[{"month":"08","day":"01","publication_identifier":{"isbn":["9781728157511"]},"article_processing_charge":"No","scopus_import":"1","conference":{"name":"ESGCO: European Study Group on Cardiovascular Oscillations","start_date":"2020-07-15","location":"Pisa, Italy","end_date":"2020-07-15"},"date_published":"2020-08-01T00:00:00Z","doi":"10.1109/ESGCO49734.2020.9158054","language":[{"iso":"eng"}],"publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","external_id":{"isi":["000621172600045"]},"citation":{"short":"G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , IEEE, 2020.","mla":"Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , 9158054, IEEE, 2020, doi:10.1109/ESGCO49734.2020.9158054.","chicago":"Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE, 2020. https://doi.org/10.1109/ESGCO49734.2020.9158054.","ama":"Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent homology in the analysis of heart rate variability. In: 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE; 2020. doi:10.1109/ESGCO49734.2020.9158054","apa":"Graff, G., Graff, B., Jablonski, G., & Narkiewicz, K. (2020). The application of persistent homology in the analysis of heart rate variability. In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . Pisa, Italy: IEEE. https://doi.org/10.1109/ESGCO49734.2020.9158054","ieee":"G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of persistent homology in the analysis of heart rate variability,” in 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , Pisa, Italy, 2020.","ista":"Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent homology in the analysis of heart rate variability. 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular Oscillations, 9158054."},"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients."}],"article_number":"9158054","type":"conference","author":[{"full_name":"Graff, Grzegorz","last_name":"Graff","first_name":"Grzegorz"},{"full_name":"Graff, Beata","first_name":"Beata","last_name":"Graff"},{"last_name":"Jablonski","first_name":"Grzegorz","orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz"},{"first_name":"Krzysztof","last_name":"Narkiewicz","full_name":"Narkiewicz, Krzysztof"}],"date_updated":"2023-08-22T09:33:34Z","date_created":"2020-09-28T08:59:27Z","oa_version":"None","_id":"8580","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2020","status":"public","title":"The application of persistent homology in the analysis of heart rate variability","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"IEEE"},{"doi":"10.1002/advs.202001724","language":[{"iso":"eng"}],"external_id":{"isi":["000573860700001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2198-3844"]},"month":"11","author":[{"full_name":"Tian, Anhao","first_name":"Anhao","last_name":"Tian"},{"full_name":"Kang, Bo","first_name":"Bo","last_name":"Kang"},{"last_name":"Li","first_name":"Baizhou","full_name":"Li, Baizhou"},{"full_name":"Qiu, Biying","first_name":"Biying","last_name":"Qiu"},{"last_name":"Jiang","first_name":"Wenhong","full_name":"Jiang, Wenhong"},{"first_name":"Fangjie","last_name":"Shao","full_name":"Shao, Fangjie"},{"first_name":"Qingqing","last_name":"Gao","full_name":"Gao, Qingqing"},{"last_name":"Liu","first_name":"Rui","full_name":"Liu, Rui"},{"last_name":"Cai","first_name":"Chengwei","full_name":"Cai, Chengwei"},{"full_name":"Jing, Rui","first_name":"Rui","last_name":"Jing"},{"last_name":"Wang","first_name":"Wei","full_name":"Wang, Wei"},{"first_name":"Pengxiang","last_name":"Chen","full_name":"Chen, Pengxiang"},{"full_name":"Liang, Qinghui","last_name":"Liang","first_name":"Qinghui"},{"full_name":"Bao, Lili","last_name":"Bao","first_name":"Lili"},{"last_name":"Man","first_name":"Jianghong","full_name":"Man, Jianghong"},{"full_name":"Wang, Yan","last_name":"Wang","first_name":"Yan"},{"full_name":"Shi, Yu","first_name":"Yu","last_name":"Shi"},{"last_name":"Li","first_name":"Jin","full_name":"Li, Jin"},{"first_name":"Minmin","last_name":"Yang","full_name":"Yang, Minmin"},{"full_name":"Wang, Lisha","last_name":"Wang","first_name":"Lisha"},{"full_name":"Zhang, Jianmin","last_name":"Zhang","first_name":"Jianmin"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"full_name":"Zhu, Junming","last_name":"Zhu","first_name":"Junming"},{"full_name":"Bian, Xiuwu","last_name":"Bian","first_name":"Xiuwu"},{"last_name":"Wang","first_name":"Ying‐Jie","full_name":"Wang, Ying‐Jie"},{"first_name":"Chong","last_name":"Liu","full_name":"Liu, Chong"}],"volume":7,"date_created":"2020-10-01T09:44:13Z","date_updated":"2023-08-22T09:53:01Z","acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","year":"2020","publisher":"Wiley","department":[{"_id":"SiHi"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-12-10T14:07:24Z","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"2001724","date_published":"2020-11-04T00:00:00Z","citation":{"apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. Wiley. https://doi.org/10.1002/advs.202001724","ieee":"A. Tian et al., “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” Advanced Science, vol. 7, no. 21. Wiley, 2020.","ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.","ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 2020;7(21). doi:10.1002/advs.202001724","chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.202001724.","short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020).","mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science, vol. 7, no. 21, 2001724, Wiley, 2020, doi:10.1002/advs.202001724."},"publication":"Advanced Science","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"04","keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"file":[{"date_created":"2020-12-10T14:07:24Z","date_updated":"2020-12-10T14:07:24Z","success":1,"checksum":"92818c23ecc70e35acfa671f3cfb9909","file_id":"8938","relation":"main_file","creator":"dernst","file_size":7835833,"content_type":"application/pdf","file_name":"2020_AdvScience_Tian.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8592","intvolume":" 7","ddc":["570"],"title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","status":"public","issue":"21","abstract":[{"lang":"eng","text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma."}],"type":"journal_article"},{"publication_identifier":{"issn":["2041-1723"]},"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000573756600004"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-020-18610-6","language":[{"iso":"eng"}],"article_number":"4838","file_date_updated":"2020-09-28T13:16:15Z","year":"2020","department":[{"_id":"StFr"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-19720-x","relation":"erratum"}]},"author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"first_name":"Harald","last_name":"Fitzek","full_name":"Fitzek, Harald"},{"full_name":"Kothleitner, Gerald","last_name":"Kothleitner","first_name":"Gerald"},{"full_name":"Presser, Volker","last_name":"Presser","first_name":"Volker"},{"full_name":"Gollas, Bernhard","last_name":"Gollas","first_name":"Bernhard"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Abbas, Qamar","last_name":"Abbas","first_name":"Qamar"}],"volume":11,"date_updated":"2023-08-22T09:37:24Z","date_created":"2020-09-25T07:23:13Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"article_processing_charge":"No","has_accepted_license":"1","day":"24","citation":{"chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer Nature, 2020, doi:10.1038/s41467-020-18610-6.","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6","ieee":"C. Prehal et al., “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 2020;11. doi:10.1038/s41467-020-18610-6"},"publication":"Nature Communications","article_type":"original","date_published":"2020-09-24T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}],"_id":"8568","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 11","status":"public","ddc":["530"],"title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","oa_version":"Published Version","file":[{"file_name":"2020_NatureComm_Prehal.pdf","access_level":"open_access","file_size":1822469,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8585","date_updated":"2020-09-28T13:16:15Z","date_created":"2020-09-28T13:16:15Z","checksum":"eada7bc8dd16a49390137cff882ef328","success":1}]},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000577142600032"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41598-020-72848-0","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["20452322"]},"acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).","year":"2020","publication_status":"published","department":[{"_id":"MaJö"}],"publisher":"Springer Nature","author":[{"full_name":"Deichler, Alfonso","first_name":"Alfonso","last_name":"Deichler"},{"full_name":"Carrasco, Denisse","last_name":"Carrasco","first_name":"Denisse"},{"last_name":"Lopez-Jury","first_name":"Luciana","full_name":"Lopez-Jury, Luciana"},{"full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A","last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marquez, Natalia","first_name":"Natalia","last_name":"Marquez"},{"full_name":"Mpodozis, Jorge","last_name":"Mpodozis","first_name":"Jorge"},{"full_name":"Marin, Gonzalo","last_name":"Marin","first_name":"Gonzalo"}],"date_updated":"2023-08-22T09:58:21Z","date_created":"2020-10-11T22:01:14Z","volume":10,"article_number":"16220","file_date_updated":"2020-10-12T12:39:10Z","publication":"Scientific Reports","citation":{"mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0.","ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0","ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220.","apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0","ieee":"A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020."},"article_type":"original","date_published":"2020-10-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","_id":"8643","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","ddc":["570"],"status":"public","intvolume":" 10","oa_version":"Published Version","file":[{"file_name":"2020_ScientificReport_Deichler.pdf","access_level":"open_access","creator":"dernst","file_size":3906744,"content_type":"application/pdf","file_id":"8651","relation":"main_file","date_created":"2020-10-12T12:39:10Z","date_updated":"2020-10-12T12:39:10Z","success":1,"checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors."}]},{"volume":36,"date_updated":"2023-08-22T09:57:29Z","date_created":"2020-10-11T22:01:14Z","author":[{"full_name":"Esteban, Laura A","first_name":"Laura A","last_name":"Esteban"},{"last_name":"Lonishin","first_name":"Lyubov R","full_name":"Lonishin, Lyubov R"},{"first_name":"Daniil M","last_name":"Bobrovskiy","full_name":"Bobrovskiy, Daniil M"},{"full_name":"Leleytner, Gregory","last_name":"Leleytner","first_name":"Gregory"},{"last_name":"Bogatyreva","first_name":"Natalya S","full_name":"Bogatyreva, Natalya S"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry N ","first_name":"Dmitry N ","last_name":"Ivankov"}],"department":[{"_id":"FyKo"}],"publisher":"Oxford Academic","publication_status":"published","pmid":1,"acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","year":"2020","license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"file_date_updated":"2020-10-12T12:02:09Z","language":[{"iso":"eng"}],"doi":"10.1093/bioinformatics/btz841","project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["31742320"],"isi":["000538696800054"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"month":"03","oa_version":"Published Version","file":[{"file_id":"8649","relation":"main_file","date_updated":"2020-10-12T12:02:09Z","date_created":"2020-10-12T12:02:09Z","success":1,"checksum":"21d6f71839deb3b83e4a356193f72767","file_name":"2020_Bioinformatics_Esteban.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":308341}],"intvolume":" 36","ddc":["000","570"],"title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8645","issue":"6","abstract":[{"lang":"eng","text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data."}],"type":"journal_article","date_published":"2020-03-15T00:00:00Z","page":"1960-1962","article_type":"original","citation":{"short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.","ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841","apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841","ieee":"L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.","ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962."},"publication":"Bioinformatics","has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1"},{"day":"23","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2020-09-23T00:00:00Z","article_type":"original","publication":"Physical Biology","citation":{"ama":"Merrin J. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 2020;17(6). doi:10.1088/1478-3975/abb2db","ieee":"J. Merrin, “Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide,” Physical Biology, vol. 17, no. 6. IOP Publishing, 2020.","apa":"Merrin, J. (2020). Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abb2db","ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005.","short":"J. Merrin, Physical Biology 17 (2020).","mla":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology, vol. 17, no. 6, 065005, IOP Publishing, 2020, doi:10.1088/1478-3975/abb2db.","chicago":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology. IOP Publishing, 2020. https://doi.org/10.1088/1478-3975/abb2db."},"abstract":[{"text":"Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_PhysBio_Merrin.pdf","creator":"dernst","content_type":"application/pdf","file_size":1667111,"file_id":"8609","relation":"main_file","success":1,"checksum":"fec9bdd355ed349f09990faab20838a7","date_created":"2020-10-05T13:53:59Z","date_updated":"2020-10-05T13:53:59Z"}],"title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide","ddc":["510","570"],"status":"public","intvolume":" 17","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8597","month":"09","publication_identifier":{"eissn":["14783975"]},"language":[{"iso":"eng"}],"doi":"10.1088/1478-3975/abb2db","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000575539700001"]},"oa":1,"file_date_updated":"2020-10-05T13:53:59Z","article_number":"065005","date_created":"2020-10-04T22:01:35Z","date_updated":"2023-08-22T09:53:29Z","volume":17,"author":[{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"NanoFab"}],"publisher":"IOP Publishing","acknowledgement":"I would especially like to thank Michael Sixt for encouraging me to think about these problems while working at home due to restrictions in place. I want to thank Nick Barton, Katka Bodova, Matthew Robinson, Simon Rella, Federico Sau, Ivan Prieto, and Pradeep Kumar for useful