED-18 16-2). We acknowledge Mrs. T. Kikitsu and Dr. D. Hashizume (RIKEN-CEMS) for access to the transmission electron microscope facility.","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Miranti, Retno","last_name":"Miranti","first_name":"Retno"},{"last_name":"Septianto","first_name":"Ricky Dwi","full_name":"Septianto, Ricky Dwi"},{"last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"full_name":"Kovalenko, Maksym V.","last_name":"Kovalenko","first_name":"Maksym V."},{"full_name":"Matsushita, Nobuhiro","first_name":"Nobuhiro","last_name":"Matsushita"},{"first_name":"Yoshihiro","last_name":"Iwasa","full_name":"Iwasa, Yoshihiro"},{"first_name":"Satria Zulkarnaen","last_name":"Bisri","full_name":"Bisri, Satria Zulkarnaen"}],"external_id":{"isi":["000591639700001"]},"isi":1,"publication_identifier":{"issn":["0003-6951"],"eissn":["1077-3118"]},"intvolume":"       117","issue":"17","_id":"8746","date_published":"2020-10-26T00:00:00Z","quality_controlled":"1","status":"public","month":"10","publisher":"AIP Publishing","citation":{"chicago":"Miranti, Retno, Ricky Dwi Septianto, Maria Ibáñez, Maksym V. Kovalenko, Nobuhiro Matsushita, Yoshihiro Iwasa, and Satria Zulkarnaen Bisri. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” <i>Applied Physics Letters</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/5.0025965\">https://doi.org/10.1063/5.0025965</a>.","short":"R. Miranti, R.D. Septianto, M. Ibáñez, M.V. Kovalenko, N. Matsushita, Y. Iwasa, S.Z. Bisri, Applied Physics Letters 117 (2020).","mla":"Miranti, Retno, et al. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” <i>Applied Physics Letters</i>, vol. 117, no. 17, 173101, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/5.0025965\">10.1063/5.0025965</a>.","ista":"Miranti R, Septianto RD, Ibáñez M, Kovalenko MV, Matsushita N, Iwasa Y, Bisri SZ. 2020. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. 117(17), 173101.","apa":"Miranti, R., Septianto, R. D., Ibáñez, M., Kovalenko, M. V., Matsushita, N., Iwasa, Y., &#38; Bisri, S. Z. (2020). Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. <i>Applied Physics Letters</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0025965\">https://doi.org/10.1063/5.0025965</a>","ama":"Miranti R, Septianto RD, Ibáñez M, et al. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. <i>Applied Physics Letters</i>. 2020;117(17). doi:<a href=\"https://doi.org/10.1063/5.0025965\">10.1063/5.0025965</a>","ieee":"R. Miranti <i>et al.</i>, “Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids,” <i>Applied Physics Letters</i>, vol. 117, no. 17. AIP Publishing, 2020."},"department":[{"_id":"MaIb"}],"date_created":"2020-11-09T08:05:43Z"},{"department":[{"_id":"MaIb"}],"date_created":"2020-11-09T08:37:51Z","publisher":"Royal Society of Chemistry","citation":{"ama":"Zhang Y, Liu Y, Calcabrini M, et al. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. <i>Journal of Materials Chemistry C</i>. 2020;8(40):14092-14099. doi:<a href=\"https://doi.org/10.1039/D0TC02182B\">10.1039/D0TC02182B</a>","ieee":"Y. Zhang <i>et al.</i>, “Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks,” <i>Journal of Materials Chemistry C</i>, vol. 8, no. 40. Royal Society of Chemistry, pp. 14092–14099, 2020.","apa":"Zhang, Y., Liu, Y., Calcabrini, M., Xing, C., Han, X., Arbiol, J., … Cabot, A. (2020). Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. <i>Journal of Materials Chemistry C</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/D0TC02182B\">https://doi.org/10.1039/D0TC02182B</a>","ista":"Zhang Y, Liu Y, Calcabrini M, Xing C, Han X, Arbiol J, Cadavid D, Ibáñez M, Cabot A. 2020. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 8(40), 14092–14099.","short":"Y. Zhang, Y. Liu, M. Calcabrini, C. Xing, X. Han, J. Arbiol, D. Cadavid, M. Ibáñez, A. Cabot, Journal of Materials Chemistry C 8 (2020) 14092–14099.","mla":"Zhang, Yu, et al. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” <i>Journal of Materials Chemistry C</i>, vol. 8, no. 40, Royal Society of Chemistry, 2020, pp. 14092–99, doi:<a href=\"https://doi.org/10.1039/D0TC02182B\">10.1039/D0TC02182B</a>.","chicago":"Zhang, Yu, Yu Liu, Mariano Calcabrini, Congcong Xing, Xu Han, Jordi Arbiol, Doris Cadavid, Maria Ibáñez, and Andreu Cabot. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” <i>Journal of Materials Chemistry C</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/D0TC02182B\">https://doi.org/10.1039/D0TC02182B</a>."},"status":"public","month":"10","page":"14092-14099","quality_controlled":"1","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_published":"2020-10-28T00:00:00Z","issue":"40","intvolume":"         8","_id":"8747","isi":1,"author":[{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"first_name":"Yu","last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mariano","last_name":"Calcabrini","full_name":"Calcabrini, Mariano"},{"full_name":"Xing, Congcong","last_name":"Xing","first_name":"Congcong"},{"full_name":"Han, Xu","first_name":"Xu","last_name":"Han"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Doris","last_name":"Cadavid","full_name":"Cadavid, Doris"},{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"external_id":{"isi":["000581559100015"]},"oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economı´a y\r\nCompetitividad through the project SEHTOP (ENE2016-77798-C4-3-R). Y. Z. and X. H., thank the China Scholarship Council for scholarship support. M. C. has received funding from the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. M. I. acknowledges financial support from IST Austria. Y. L. acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement no. 754411. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat \r\nAuto`noma de Barcelona Materials Science PhD program.","article_processing_charge":"No","article_type":"original","date_updated":"2025-04-14T07:43:50Z","publication":"Journal of Materials Chemistry C","type":"journal_article","scopus_import":"1","ec_funded":1,"doi":"10.1039/D0TC02182B","publication_status":"published","day":"28","volume":8,"title":"Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks","year":"2020","language":[{"iso":"eng"}],"abstract":[{"text":"Appropriately designed nanocomposites allow improving the thermoelectric performance by several mechanisms, including phonon scattering, modulation doping and energy filtering, while additionally promoting better mechanical properties than those of crystalline materials. Here, a strategy for producing Bi2Te3–Cu2xTe nanocomposites based on the consolidation of heterostructured nanoparticles is described and the thermoelectric properties of the obtained materials are investigated. We first detail a two-step solution-based process to produce Bi2Te3–Cu2xTe heteronanostructures, based on the growth of Cu2xTe nanocrystals on the surface of Bi2Te3 nanowires. We characterize the structural and chemical properties of the synthesized nanostructures and of the nanocomposites\r\nproduced by hot-pressing the particles at moderate temperatures. Besides, the transport properties of the nanocomposites are investigated as a function of the amount of Cu introduced. Overall, the presence of Cu decreases the material thermal conductivity through promotion of phonon scattering, modulates the charge carrier concentration through electron spillover, and increases the Seebeck coefficient through filtering of charge carriers at energy barriers. These effects result in an improvement of over 50% of the thermoelectric figure of merit of Bi2Te3.","lang":"eng"}],"corr_author":"1"},{"date_published":"2020-12-04T00:00:00Z","quality_controlled":"1","project":[{"grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"isbn":["9781728191485"]},"_id":"8750","publisher":"IEEE","citation":{"chicago":"Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with  Time-Triggered Transitions.” In <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/MEMOCODE51338.2020.9314994\">https://doi.org/10.1109/MEMOCODE51338.2020.9314994</a>.","mla":"Forets, Marcelo, et al. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with  Time-Triggered Transitions.” <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>, 9314994, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/MEMOCODE51338.2020.9314994\">10.1109/MEMOCODE51338.2020.9314994</a>.","short":"M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020.","ista":"Forets M, Freire D, Schilling C. 2020. Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. MEMOCODE: Conference on Formal Methods and Models for System Design, 9314994.","ama":"Forets M, Freire D, Schilling C. Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. In: <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/MEMOCODE51338.2020.9314994\">10.1109/MEMOCODE51338.2020.9314994</a>","apa":"Forets, M., Freire, D., &#38; Schilling, C. (2020). Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. In <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>. Virtual Conference: IEEE. <a href=\"https://doi.org/10.1109/MEMOCODE51338.2020.9314994\">https://doi.org/10.1109/MEMOCODE51338.2020.9314994</a>","ieee":"M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions,” in <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>, Virtual Conference, 2020."},"department":[{"_id":"ToHe"}],"date_created":"2020-11-10T07:04:57Z","status":"public","month":"12","author":[{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"last_name":"Freire","first_name":"Daniel","full_name":"Freire, Daniel"},{"full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","last_name":"Schilling","first_name":"Christian"}],"external_id":{"isi":["000661920400013"],"arxiv":["2006.12325"]},"arxiv":1,"isi":1,"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-04-15T06:26:12Z","type":"conference","publication":"18th ACM-IEEE International Conference on Formal Methods and Models for System Design","scopus_import":"1","article_processing_charge":"No","title":"Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions","year":"2020","day":"04","conference":{"end_date":"2020-12-04","name":"MEMOCODE: Conference on Formal Methods and Models for System Design","location":"Virtual Conference","start_date":"2020-12-02"},"oa":1,"abstract":[{"lang":"eng","text":"Efficiently handling time-triggered and possibly nondeterministic switches\r\nfor hybrid systems reachability is a challenging task. In this paper we present\r\nan approach based on conservative set-based enclosure of the dynamics that can\r\nhandle systems with uncertain parameters and inputs, where the uncertainties\r\nare bound to given intervals. The method is evaluated on the plant model of an\r\nexperimental electro-mechanical braking system with periodic controller. In\r\nthis model, the fast-switching controller dynamics requires simulation time\r\nscales of the order of nanoseconds. Accurate set-based computations for\r\nrelatively large time horizons are known to be expensive. However, by\r\nappropriately decoupling the time variable with respect to the spatial\r\nvariables, and enclosing the uncertain parameters using interval matrix maps\r\nacting on zonotopes, we show that the computation time can be lowered to 5000\r\ntimes faster with respect to previous works. This is a step forward in formal\r\nverification of hybrid systems because reduced run-times allow engineers to\r\nintroduce more expressiveness in their models with a relatively inexpensive\r\ncomputational cost."}],"language":[{"iso":"eng"}],"article_number":"9314994","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/2006.12325","open_access":"1"}],"publication_status":"published","doi":"10.1109/MEMOCODE51338.2020.9314994"},{"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F06504"}],"quality_controlled":"1","date_published":"2020-12-01T00:00:00Z","_id":"8758","issue":"6","intvolume":"       181","publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"date_created":"2020-11-15T23:01:18Z","department":[{"_id":"JaMa"}],"citation":{"apa":"Maas, J., &#38; Mielke, A. (2020). Modeling of chemical reaction systems with detailed balance using gradient structures. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-020-02663-4\">https://doi.org/10.1007/s10955-020-02663-4</a>","ieee":"J. Maas and A. Mielke, “Modeling of chemical reaction systems with detailed balance using gradient structures,” <i>Journal of Statistical Physics</i>, vol. 181, no. 6. Springer Nature, pp. 2257–2303, 2020.","ama":"Maas J, Mielke A. Modeling of chemical reaction systems with detailed balance using gradient structures. <i>Journal of Statistical Physics</i>. 2020;181(6):2257-2303. doi:<a href=\"https://doi.org/10.1007/s10955-020-02663-4\">10.1007/s10955-020-02663-4</a>","chicago":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” <i>Journal of Statistical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10955-020-02663-4\">https://doi.org/10.1007/s10955-020-02663-4</a>.","mla":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” <i>Journal of Statistical Physics</i>, vol. 181, no. 6, Springer Nature, 2020, pp. 2257–303, doi:<a href=\"https://doi.org/10.1007/s10955-020-02663-4\">10.1007/s10955-020-02663-4</a>.","short":"J. Maas, A. Mielke, Journal of Statistical Physics 181 (2020) 2257–2303.","ista":"Maas J, Mielke A. 2020. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 181(6), 2257–2303."},"publisher":"Springer Nature","month":"12","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"2257-2303","file":[{"success":1,"file_size":753596,"checksum":"bc2b63a90197b97cbc73eccada4639f5","file_name":"2020_JourStatPhysics_Maas.pdf","relation":"main_file","access_level":"open_access","date_created":"2021-02-04T10:29:11Z","content_type":"application/pdf","creator":"dernst","date_updated":"2021-02-04T10:29:11Z","file_id":"9087"}],"acknowledgement":"The research of A.M. was partially supported by the Deutsche Forschungsgemeinschaft (DFG) via the Collaborative Research Center SFB 1114 Scaling Cascades in Complex Systems (Project No. 235221301), through the Subproject C05 Effective models for materials and interfaces with multiple scales. 