discussions.","year":"2020"},{"external_id":{"isi":["000603428000010"],"pmid":["32976770"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1016/j.neuron.2020.08.030","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"year":"2020","acknowledgement":"We thank J. Angibaud for organotypic cultures and R. Chereau and J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping. This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251, ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950, and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program (C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995 (A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01, Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O., and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and FP7 MemStick Project No. 201600 (M.G.S.).","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"HaJa"}],"author":[{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"full_name":"Bard, Lucie","first_name":"Lucie","last_name":"Bard"},{"last_name":"Panatier","first_name":"Aude","full_name":"Panatier, Aude"},{"first_name":"James P.","last_name":"Reynolds","full_name":"Reynolds, James P."},{"full_name":"Kopach, Olga","first_name":"Olga","last_name":"Kopach"},{"full_name":"Medvedev, Nikolay I.","last_name":"Medvedev","first_name":"Nikolay I."},{"full_name":"Minge, Daniel","first_name":"Daniel","last_name":"Minge"},{"full_name":"Herde, Michel K.","last_name":"Herde","first_name":"Michel K."},{"first_name":"Stefanie","last_name":"Anders","full_name":"Anders, Stefanie"},{"last_name":"Kraev","first_name":"Igor","full_name":"Kraev, Igor"},{"full_name":"Heller, Janosch P.","last_name":"Heller","first_name":"Janosch P."},{"full_name":"Rama, Sylvain","first_name":"Sylvain","last_name":"Rama"},{"last_name":"Zheng","first_name":"Kaiyu","full_name":"Zheng, Kaiyu"},{"last_name":"Jensen","first_name":"Thomas P.","full_name":"Jensen, Thomas P."},{"first_name":"Inmaculada","last_name":"Sanchez-Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez-Romero, Inmaculada"},{"full_name":"Jackson, Colin J.","first_name":"Colin J.","last_name":"Jackson"},{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L"},{"first_name":"Ole Petter","last_name":"Ottersen","full_name":"Ottersen, Ole Petter"},{"full_name":"Nagelhus, Erlend Arnulf","last_name":"Nagelhus","first_name":"Erlend Arnulf"},{"first_name":"Stephane H.R.","last_name":"Oliet","full_name":"Oliet, Stephane H.R."},{"full_name":"Stewart, Michael G.","last_name":"Stewart","first_name":"Michael G."},{"first_name":"U. VAlentin","last_name":"Nägerl","full_name":"Nägerl, U. VAlentin"},{"last_name":"Rusakov","first_name":"Dmitri A. ","full_name":"Rusakov, Dmitri A. "}],"date_updated":"2023-08-22T09:59:29Z","date_created":"2020-10-18T22:01:38Z","volume":108,"file_date_updated":"2020-12-10T14:42:09Z","publication":"Neuron","citation":{"ama":"Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11. doi:10.1016/j.neuron.2020.08.030","apa":"Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev, N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030","ieee":"C. Henneberger et al., “LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5. Elsevier, p. P919–936.E11, 2020.","ista":"Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 108(5), P919–936.E11.","short":"C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev, D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P. Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus, S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11.","mla":"Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5, Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030.","chicago":"Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.08.030."},"article_type":"original","page":"P919-936.E11","date_published":"2020-12-09T00:00:00Z","scopus_import":"1","day":"09","has_accepted_license":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8674","ddc":["570"],"title":"LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia","status":"public","intvolume":" 108","file":[{"content_type":"application/pdf","file_size":7518960,"creator":"dernst","file_name":"2020_Neuron_Henneberger.pdf","access_level":"open_access","date_updated":"2020-12-10T14:42:09Z","date_created":"2020-12-10T14:42:09Z","checksum":"054562bb50165ef9a1f46631c1c5e36b","success":1,"relation":"main_file","file_id":"8939"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections."}],"issue":"5"},{"month":"10","publication_identifier":{"issn":["2399-3650"]},"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"},{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000581681000001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s42005-020-00445-8","article_number":"178","file_date_updated":"2020-10-14T15:16:28Z","ec_funded":1,"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"Springer Nature","acknowledgement":"This work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting\r\nGrant No. 801770 (ANGULON).","year":"2020","date_created":"2020-10-13T09:48:59Z","date_updated":"2023-08-22T09:58:46Z","volume":3,"author":[{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"scopus_import":"1","day":"09","article_processing_charge":"Yes","has_accepted_license":"1","article_type":"original","publication":"Communications Physics","citation":{"ama":"Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8","ista":"Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178.","apa":"Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by scattering from a lattice of point magnets. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-00445-8","ieee":"A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering from a lattice of point magnets,” Communications Physics, vol. 3. Springer Nature, 2020.","mla":"Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8.","short":"A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020).","chicago":"Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8."},"date_published":"2020-10-09T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules."}],"title":"Filtering spins by scattering from a lattice of point magnets","ddc":["530"],"status":"public","intvolume":" 3","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8652","oa_version":"Published Version","file":[{"file_id":"8662","relation":"main_file","date_created":"2020-10-14T15:16:28Z","date_updated":"2020-10-14T15:16:28Z","success":1,"checksum":"60cd35b99f0780acffc7b6060e49ec8b","file_name":"2020_CommPhysics_Ghazaryan.pdf","access_level":"open_access","creator":"dernst","file_size":1462934,"content_type":"application/pdf"}]},{"article_number":"5037","file_date_updated":"2020-10-19T11:27:46Z","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","author":[{"full_name":"Sznurkowska, Magdalena K.","last_name":"Sznurkowska","first_name":"Magdalena K."