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), and by the Austrian Science Fund (FWF), Project SFB F65. The authors thank Christof Schütte, Robert I. A. Patterson, and Stefanie Winkelmann for helpful and stimulating discussions. Open access funding provided by Austrian Science Fund (FWF).","has_accepted_license":"1","isi":1,"external_id":{"isi":["000587107200002"],"pmid":["33268907"],"arxiv":["2004.02831"]},"arxiv":1,"author":[{"last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"},{"last_name":"Mielke","first_name":"Alexander","full_name":"Mielke, Alexander"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","publication":"Journal of Statistical Physics","type":"journal_article","date_updated":"2025-06-12T07:01:39Z","scopus_import":"1","ddc":["510"],"article_processing_charge":"No","article_type":"original","oa":1,"day":"01","year":"2020","title":"Modeling of chemical reaction systems with detailed balance using gradient structures","volume":181,"language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"lang":"eng","text":"We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ-convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels."}],"file_date_updated":"2021-02-04T10:29:11Z","ec_funded":1,"doi":"10.1007/s10955-020-02663-4","publication_status":"published"},{"ec_funded":1,"author":[{"last_name":"Guseinov","first_name":"Ruslan","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-11-18T10:04:59Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8562"}],"link":[{"url":"https://github.com/russelmann/cold-glass-acm","relation":"software"}]},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:ISTA:8761","title":"Supplementary data for \"Computational design of cold bent glass façades\"","year":"2020","day":"23","oa":1,"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"creator":"rguseino","content_type":"application/x-gzip","file_id":"8762","date_updated":"2020-11-16T10:31:29Z","file_name":"mdn_model.tar.gz","success":1,"file_size":15378270,"checksum":"f5ae57b97017b9f61081032703361233","date_created":"2020-11-16T10:31:29Z","access_level":"open_access","relation":"main_file"},{"creator":"rguseino","content_type":"application/x-gzip","file_id":"8763","date_updated":"2020-11-16T10:43:23Z","file_name":"optimal_panels_data.tar.gz","checksum":"b0d25e04060ee78c585ee2f23542c744","file_size":615387734,"success":1,"date_created":"2020-11-16T10:43:23Z","access_level":"open_access","relation":"main_file"},{"date_updated":"2020-11-18T10:04:59Z","file_id":"8770","content_type":"text/plain","creator":"rguseino","access_level":"open_access","relation":"main_file","date_created":"2020-11-18T10:04:59Z","file_name":"readme.txt","success":1,"file_size":1228,"checksum":"69c1dde3434ada86d125e0c2588caf1e"}],"corr_author":"1","citation":{"ama":"Guseinov R. 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Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020.","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">https://doi.org/10.15479/AT:ISTA:8761</a>.","mla":"Guseinov, Ruslan. <i>Supplementary Data for “Computational Design of Cold Bent Glass Façades.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>.","short":"R. Guseinov, (2020).","ista":"Guseinov R. 2020. 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We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re‐use popular isotropic plasticity models like the Drucker‐Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"file_date_updated":"2020-11-23T09:05:13Z","ec_funded":1,"doi":"10.1111/cgf.13914","publication_status":"published","type":"journal_article","publication":"Computer Graphics Forum","date_updated":"2024-10-22T09:58:14Z","scopus_import":"1","ddc":["000"],"article_processing_charge":"No","article_type":"original","keyword":["Computer Networks and Communications"],"file":[{"content_type":"application/pdf","creator":"dernst","file_id":"8796","date_updated":"2020-11-23T09:05:13Z","file_name":"2020_poff_revisited.pdf","file_size":38969122,"checksum":"7605f605acd84d0942b48bc7a1c2d72e","success":1,"access_level":"open_access","relation":"main_file","date_created":"2020-11-23T09:05:13Z"}],"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would also like to thank Joseph Teran and Chenfanfu Jiang for the helpful discussions.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176.","has_accepted_license":"1","isi":1,"external_id":{"isi":["000548709600008"]},"author":[{"first_name":"Camille","last_name":"Schreck","full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","project":[{"grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"quality_controlled":"1","date_published":"2020-05-01T00:00:00Z","_id":"8765","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"issue":"2","intvolume":"        39","date_created":"2020-11-17T09:35:10Z","department":[{"_id":"ChWo"}],"publisher":"Wiley","citation":{"apa":"Schreck, C., &#38; Wojtan, C. (2020). A practical method for animating anisotropic elastoplastic materials. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13914\">https://doi.org/10.1111/cgf.13914</a>","ama":"Schreck C, Wojtan C. A practical method for animating anisotropic elastoplastic materials. <i>Computer Graphics Forum</i>. 2020;39(2):89-99. doi:<a href=\"https://doi.org/10.1111/cgf.13914\">10.1111/cgf.13914</a>","ieee":"C. Schreck and C. Wojtan, “A practical method for animating anisotropic elastoplastic materials,” <i>Computer Graphics Forum</i>, vol. 39, no. 2. Wiley, pp. 89–99, 2020.","chicago":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” <i>Computer Graphics Forum</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/cgf.13914\">https://doi.org/10.1111/cgf.13914</a>.","mla":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” <i>Computer Graphics Forum</i>, vol. 39, no. 2, Wiley, 2020, pp. 89–99, doi:<a href=\"https://doi.org/10.1111/cgf.13914\">10.1111/cgf.13914</a>.","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 39 (2020) 89–99.","ista":"Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99."},"month":"05","status":"public","page":"89-99"},{"project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"quality_controlled":"1","date_published":"2020-12-01T00:00:00Z","_id":"8766","issue":"8","intvolume":"        39","department":[{"_id":"ChWo"},{"_id":"BeBi"}],"date_created":"2020-11-17T10:47:48Z","publisher":"Wiley","citation":{"ama":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. Making procedural water waves boundary-aware. <i>Computer Graphics forum</i>. 