},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Azzarelli, Roberta","first_name":"Roberta","last_name":"Azzarelli"},{"last_name":"Chatzeli","first_name":"Lemonia","full_name":"Chatzeli, Lemonia"},{"full_name":"Ikeda, Tatsuro","first_name":"Tatsuro","last_name":"Ikeda"},{"last_name":"Yoshida","first_name":"Shosei","full_name":"Yoshida, Shosei"},{"first_name":"Anna","last_name":"Philpott","full_name":"Philpott, Anna"},{"full_name":"Simons, Benjamin D","last_name":"Simons","first_name":"Benjamin D"}],"date_created":"2020-10-18T22:01:35Z","date_updated":"2023-08-22T10:18:17Z","volume":11,"month":"10","publication_identifier":{"eissn":["20411723"]},"external_id":{"isi":["000577244600003"],"pmid":["33028844"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-020-18837-3","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8669","status":"public","ddc":["570"],"title":"Tracing the cellular basis of islet specification in mouse pancreas","intvolume":" 11","oa_version":"Published Version","file":[{"file_size":5540540,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_NatureComm_Sznurkowska.pdf","checksum":"0ecc0eab72d2d50694852579611a6624","success":1,"date_updated":"2020-10-19T11:27:46Z","date_created":"2020-10-19T11:27:46Z","relation":"main_file","file_id":"8677"}],"scopus_import":"1","day":"07","article_processing_charge":"No","has_accepted_license":"1","publication":"Nature Communications","citation":{"ista":"Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037.","apa":"Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","ama":"Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3","chicago":"Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.","mla":"Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3.","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020)."},"article_type":"original","date_published":"2020-10-07T00:00:00Z"},{"external_id":{"pmid":["32979313"],"isi":["000582501100012"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1016/j.devcel.2020.09.001","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"acknowledgement":"This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015).","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Elsevier","author":[{"last_name":"Chaigne","first_name":"Agathe","full_name":"Chaigne, Agathe"},{"full_name":"Labouesse, Céline","last_name":"Labouesse","first_name":"Céline"},{"full_name":"White, Ian J.","first_name":"Ian J.","last_name":"White"},{"last_name":"Agnew","first_name":"Meghan","full_name":"Agnew, Meghan"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"full_name":"Chalut, Kevin J.","first_name":"Kevin J.","last_name":"Chalut"},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."}],"date_updated":"2023-08-22T10:16:58Z","date_created":"2020-10-18T22:01:37Z","volume":55,"file_date_updated":"2021-02-04T10:20:02Z","publication":"Developmental Cell","citation":{"mla":"Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:10.1016/j.devcel.2020.09.001.","short":"A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208.","chicago":"Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001.","ama":"Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001","ista":"Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208.","ieee":"A. Chaigne et al., “Abscission couples cell division to embryonic stem cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208, 2020.","apa":"Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001"},"article_type":"original","page":"195-208","date_published":"2020-10-26T00:00:00Z","scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"No","_id":"8672","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Abscission couples cell division to embryonic stem cell fate","intvolume":" 55","file":[{"file_size":6929686,"content_type":"application/pdf","creator":"dernst","file_name":"2020_DevelopmCell_Chaigne.pdf","access_level":"open_access","date_updated":"2021-02-04T10:20:02Z","date_created":"2021-02-04T10:20:02Z","checksum":"88e1a031a61689165d19a19c2f16d795","success":1,"relation":"main_file","file_id":"9086"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions.","lang":"eng"}],"issue":"2"},{"file_date_updated":"2020-10-27T12:09:57Z","license":"https://creativecommons.org/licenses/by/3.0/","year":"2020","publication_status":"published","publisher":"IOP Publishing","department":[{"_id":"JuFi"}],"author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L"},{"full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","first_name":"Michael"}],"date_created":"2020-10-25T23:01:16Z","date_updated":"2023-08-22T10:38:38Z","volume":33,"month":"11","publication_identifier":{"issn":["09517715"],"eissn":["13616544"]},"external_id":{"arxiv":["1906.12245"],"isi":["000576492700001"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1088/1361-6544/ab9728","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest.","lang":"eng"}],"issue":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8697","ddc":["510"],"title":"Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model","status":"public","intvolume":" 33","oa_version":"Published Version","file":[{"file_name":"2020_Nonlinearity_Fischer.pdf","access_level":"open_access","file_size":1223899,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","file_id":"8710","date_updated":"2020-10-27T12:09:57Z","date_created":"2020-10-27T12:09:57Z","checksum":"ed90bc6eb5f32ee6157fef7f3aabc057","success":1}],"scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Nonlinearity","citation":{"ama":"Fischer JL, Kniely M. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772. doi:10.1088/1361-6544/ab9728","ieee":"J. L. Fischer and M. Kniely, “Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity, vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020.","apa":"Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728","ista":"Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772.","short":"J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.","mla":"Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity, vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728.","chicago":"Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728."},"article_type":"original","page":"5733-5772","date_published":"2020-11-01T00:00:00Z"},{"doi":"10.1126/science.aba6637","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/803635v1"}],"oa":1,"external_id":{"isi":["000579169000053"]},"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"10","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/sticking-together/"}]},"author":[{"last_name":"Tsai","first_name":"Tony Y.-C.","full_name":"Tsai, Tony Y.-C."},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K"},{"full_name":"Xia, Peng","first_name":"Peng","last_name":"Xia","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5419-7756"},{"last_name":"Colak-Champollion","first_name":"Tugba","full_name":"Colak-Champollion, Tugba"},{"full_name":"Knaut, Holger","last_name":"Knaut","first_name":"Holger"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Megason, Sean G.","last_name":"Megason","first_name":"Sean G."}],"volume":370,"date_created":"2020-10-19T14:09:38Z","date_updated":"2023-08-22T10:36:35Z","acknowledgement":"We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.).","year":"2020","publisher":"American Association for the Advancement of Science","department":[{"_id":"CaHe"}],"publication_status":"published","ec_funded":1,"date_published":"2020-10-02T00:00:00Z","citation":{"ieee":"T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020.","apa":"Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637","ista":"Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116.","ama":"Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637","chicago":"Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.","short":"T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116.","mla":"Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637."},"publication":"Science","page":"113-116","article_type":"original","article_processing_charge":"No","day":"02","scopus_import":"1","keyword":["Multidisciplinary"],"oa_version":"Preprint","_id":"8680","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 370","title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","status":"public","issue":"6512","abstract":[{"lang":"eng","text":"Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning."}],"type":"journal_article"},{"year":"2020","acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","pmid":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","author":[{"first_name":"Silvia","last_name":" Galan","full_name":" Galan, Silvia"},{"full_name":"Machnik, Nick N","first_name":"Nick N","last_name":"Machnik","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6617-9742"},{"full_name":"Kruse, Kai","last_name":"Kruse","first_name":"Kai"},{"last_name":"Díaz","first_name":"Noelia","full_name":"Díaz, Noelia"},{"last_name":"Marti-Renom","first_name":"Marc A","full_name":"Marti-Renom, Marc A"},{"full_name":"Vaquerizas, Juan M","first_name":"Juan M","last_name":"Vaquerizas"}],"date_created":"2020-10-25T23:01:20Z","date_updated":"2023-08-22T10:37:10Z","volume":52,"external_id":{"isi":["000579693500004"],"pmid":["33077914"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41588-020-00712-y","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["15461718"],"issn":["10614036"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8707","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","status":"public","intvolume":" 52","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data."}],"publication":"Nature Genetics","citation":{"ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y","ieee":"S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature, pp. 1247–1255, 2020.","apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y","ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","short":"S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.","chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature, 2020. https://doi.org/10.1038/s41588-020-00712-y."},"article_type":"original","page":"1247-1255","date_published":"2020-10-19T00:00:00Z","scopus_import":"1","day":"19","article_processing_charge":"No"},{"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ieee":"M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural circuit policies enabling auditable autonomy,” Nature Machine Intelligence, vol. 2. Springer Nature, pp. 642–652, 2020.","apa":"Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu, R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3","ista":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652.","ama":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652. doi:10.1038/s42256-020-00237-3","chicago":"Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3.","short":"M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 642–652.","mla":"Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52, doi:10.1038/s42256-020-00237-3."},"publication":"Nature Machine Intelligence","page":"642-652","article_type":"original","date_published":"2020-10-01T00:00:00Z","type":"journal_article","abstract":[{"text":"A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8679","intvolume":" 2","status":"public","title":"Neural circuit policies enabling auditable autonomy","oa_version":"None","publication_identifier":{"eissn":["2522-5839"]},"month":"10","external_id":{"isi":["000583337200011"]},"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"isi":1,"quality_controlled":"1","doi":"10.1038/s42256-020-00237-3","language":[{"iso":"eng"}],"year":"2020","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-deep-learning-models/"}]},"author":[{"full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hasani","first_name":"Ramin","full_name":"Hasani, Ramin"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"}],"volume":2,"date_updated":"2023-08-22T10:36:06Z","date_created":"2020-10-19T13:46:06Z"},{"article_type":"original","publication":"Journal of Mathematical Physics","citation":{"chicago":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0022787.","short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","mla":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:10.1063/5.0022787.","ieee":"H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10. AIP Publishing, 2020.","apa":"Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0022787","ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201.","ama":"Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787"},"date_published":"2020-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Equality conditions of data processing inequality for α-z Rényi relative entropies","status":"public","intvolume":" 61","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8670","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].","lang":"eng"}],"issue":"10","quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"main_file_link":[{"url":"https://arxiv.org/abs/2007.06644","open_access":"1"}],"external_id":{"isi":["000578529200001"],"arxiv":["2007.06644"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1063/5.0022787","month":"10","publication_identifier":{"issn":["00222488"]},"publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"JaMa"}],"acknowledgement":"This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments.","year":"2020","date_updated":"2023-08-22T10:32:29Z","date_created":"2020-10-18T22:01:36Z","volume":61,"author":[{"full_name":"Zhang, Haonan","first_name":"Haonan","last_name":"Zhang","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"article_number":"102201","ec_funded":1},{"doi":"10.1073/pnas.1912804117","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["32948691"],"isi":["000579045200012"]},"quality_controlled":"1","isi":1,"month":"10","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"author":[{"full_name":"Maoz, Ori","last_name":"Maoz","first_name":"Ori"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"},{"last_name":"Esteki","first_name":"Mohamad Saleh","full_name":"Esteki, Mohamad Saleh"},{"first_name":"Roozbeh","last_name":"Kiani","full_name":"Kiani, Roozbeh"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"}],"date_updated":"2023-08-22T12:11:23Z","date_created":"2020-10-25T23:01:16Z","volume":117,"acknowledgement":"We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.).","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","file_date_updated":"2020-10-27T14:57:50Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2020-10-06T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ama":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117","ieee":"O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.","apa":"Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117","ista":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073.","short":"O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.","mla":"Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117.","chicago":"Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117."