2020;39(8):47-54. doi:<a href=\"https://doi.org/10.1111/cgf.14100\">10.1111/cgf.14100</a>","apa":"Jeschke, S., Hafner, C., Chentanez, N., Macklin, M., Müller-Fischer, M., &#38; Wojtan, C. (2020). Making procedural water waves boundary-aware. <i>Computer Graphics Forum</i>. Online Symposium: Wiley. <a href=\"https://doi.org/10.1111/cgf.14100\">https://doi.org/10.1111/cgf.14100</a>","ieee":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, and C. Wojtan, “Making procedural water waves boundary-aware,” <i>Computer Graphics forum</i>, vol. 39, no. 8. Wiley, pp. 47–54, 2020.","chicago":"Jeschke, Stefan, Christian Hafner, Nuttapong Chentanez, Miles Macklin, Matthias Müller-Fischer, and Chris Wojtan. “Making Procedural Water Waves Boundary-Aware.” <i>Computer Graphics Forum</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/cgf.14100\">https://doi.org/10.1111/cgf.14100</a>.","ista":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. 2020. Making procedural water waves boundary-aware. Computer Graphics forum. 39(8), 47–54.","short":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, C. Wojtan, Computer Graphics Forum 39 (2020) 47–54.","mla":"Jeschke, Stefan, et al. “Making Procedural Water Waves Boundary-Aware.” <i>Computer Graphics Forum</i>, vol. 39, no. 8, Wiley, 2020, pp. 47–54, doi:<a href=\"https://doi.org/10.1111/cgf.14100\">10.1111/cgf.14100</a>."},"month":"12","status":"public","page":"47-54","isi":1,"external_id":{"isi":["000591780400005"]},"author":[{"last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"},{"last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"full_name":"Chentanez, Nuttapong","first_name":"Nuttapong","last_name":"Chentanez"},{"first_name":"Miles","last_name":"Macklin","full_name":"Macklin, Miles"},{"first_name":"Matthias","last_name":"Müller-Fischer","full_name":"Müller-Fischer, Matthias"},{"first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication":"Computer Graphics forum","type":"journal_article","date_updated":"2024-10-22T09:58:15Z","scopus_import":"1","article_processing_charge":"No","article_type":"original","day":"01","conference":{"start_date":"2020-10-06","location":"Online Symposium","name":"SCA: Symposium on Computer Animation","end_date":"2020-10-09"},"year":"2020","title":"Making procedural water waves boundary-aware","volume":39,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The “procedural” approach to animating ocean waves is the dominant algorithm for animating larger bodies of water in\r\ninteractive applications as well as in off-line productions — it provides high visual quality with a low computational demand. In this paper, we widen the applicability of procedural water wave animation with an extension that guarantees the satisfaction of boundary conditions imposed by terrain while still approximating physical wave behavior. In combination with a particle system that models wave breaking, foam, and spray, this allows us to naturally model waves interacting with beaches and rocks. Our system is able to animate waves at large scales at interactive frame rates on a commodity PC."}],"ec_funded":1,"doi":"10.1111/cgf.14100","publication_status":"published"},{"date_updated":"2025-06-12T07:02:01Z","publication":"PLOS Computational Biology","type":"journal_article","ddc":["000"],"scopus_import":"1","article_processing_charge":"No","article_type":"original","day":"05","oa":1,"title":"The Moran process on 2-chromatic graphs","volume":16,"year":"2020","article_number":"e1008402","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring."}],"file_date_updated":"2020-11-18T07:26:10Z","doi":"10.1371/journal.pcbi.1008402","publication_status":"published","quality_controlled":"1","date_published":"2020-11-05T00:00:00Z","issue":"11","intvolume":"        16","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"_id":"8767","date_created":"2020-11-18T07:20:23Z","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","citation":{"chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>.","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., &#38; Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. 2020;16(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>","ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” <i>PLOS Computational Biology</i>, vol. 16, no. 11. Public Library of Science, 2020."},"status":"public","month":"11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","has_accepted_license":"1","file":[{"content_type":"application/pdf","creator":"dernst","date_updated":"2020-11-18T07:26:10Z","file_id":"8768","file_name":"2020_PlosCompBio_Kaveh.pdf","checksum":"555456dd0e47bcf9e0994bcb95577e88","success":1,"file_size":2498594,"access_level":"open_access","relation":"main_file","date_created":"2020-11-18T07:26:10Z"}],"isi":1,"author":[{"full_name":"Kaveh, Kamran","first_name":"Kamran","last_name":"Kaveh"},{"full_name":"McAvoy, Alex","last_name":"McAvoy","first_name":"Alex"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"pmid":1,"external_id":{"pmid":["33151935"],"isi":["000591317200004"]},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"8769","issue":"14","intvolume":"       102","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"quality_controlled":"1","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"},{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"date_published":"2020-10-01T00:00:00Z","month":"10","status":"public","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"date_created":"2020-11-18T07:34:17Z","publisher":"American Physical Society","citation":{"ista":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. 2020. Quantum impurity model for anyons. Physical Review B. 102(14), 144109.","short":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, R. Seiringer, Physical Review B 102 (2020).","mla":"Yakaboylu, Enderalp, et al. “Quantum Impurity Model for Anyons.” <i>Physical Review B</i>, vol. 102, no. 14, 144109, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.144109\">10.1103/physrevb.102.144109</a>.","chicago":"Yakaboylu, Enderalp, Areg Ghazaryan, D. Lundholm, N. Rougerie, Mikhail Lemeshko, and Robert Seiringer. “Quantum Impurity Model for Anyons.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.144109\">https://doi.org/10.1103/physrevb.102.144109</a>.","ieee":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, and R. Seiringer, “Quantum impurity model for anyons,” <i>Physical Review B</i>, vol. 102, no. 14. American Physical Society, 2020.","ama":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. Quantum impurity model for anyons. <i>Physical Review B</i>. 2020;102(14). doi:<a href=\"https://doi.org/10.1103/physrevb.102.144109\">10.1103/physrevb.102.144109</a>","apa":"Yakaboylu, E., Ghazaryan, A., Lundholm, D., Rougerie, N., Lemeshko, M., &#38; Seiringer, R. (2020). Quantum impurity model for anyons. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.144109\">https://doi.org/10.1103/physrevb.102.144109</a>"},"acknowledgement":"We are grateful to M. Correggi, A. Deuchert, and P. Schmelcher for valuable discussions. We also thank the anonymous referees for helping to clarify a few important points in the experimental realization. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement\r\nNo 754411. D.L. acknowledges financial support from the Goran Gustafsson Foundation (grant no. 1804) and LMU Munich. R.S., M.L., and N.R. gratefully acknowledge financial support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 694227, No 801770, and No 758620, respectively).","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","isi":1,"arxiv":1,"external_id":{"arxiv":["1912.07890"],"isi":["000582563300001"]},"author":[{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","first_name":"Enderalp"},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan"},{"first_name":"D.","last_name":"Lundholm","full_name":"Lundholm, D."},{"full_name":"Rougerie, N.","last_name":"Rougerie","first_name":"N."},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail"},{"first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"scopus_import":"1","type":"journal_article","publication":"Physical Review B","date_updated":"2025-04-14T07:26:54Z","article_processing_charge":"No","article_type":"original","article_number":"144109","language":[{"iso":"eng"}],"abstract":[{"text":"One of the hallmarks of quantum statistics, tightly entwined with the concept of topological phases of matter, is the prediction of anyons. Although anyons are predicted to be realized in certain fractional quantum Hall systems, they have not yet been unambiguously detected in experiment. Here we introduce a simple quantum impurity model, where bosonic or fermionic impurities turn into anyons as a consequence of their interaction with the surrounding many-particle bath. A cloud of phonons dresses each impurity in such a way that it effectively attaches fluxes or vortices to it and thereby converts it into an Abelian anyon. The corresponding quantum impurity model, first, provides a different approach to the numerical solution of the many-anyon problem, along with a concrete perspective of anyons as emergent quasiparticles built from composite bosons or fermions. More importantly, the model paves the way toward realizing anyons using impurities in crystal lattices as well as ultracold gases. In particular, we consider two heavy electrons interacting with a two-dimensional lattice crystal in a magnetic field, and show that when the impurity-bath system is rotated at the cyclotron frequency, impurities behave as anyons as a consequence of the angular momentum exchange between the impurities and the bath. A possible experimental realization is proposed by identifying the statistics parameter in terms of the mean-square distance of the impurities and the magnetization of the impurity-bath system, both of which are accessible to experiment. Another proposed application is impurities immersed in a two-dimensional weakly interacting Bose gas.","lang":"eng"}],"oa":1,"day":"01","year":"2020","volume":102,"title":"Quantum impurity model for anyons","doi":"10.1103/physrevb.102.144109","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.07890"}],"ec_funded":1},{"license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2020-07-01T00:00:00Z","type":"research_data_reference","date_updated":"2025-07-10T11:54:59Z","_id":"8809","citation":{"ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>.","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","mla":"Perini, Samuel, et al. <i>Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>.","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>.","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>"},"publisher":"Dryad","date_created":"2020-11-25T11:07:25Z","department":[{"_id":"NiBa"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"article_processing_charge":"No","month":"07","status":"public","year":"2020","title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","oa":1,"day":"01","abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"has_accepted_license":"1","author":[{"full_name":"Perini, Samuel","first_name":"Samuel","last_name":"Perini"},{"last_name":"Rafajlovic","first_name":"Marina","full_name":"Rafajlovic, Marina"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.qrfj6q5cn"}],"doi":"10.5061/dryad.qrfj6q5cn","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","id":"7995","relation":"used_in_publication"}]},"oa_version":"Published Version"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1101/2020.11.03.366948","publication_status":"submitted","pmid":1,"author":[{"first_name":"Laura","last_name":"Santini","full_name":"Santini, Laura"},{"last_name":"Halbritter","first_name":"Florian","full_name":"Halbritter, Florian"},{"full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira","first_name":"Fabian"},{"last_name":"Suzuki","first_name":"Toru","full_name":"Suzuki, Toru"},{"last_name":"Asami","first_name":"Maki","full_name":"Asami, Maki"},{"full_name":"Ramesmayer, Julia","last_name":"Ramesmayer","first_name":"Julia"},{"first_name":"Xiaoyan","last_name":"Ma","full_name":"Ma, Xiaoyan"},{"first_name":"Andreas","last_name":"Lackner","full_name":"Lackner, Andreas"},{"full_name":"Warr, Nick","last_name":"Warr","first_name":"Nick"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ernest","last_name":"Laue","full_name":"Laue, Ernest"},{"full_name":"Farlik, Matthias","first_name":"Matthias","last_name":"Farlik"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"full_name":"Beyer, Andreas","last_name":"Beyer","first_name":"Andreas"},{"last_name":"Perry","first_name":"Anthony C. F.","full_name":"Perry, Anthony C. F."},{"full_name":"Leeb, Martin","first_name":"Martin","last_name":"Leeb"}],"main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"external_id":{"pmid":["PPR234457 "]},"language":[{"iso":"eng"}],"abstract":[{"text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"day":"05","oa":1,"title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","year":"2020","status":"public","month":"11","article_processing_charge":"No","department":[{"_id":"SiHi"}],"date_created":"2020-11-26T07:17:19Z","publisher":"Cold Spring Harbor Laboratory","citation":{"ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>","ieee":"L. Santini <i>et al.</i>, “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, <a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>."},"_id":"8813","date_updated":"2023-09-12T11:05:28Z","publication":"bioRxiv","type":"preprint","date_published":"2020-11-05T00:00:00Z"},{"_id":"8834","ddc":["530"],"date_updated":"2025-04-15T08:38:16Z","type":"research_data","date_published":"2020-12-02T00:00:00Z","contributor":[{"first_name":"Kushagra","last_name":"Aggarwal","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","contributor_type":"project_member"},{"first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"contributor_type":"project_member","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","first_name":"Ivan"},{"first_name":"Amir","last_name":"Sammak","contributor_type":"project_member"},{"first_name":"Marc","last_name":"Botifoll","contributor_type":"project_member"},{"first_name":"Sara","last_name":"Marti-Sanchez","contributor_type":"project_member"},{"first_name":"Menno","last_name":"Veldhorst","contributor_type":"project_member"},{"contributor_type":"project_member","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Scappucci","first_name":"Giordano","contributor_type":"project_member"},{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader"}],"status":"public","month":"12","article_processing_charge":"No","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"department":[{"_id":"GeKa"}],"date_created":"2020-12-02T10:49:30Z","citation":{"ama":"Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">https://doi.org/10.15479/AT:ISTA:8834</a>","chicago":"Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">https://doi.org/10.15479/AT:ISTA:8834</a>.","ista":"Katsaros G. 2020. Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>.","short":"G. Katsaros, (2020).","mla":"Katsaros, Georgios. <i>Enhancement of Proximity Induced Superconductivity in Planar Germanium</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>."},"publisher":"Institute of Science and Technology 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data collection contains the transport data for figures presented in the supplementary material of \"Enhancement of Proximity Induced Superconductivity in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).\r\n","lang":"eng"}],"day":"02","oa":1,"title":"Enhancement of proximity induced superconductivity in planar Germanium","year":"2020","oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10559"},{"status":"public","id":"8831","relation":"used_in_publication"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:ISTA:8834","file_date_updated":"2020-12-02T10:46:27Z","author":[{"last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}]},{"date_published":"2020-12-01T00:00:00Z","quality_controlled":"1","_id":"8914","intvolume":"       450","publication_identifier":{"issn":["0306-4522"]},"citation":{"short":"A. Salamatina, J.H. Yang, S. Brenner-Morton, J.B. Bikoff, L. Fang, C.R. Kintner, T.M. Jessell, L.B. Sweeney, Neuroscience 450 (2020) 81–95.","mla":"Salamatina, Alina, et al. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” <i>Neuroscience</i>, vol. 450, Elsevier, 2020, pp. 81–95, doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">10.1016/j.neuroscience.2020.08.011</a>.","ista":"Salamatina A, Yang JH, Brenner-Morton S, Bikoff JB, Fang L, Kintner CR, Jessell TM, Sweeney LB. 2020. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 450, 81–95.","chicago":"Salamatina, Alina, Jerry H Yang, Susan Brenner-Morton, Jay B  Bikoff, Linjing Fang, Christopher R Kintner, Thomas M Jessell, and Lora B. Sweeney. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” <i>Neuroscience</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">https://doi.org/10.1016/j.neuroscience.2020.08.011</a>.","ama":"Salamatina A, Yang JH, Brenner-Morton S, et al. Differential loss of spinal interneurons in a mouse model of ALS. <i>Neuroscience</i>. 2020;450:81-95. doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">10.1016/j.neuroscience.2020.08.011</a>","ieee":"A. Salamatina <i>et al.</i>, “Differential loss of spinal interneurons in a mouse model of ALS,” <i>Neuroscience</i>, vol. 450. Elsevier, pp. 81–95, 2020.","apa":"Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner, C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a mouse model of ALS. <i>Neuroscience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">https://doi.org/10.1016/j.neuroscience.2020.08.011</a>"},"publisher":"Elsevier","date_created":"2020-12-03T11:47:31Z","department":[{"_id":"LoSw"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"page":"81-95","month":"12","status":"public","file":[{"creator":"dernst","content_type":"application/pdf","date_updated":"2020-12-03T11:45:26Z","file_id":"8915","checksum":"da7413c819e079720669c82451b49294","success":1,"file_size":4071247,"file_name":"2020_Neuroscience_Salamatina.pdf","date_created":"2020-12-03T11:45:26Z","relation":"main_file","access_level":"open_access"}],"acknowledgement":"This work was made possible by the generous support of Project ALS. Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. This manuscript is dedicated to Tom Jessell, an inspirational scientist, friend and mentor.","has_accepted_license":"1","external_id":{"pmid":["32858144"],"isi":["000595588700008"]},"author":[{"last_name":"Salamatina","first_name":"Alina","full_name":"Salamatina, Alina"},{"full_name":"Yang, Jerry H","last_name":"Yang","first_name":"Jerry H"},{"full_name":"Brenner-Morton, Susan","last_name":"Brenner-Morton","first_name":"Susan"},{"full_name":"Bikoff, Jay B ","first_name":"Jay B ","last_name":"Bikoff"},{"last_name":"Fang","first_name":"Linjing","full_name":"Fang, Linjing"},{"full_name":"Kintner, Christopher R","last_name":"Kintner","first_name":"Christopher R"},{"first_name":"Thomas M","last_name":"Jessell","full_name":"Jessell, Thomas M"},{"last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","orcid":"0000-0001-9242-5601"}],"pmid":1,"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","publication":"Neuroscience","date_updated":"2024-10-09T21:00:14Z","scopus_import":"1","ddc":["570"],"article_type":"original","article_processing_charge":"Yes (via OA deal)","year":"2020","title":"Differential loss of spinal interneurons in a mouse model of ALS","volume":450,"oa":1,"day":"01","abstract":[{"text":"Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron populations in the spinal cord and cortex. Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord.","lang":"eng"}],"corr_author":"1","language":[{"iso":"eng"}],"file_date_updated":"2020-12-03T11:45:26Z","publication_status":"published","doi":"10.1016/j.neuroscience.2020.08.011"},{"date_created":"2020-12-06T23:01:14Z","department":[{"_id":"EvBe"}],"publisher":"Frontiers","citation":{"short":"C. Nibau, D. Dadarou, N. Kargios, A. Mallioura, N. Fernandez-Fuentes, N. Cavallari, J.H. Doonan, Frontiers in Plant Science 11 (2020).","mla":"Nibau, Candida, et al. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” <i>Frontiers in Plant Science</i>, vol. 11, 586870, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2020.586870\">10.3389/fpls.2020.586870</a>.","ista":"Nibau C, Dadarou D, Kargios N, Mallioura A, Fernandez-Fuentes N, Cavallari N, Doonan JH. 2020. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 11, 586870.","chicago":"Nibau, Candida, Despoina Dadarou, Nestoras Kargios, Areti Mallioura, Narcis Fernandez-Fuentes, Nicola Cavallari, and John H. Doonan. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” <i>Frontiers in Plant Science</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fpls.2020.586870\">https://doi.org/10.3389/fpls.2020.586870</a>.","ieee":"C. Nibau <i>et al.</i>, “A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020.","ama":"Nibau C, Dadarou D, Kargios N, et al. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fpls.2020.586870\">10.3389/fpls.2020.586870</a>","apa":"Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N., Cavallari, N., &#38; Doonan, J. H. (2020). A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2020.586870\">https://doi.org/10.3389/fpls.2020.586870</a>"},"month":"11","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","date_published":"2020-11-10T00:00:00Z","_id":"8924","intvolume":"        11","publication_identifier":{"eissn":["1664-462X"]},"isi":1,"external_id":{"pmid":["33240303"],"isi":["000591637000001"]},"pmid":1,"author":[{"full_name":"Nibau, Candida","first_name":"Candida","last_name":"Nibau"},{"last_name":"Dadarou","first_name":"Despoina","full_name":"Dadarou, Despoina"},{"full_name":"Kargios, Nestoras","first_name":"Nestoras","last_name":"Kargios"},{"first_name":"Areti","last_name":"Mallioura","full_name":"Mallioura, Areti"},{"last_name":"Fernandez-Fuentes","first_name":"Narcis","full_name":"Fernandez-Fuentes, Narcis"},{"first_name":"Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"full_name":"Doonan, John H.","first_name":"John H.","last_name":"Doonan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"1c0ee6ce9950aa665d6a5cc64aa6b752","success":1,"file_size":1833244,"file_name":"2020_Frontiers_Nibau.pdf","relation":"main_file","access_level":"open_access","date_created":"2020-12-09T09:14:19Z","content_type":"application/pdf","creator":"dernst","date_updated":"2020-12-09T09:14:19Z","file_id":"8929"}],"acknowledgement":"CN, DD, NF-F, and JD were funded by the BBSRC (grant number BB/M009459/1). NK and AM were funded through the ERASMUS+Program. NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna.","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","type":"journal_article","publication":"Frontiers in Plant Science","date_updated":"2025-06-12T07:02:22Z","scopus_import":"1","ddc":["580"],"file_date_updated":"2020-12-09T09:14:19Z","doi":"10.3389/fpls.2020.586870","publication_status":"published","oa":1,"day":"10","year":"2020","volume":11,"title":"A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis","article_number":"586870","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Maintaining fertility in a fluctuating environment is key to the reproductive success of flowering plants. Meiosis and pollen formation are particularly sensitive to changes in growing conditions, especially temperature. We have previously identified cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent meiosis and this may involve the regulation of alternative splicing (AS), including of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain which may be involved in co-factor interaction. In leaves, both isoforms have distinct temperature-dependent functions on target mRNA processing, but their role in pollen development is unknown. In the present study, we characterize the role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the long (L) form is necessary and sufficient to rescue the fertility defects of the cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of the ATP binding pocket of the kinase indicates that kinase activity is necessary for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore, we show that there is partial functional overlap between CDKG1 and its paralog CDKG2 that could in part be explained by overlapping gene expression."}]},{"contributor":[{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor"},{"first_name":"Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor"}],"date_published":"2020-12-10T00:00:00Z","type":"research_data","date_updated":"2025-06-12T06:33:18Z","ddc":["570"],"_id":"8930","citation":{"apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","short":"B. Kavcic, (2020).","mla":"Kavcic, Bor. <i>Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>."},"publisher":"Institute of Science and Technology Austria","date_created":"2020-12-09T15:04:02Z","department":[{"_id":"GaTk"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"month":"12","article_processing_charge":"No","status":"public","year":"2020","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","oa":1,"day":"10","file":[{"date_created":"2020-12-09T15:00:19Z","access_level":"open_access","relation":"main_file","file_name":"PLoSCompBiol2020_datarep.zip","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","file_size":315494370,"date_updated":"2020-12-09T15:00:19Z","file_id":"8932","creator":"bkavcic","content_type":"application/zip"}],"corr_author":"1","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"has_accepted_license":"1","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"author":[{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","last_name":"Kavcic","first_name":"Bor"}],"file_date_updated":"2020-12-09T15:00:19Z","doi":"10.15479/AT:ISTA:8930","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"8997","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2."}],"language":[{"iso":"eng"}],"article_number":"180508","year":"2020","volume":102,"title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","oa":1,"day":"01","publication_status":"published","doi":"10.1103/PhysRevB.102.180508","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.04329"}],"scopus_import":"1","type":"journal_article","publication":"Physical Review B","date_updated":"2025-07-10T12:01:27Z","article_type":"original","article_processing_charge":"No","acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","external_id":{"isi":["000591509900003"],"arxiv":["2011.04329"]},"arxiv":1,"author":[{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","first_name":"Martin","last_name":"Zemlicka"},{"first_name":"M.","last_name":"Kopčík","full_name":"Kopčík, M."},{"full_name":"Szabó, P.","first_name":"P.","last_name":"Szabó"},{"first_name":"T.","last_name":"Samuely","full_name":"Samuely, T."},{"first_name":"J.","last_name":"Kačmarčík","full_name":"Kačmarčík, J."},{"full_name":"Neilinger, P.","first_name":"P.","last_name":"Neilinger"},{"last_name":"Grajcar","first_name":"M.","full_name":"Grajcar, M."},{"full_name":"Samuely, P.","first_name":"P.","last_name":"Samuely"}],"isi":1,"_id":"8944","intvolume":"       102","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"issue":"18","date_published":"2020-11-01T00:00:00Z","quality_controlled":"1","month":"11","status":"public","publisher":"American Physical Society","citation":{"chicago":"Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020).","mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>.","ista":"Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508.","ieee":"M. Zemlicka <i>et al.</i>, “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” <i>Physical Review B</i>, vol. 102, no. 18. American Physical Society, 2020.","apa":"Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>","ama":"Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. 2020;102(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>"},"department":[{"_id":"JoFi"}],"date_created":"2020-12-13T23:01:21Z"},{"oa":1,"day":"11","year":"2020","title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","volume":9,"article_number":"2662","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"<jats:p>Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.</jats:p>"}],"file_date_updated":"2020-12-14T08:09:43Z","ec_funded":1,"doi":"10.3390/cells9122662","publication_status":"published","type":"journal_article","publication":"Cells","date_updated":"2025-06-12T07:02:43Z","scopus_import":"1","ddc":["570"],"article_processing_charge":"No","article_type":"original","file":[{"access_level":"open_access","relation":"main_file","date_created":"2020-12-14T08:09:43Z","file_name":"2020_Cells_Zhang.pdf","success":1,"file_size":3504525,"checksum":"5095cbdc728c9a510c5761cf60a8861c","file_id":"8950","date_updated":"2020-12-14T08:09:43Z","content_type":"application/pdf","creator":"dernst"}],"has_accepted_license":"1","acknowledgement":"This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript.","isi":1,"external_id":{"isi":["000601787300001"],"pmid":["33322301"]},"pmid":1,"author":[{"full_name":"Zhang, Xuying","last_name":"Zhang","first_name":"Xuying"},{"full_name":"Mennicke, Christine V.","last_name":"Mennicke","first_name":"Christine V."},{"full_name":"Xiao, Guanxi","first_name":"Guanxi","last_name":"Xiao"},{"last_name":"Beattie","first_name":"Robert J","full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753"},{"first_name":"Mansoor","last_name":"Haider","full_name":"Haider, Mansoor"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer"},{"last_name":"Ghashghaei","first_name":"H. Troy","full_name":"Ghashghaei, H. Troy"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","call_identifier":"FWF"},{"grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"date_published":"2020-12-11T00:00:00Z","_id":"8949","issue":"12","intvolume":"         9","publication_identifier":{"issn":["2073-4409"]},"department":[{"_id":"SiHi"}],"date_created":"2020-12-14T08:04:03Z","citation":{"chicago":"Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>.","mla":"Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>, vol. 9, no. 12, 2662, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>.","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020).","ista":"Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662.","apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., &#38; Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>","ama":"Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. 2020;9(12). doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>","ieee":"X. Zhang <i>et al.</i>, “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” <i>Cells</i>, vol. 9, no. 12. MDPI, 2020."},"publisher":"MDPI","month":"12","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","month":"12","status":"public","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>.","mla":"Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","short":"A.A. Nagy-Staron, (2020).","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>."},"date_created":"2020-12-20T10:00:26Z","department":[{"_id":"CaGu"}],"ddc":["570"],"_id":"8951","contributor":[{"first_name":"Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"first_name":"Kathrin","last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Caroline","last_name":"Caruso Carter"},{"last_name":"Sonnleitner","first_name":"Elisabeth","contributor_type":"project_member"},{"last_name":"Kavcic","first_name":"Bor","contributor_type":"project_member","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tiago","last_name":"Paixão","contributor_type":"project_member"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","contributor_type":"project_manager","first_name":"Calin C","last_name":"Guet"}],"date_published":"2020-12-21T00:00:00Z","type":"research_data","date_updated":"2025-06-12T06:36:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:ISTA:8951","oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","id":"9283","status":"public"}]},"author":[{"last_name":"Nagy-Staron","first_name":"Anna A","full_name":"Nagy-Staron, Anna A","orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-12-20T22:01:44Z","file":[{"file_name":"readme.txt","checksum":"f57862aeee1690c7effd2b1117d40ed1","success":1,"file_size":523,"date_created":"2020-12-20T09:52:52Z","access_level":"open_access","relation":"main_file","creator":"bkavcic","content_type":"text/plain","file_id":"8952","date_updated":"2020-12-20T09:52:52Z"},{"relation":"main_file","access_level":"open_access","date_created":"2020-12-20T22:01:44Z","checksum":"f2c6d5232ec6d551b6993991e8689e9f","success":1,"file_size":379228,"file_name":"GRNs Research depository.gb","file_id":"8954","date_updated":"2020-12-20T22:01:44Z","content_type":"application/octet-stream","creator":"bkavcic"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"has_accepted_license":"1","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"year":"2020","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","oa":1,"day":"21"},{"acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","date_created":"2020-12-21T10:37:50Z","success":1,"file_size":13380030,"checksum":"ef9515b28c5619b7126c0f347958bcb3","file_name":"2020_Frontiers_Rizzo.pdf","file_id":"8961","date_updated":"2020-12-21T10:37:50Z","content_type":"application/pdf","creator":"dernst"}],"pmid":1,"author":[{"first_name":"Rossella","last_name":"Rizzo","full_name":"Rizzo, Rossella"},{"full_name":"Zhang, Xiyun","first_name":"Xiyun","last_name":"Zhang"},{"full_name":"Wang, Jilin W.J.L.","first_name":"Jilin W.J.L.","last_name":"Wang"},{"last_name":"Lombardi","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio"},{"full_name":"Ivanov, Plamen Ch","last_name":"Ivanov","first_name":"Plamen Ch"}],"external_id":{"pmid":["33324233"],"isi":["000596849400001"]},"isi":1,"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-11-26T00:00:00Z","quality_controlled":"1","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"publication_identifier":{"eissn":["1664042X"]},"intvolume":"        11","_id":"8955","citation":{"chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>.","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>, vol. 11, 558070, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>.","short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).","ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” <i>Frontiers in Physiology</i>, vol. 11. Frontiers, 2020.","apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., &#38; Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>"},"publisher":"Frontiers","department":[{"_id":"GaTk"}],"date_created":"2020-12-20T23:01:18Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","month":"11","title":"Network physiology of cortico–muscular interactions","volume":11,"year":"2020","day":"26","oa":1,"abstract":[{"text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies.","lang":"eng"}],"article_number":"558070","language":[{"iso":"eng"}],"ec_funded":1,"file_date_updated":"2020-12-21T10:37:50Z","publication_status":"published","doi":"10.3389/fphys.2020.558070","date_updated":"2025-04-14T07:43:50Z","publication":"Frontiers in Physiology","type":"journal_article","ddc":["570"],"scopus_import":"1","article_type":"original","article_processing_charge":"No"}]