},"article_type":"original","page":"25066-25073","day":"06","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1755359,"creator":"cziletti","file_name":"2020_PNAS_Maoz.pdf","access_level":"open_access","date_created":"2020-10-27T14:57:50Z","date_updated":"2020-10-27T14:57:50Z","checksum":"c6a24fdecf3f28faf447078e7a274a88","success":1,"relation":"main_file","file_id":"8713"}],"_id":"8698","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Learning probabilistic neural representations with randomly connected circuits","ddc":["570"],"status":"public","intvolume":" 117","abstract":[{"text":"The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation.","lang":"eng"}],"issue":"40","type":"journal_article"},{"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias","full_name":"Lechner, Mathias"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"}],"date_created":"2020-10-25T23:01:19Z","date_updated":"2023-08-22T10:40:15Z","acknowledgement":"M.L. is supported in parts by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing Company.","year":"2020","department":[{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","file_date_updated":"2020-11-06T10:58:49Z","doi":"10.1109/ICRA40945.2020.9196608","conference":{"name":"ICRA: International Conference on Robotics and Automation","end_date":"2020-08-31","start_date":"2020-05-31","location":"Paris, France"},"language":[{"iso":"eng"}],"external_id":{"isi":["000712319503110"]},"oa":1,"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["10504729"],"isbn":["9781728173955"]},"month":"05","file":[{"relation":"main_file","file_id":"8733","date_updated":"2020-11-06T10:58:49Z","date_created":"2020-11-06T10:58:49Z","checksum":"fccf7b986ac78046918a298cc6849a50","success":1,"file_name":"2020_ICRA_Lechner.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1070010,"creator":"dernst"}],"oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8704","ddc":["000"],"status":"public","title":"Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme","abstract":[{"text":"Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E.","lang":"eng"}],"type":"conference","alternative_title":["ICRA"],"date_published":"2020-05-01T00:00:00Z","citation":{"short":"M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452.","mla":"Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–52, doi:10.1109/ICRA40945.2020.9196608.","chicago":"Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” In Proceedings - IEEE International Conference on Robotics and Automation, 5446–52. IEEE, 2020. https://doi.org/10.1109/ICRA40945.2020.9196608.","ama":"Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In: Proceedings - IEEE International Conference on Robotics and Automation. IEEE; 2020:5446-5452. doi:10.1109/ICRA40945.2020.9196608","ieee":"M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme,” in Proceedings - IEEE International Conference on Robotics and Automation, Paris, France, 2020, pp. 5446–5452.","apa":"Lechner, M., Hasani, R., Rus, D., & Grosu, R. (2020). Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In Proceedings - IEEE International Conference on Robotics and Automation (pp. 5446–5452). Paris, France: IEEE. https://doi.org/10.1109/ICRA40945.2020.9196608","ista":"Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, , 5446–5452."},"publication":"Proceedings - IEEE International Conference on Robotics and Automation","page":"5446-5452","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8700","status":"public","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","intvolume":" 54","abstract":[{"text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.","lang":"eng"}],"issue":"5","type":"journal_article","date_published":"2020-09-01T00:00:00Z","publication":"Molecular Biology","citation":{"chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320050088.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748.","mla":"Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320050088","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020.","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748.","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088"},"article_type":"original","page":"739-748","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Sokolova, E. E.","first_name":"E. E.","last_name":"Sokolova"},{"full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Vlasov"},{"full_name":"Egorova, T. V.","first_name":"T. V.","last_name":"Egorova"},{"full_name":"Shuvalov, A. V.","last_name":"Shuvalov","first_name":"A. V."},{"first_name":"E. Z.","last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z."}],"related_material":{"record":[{"id":"8701","status":"public","relation":"original"}]},"date_created":"2020-10-25T23:01:17Z","date_updated":"2023-08-22T10:39:38Z","volume":54,"year":"2020","acknowledgement":"We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work.","publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","doi":"10.1134/S0026893320050088","language":[{"iso":"eng"}],"external_id":{"isi":["000579441200009"]},"isi":1,"quality_controlled":"1","month":"09","publication_identifier":{"eissn":["16083245"],"issn":["00268933"]}},{"oa_version":"None","_id":"8701","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","status":"public","intvolume":" 54","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"issue":"5","type":"journal_article","date_published":"2020-09-01T00:00:00Z","publication":"Molekuliarnaia biologiia","citation":{"ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420050080","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848.","mla":"Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:10.31857/S0026898420050080.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080."},"article_type":"original","page":"837-848","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"E. E.","last_name":"Sokolova","full_name":"Sokolova, E. E."},{"last_name":"Vlasov","first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","full_name":"Vlasov, Petr"},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"full_name":"Shuvalov, A. V.","last_name":"Shuvalov","first_name":"A. V."},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"related_material":{"record":[{"id":"8700","relation":"translation","status":"public"}]},"date_created":"2020-10-25T23:01:17Z","date_updated":"2023-08-22T10:39:37Z","volume":54,"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Russian Academy of Sciences","doi":"10.31857/S0026898420050080","language":[{"iso":"rus"}],"external_id":{"pmid":["33009793"]},"quality_controlled":"1","month":"09","publication_identifier":{"issn":["00268984"]}},{"article_processing_charge":"No","day":"12","month":"11","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2011.06630","date_published":"2020-11-12T00:00:00Z","external_id":{"arxiv":["2011.06630"]},"citation":{"ista":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, Mink SE de, Son LAC van, Götberg YLL, Zellmann S, Alejandro Vigna-Gómez AV-G, Renzo M, Wu S, Schrøder SL, Foley RJ, Tenley Hutchinson-Smith TH-S. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv, 2011.06630.","ieee":"J. A. P. L.-S. Jamie A. P. Law-Smith et al., “Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics,” arXiv. .","apa":"Jamie A. P. Law-Smith, J. A. P. L.-S., Everson, R. W., Enrico Ramirez-Ruiz, E. R.-R., Mink, S. E. de, Son, L. A. C. van, Götberg, Y. L. L., … Tenley Hutchinson-Smith, T. H.-S. (n.d.). Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. https://doi.org/10.48550/arXiv.2011.06630","ama":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, et al. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. doi:10.48550/arXiv.2011.06630","chicago":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, Rosa Wallace Everson, Enrico Ramirez-Ruiz Enrico Ramirez-Ruiz, Selma E. de Mink, Lieke A. C. van Son, Ylva Louise Linsdotter Götberg, Stefan Zellmann, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2011.06630.","mla":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, 2011.06630, doi:10.48550/arXiv.2011.06630.","short":"J.A.P.L.-S. Jamie A. P. Law-Smith, R.W. Everson, E.R.-R. Enrico Ramirez-Ruiz, S.E. de Mink, L.A.C. van Son, Y.L.L. Götberg, S. Zellmann, A.V.-G. Alejandro Vigna-Gómez, M. Renzo, S. Wu, S.L. Schrøder, R.J. Foley, T.H.-S. Tenley Hutchinson-Smith, ArXiv (n.d.)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2011.06630"}],"oa":1,"publication":"arXiv","abstract":[{"lang":"eng","text":"A binary neutron star merger has been observed in a multi-messenger detection of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron stars that merge within a Hubble time, as well as many other compact binaries, are expected to form via common envelope evolution. Yet five decades of research on common envelope evolution have not yet resulted in a satisfactory understanding of the multi-spatial multi-timescale evolution for the systems that lead to compact binaries. In this paper, we report on the first successful simulations of common envelope ejection leading to binary neutron star formation in 3D hydrodynamics. We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red supergiant and a 1.4M⊙ neutron star for different initial separations and initial conditions. For all of our simulations, we find complete envelope ejection and final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion, leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may be specific for these extended progenitors. We fully resolve the core of the star to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive computational cost of simulating these systems. The framework we develop in this paper can be used to simulate a wide variety of interactions between stars, from stellar mergers to common envelope episodes leading to GW sources."}],"type":"preprint","article_number":"2011.06630","oa_version":"Preprint","date_created":"2023-08-21T10:10:41Z","date_updated":"2023-08-22T11:03:00Z","author":[{"full_name":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith","last_name":"Jamie A. P. Law-Smith","first_name":"Jamie A. P. Law-Smith"},{"full_name":"Everson, Rosa Wallace","last_name":"Everson","first_name":"Rosa Wallace"},{"full_name":"Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz","first_name":"Enrico Ramirez-Ruiz","last_name":"Enrico Ramirez-Ruiz"},{"full_name":"Mink, Selma E. de","last_name":"Mink","first_name":"Selma E. de"},{"full_name":"Son, Lieke A. C. van","last_name":"Son","first_name":"Lieke A. C. van"},{"last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter"},{"full_name":"Zellmann, Stefan","last_name":"Zellmann","first_name":"Stefan"},{"full_name":"Alejandro Vigna-Gómez, Alejandro Vigna-Gómez","first_name":"Alejandro Vigna-Gómez","last_name":"Alejandro Vigna-Gómez"},{"first_name":"Mathieu","last_name":"Renzo","full_name":"Renzo, Mathieu"},{"full_name":"Wu, Samantha","first_name":"Samantha","last_name":"Wu"},{"full_name":"Schrøder, Sophie L.","first_name":"Sophie L.","last_name":"Schrøder"},{"full_name":"Foley, Ryan J.","last_name":"Foley","first_name":"Ryan J."},{"full_name":"Tenley Hutchinson-Smith, Tenley Hutchinson-Smith","first_name":"Tenley Hutchinson-Smith","last_name":"Tenley Hutchinson-Smith"}],"title":"Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics","status":"public","publication_status":"submitted","_id":"14096","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["32958669"],"isi":["000579059100029"],"arxiv":["2009.12262"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2012043117","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"month":"10","department":[{"_id":"MiLe"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"acknowledgement":"We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.","year":"2020","volume":117,"date_updated":"2023-08-22T12:11:52Z","date_created":"2020-10-25T23:01:17Z","author":[{"last_name":"Paris","first_name":"Eugenio","full_name":"Paris, Eugenio"},{"full_name":"Tseng, Yi","last_name":"Tseng","first_name":"Yi"},{"orcid":"0000-0003-0853-8182","id":"8275014E-6063-11E9-9B7F-6338E6697425","last_name":"Paerschke","first_name":"Ekaterina","full_name":"Paerschke, Ekaterina"},{"full_name":"Zhang, Wenliang","first_name":"Wenliang","last_name":"Zhang"},{"first_name":"Mary H","last_name":"Upton","full_name":"Upton, Mary H"},{"first_name":"Anna","last_name":"Efimenko","full_name":"Efimenko, Anna"},{"full_name":"Rolfs, Katharina","last_name":"Rolfs","first_name":"Katharina"},{"full_name":"McNally, Daniel E","last_name":"McNally","first_name":"Daniel E"},{"full_name":"Maurel, Laura","first_name":"Laura","last_name":"Maurel"},{"last_name":"Naamneh","first_name":"Muntaser","full_name":"Naamneh, Muntaser"},{"full_name":"Caputo, Marco","first_name":"Marco","last_name":"Caputo"},{"full_name":"Strocov, Vladimir N","first_name":"Vladimir N","last_name":"Strocov"},{"full_name":"Wang, Zhiming","first_name":"Zhiming","last_name":"Wang"},{"first_name":"Diego","last_name":"Casa","full_name":"Casa, Diego"},{"first_name":"Christof W","last_name":"Schneider","full_name":"Schneider, Christof W"},{"full_name":"Pomjakushina, Ekaterina","last_name":"Pomjakushina","first_name":"Ekaterina"},{"first_name":"Krzysztof","last_name":"Wohlfeld","full_name":"Wohlfeld, Krzysztof"},{"full_name":"Radovic, Milan","last_name":"Radovic","first_name":"Milan"},{"first_name":"Thorsten","last_name":"Schmitt","full_name":"Schmitt, Thorsten"}],"ec_funded":1,"file_date_updated":"2020-10-28T11:53:12Z","page":"24764-24770","article_type":"original","citation":{"short":"E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770.","mla":"Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:10.1073/pnas.2012043117.","chicago":"Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117.","ama":"Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117","apa":"Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117","ieee":"E. Paris et al., “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020.","ista":"Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2020-10-06T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"06","intvolume":" 117","ddc":["530"],"status":"public","title":"Strain engineering of the charge and spin-orbital interactions in Sr2IrO4","_id":"8699","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":1176522,"creator":"cziletti","access_level":"open_access","file_name":"2020_PNAS_Paris.pdf","checksum":"1638fa36b442e2868576c6dd7d6dc505","success":1,"date_created":"2020-10-28T11:53:12Z","date_updated":"2020-10-28T11:53:12Z","relation":"main_file","file_id":"8715"}],"oa_version":"Published Version","type":"journal_article","issue":"40","abstract":[{"lang":"eng","text":"In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling."}]},{"quality_controlled":"1","isi":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"external_id":{"pmid":["32972993"],"isi":["000583031800004"]},"oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1126/science.abc4209","month":"10","publication_identifier":{"eissn":["10959203"]},"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"American Association for the Advancement of Science","acknowledgement":"We thank J. Novacek (CEITEC Brno) and V.-V. Hodirnau (IST Austria) for their help with collecting cryo-EM datasets. We thank the IST Life Science and Electron Microscopy Facilities for providing equipment. This work has been supported by iNEXT,project number 653706, funded by the Horizon 2020 program of the European Union. This article reflects only the authors’view,and the European Commission is not responsible for any use that may be made of the information it contains. CIISB research infrastructure project LM2015043 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography CEITEC MU.This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385","year":"2020","pmid":1,"date_created":"2020-11-08T23:01:23Z","date_updated":"2023-08-22T12:35:38Z","volume":370,"author":[{"last_name":"Kampjut","first_name":"Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"article_number":"eabc4209","file_date_updated":"2020-11-26T18:47:58Z","ec_funded":1,"article_type":"original","publication":"Science","citation":{"ama":"Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex I. Science. 2020;370(6516). doi:10.1126/science.abc4209","ieee":"D. Kampjut and L. A. Sazanov, “The coupling mechanism of mammalian respiratory complex I,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, 2020.","apa":"Kampjut, D., & Sazanov, L. A. (2020). The coupling mechanism of mammalian respiratory complex I. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abc4209","ista":"Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory complex I. Science. 370(6516), eabc4209.","short":"D. Kampjut, L.A. Sazanov, Science 370 (2020).","mla":"Kampjut, Domen, and Leonid A. Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science, vol. 370, no. 6516, eabc4209, American Association for the Advancement of Science, 2020, doi:10.1126/science.abc4209.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.abc4209."},"date_published":"2020-10-30T00:00:00Z","scopus_import":"1","day":"30","article_processing_charge":"No","has_accepted_license":"1","ddc":["572"],"status":"public","title":"The coupling mechanism of mammalian respiratory complex I","intvolume":" 370","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8737","file":[{"relation":"main_file","file_id":"8820","date_created":"2020-11-26T18:47:58Z","date_updated":"2020-11-26T18:47:58Z","checksum":"658ba90979ca9528a2efdfac8547047a","success":1,"file_name":"Full_manuscript_with_SI_opt_red.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7618987,"creator":"lsazanov"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.","lang":"eng"}],"issue":"6516"},{"oa_version":"Preprint","status":"public","title":"Taming unbalanced training workloads in deep learning with partial collective operations","_id":"8722","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for\r\ndecentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy."}],"type":"conference","date_published":"2020-02-01T00:00:00Z","page":"45-61","publication":"Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","citation":{"ama":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced training workloads in deep learning with partial collective operations. In: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:45-61. doi:10.1145/3332466.3374528","apa":"Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., & Hoefler, T. (2020). Taming unbalanced training workloads in deep learning with partial collective operations. In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 45–61). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374528","ieee":"S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler, “Taming unbalanced training workloads in deep learning with partial collective operations,” in Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 45–61.","ista":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming unbalanced training workloads in deep learning with partial collective operations. Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 45–61.","short":"S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:, Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61.","mla":"Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61, doi:10.1145/3332466.3374528.","chicago":"Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 45–61. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374528."},"day":"01","article_processing_charge":"No","date_updated":"2023-08-22T12:13:48Z","date_created":"2020-11-05T15:25:30Z","author":[{"first_name":"Shigang","last_name":"Li","full_name":"Li, Shigang"},{"last_name":"Tal Ben-Nun","first_name":"Tal Ben-Nun","full_name":"Tal Ben-Nun, Tal Ben-Nun"},{"first_name":"Salvatore Di","last_name":"Girolamo","full_name":"Girolamo, Salvatore Di"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Hoefler, Torsten","first_name":"Torsten","last_name":"Hoefler"}],"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"year":"2020","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2020-02-22","location":"San Diego, CA, United States","end_date":"2020-02-26","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"doi":"10.1145/3332466.3374528","quality_controlled":"1","isi":1,"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"oa":1,"external_id":{"arxiv":["1908.04207"],"isi":["000564476500004"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.04207"}],"month":"02"},{"doi":"10.1038/s41467-020-19372-x","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000592028600001"]},"oa":1,"isi":1,"quality_controlled":"1","month":"11","publication_identifier":{"issn":["2041-1723"]},"author":[{"full_name":"Schulte, Linda","first_name":"Linda","last_name":"Schulte"},{"full_name":"Mao, Jiafei","first_name":"Jiafei","last_name":"Mao"},{"full_name":"Reitz, Julian","first_name":"Julian","last_name":"Reitz"},{"full_name":"Sreeramulu, Sridhar","last_name":"Sreeramulu","first_name":"Sridhar"},{"full_name":"Kudlinzki, Denis","last_name":"Kudlinzki","first_name":"Denis"},{"last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Meier-Credo","first_name":"Jakob","full_name":"Meier-Credo, Jakob"},{"last_name":"Saxena","first_name":"Krishna","full_name":"Saxena, Krishna"},{"full_name":"Buhr, Florian","first_name":"Florian","last_name":"Buhr"},{"last_name":"Langer","first_name":"Julian D.","full_name":"Langer, Julian D."},{"full_name":"Blackledge, Martin","last_name":"Blackledge","first_name":"Martin"},{"full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S.","last_name":"Frangakis"},{"last_name":"Glaubitz","first_name":"Clemens","full_name":"Glaubitz, Clemens"},{"full_name":"Schwalbe, Harald","first_name":"Harald","last_name":"Schwalbe"}],"date_created":"2020-11-09T07:49:36Z","date_updated":"2023-08-22T12:36:07Z","volume":11,"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.","year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EM-Fac"}],"file_date_updated":"2020-11-09T07:56:24Z","article_number":"5569","date_published":"2020-11-04T00:00:00Z","publication":"Nature Communications","citation":{"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.","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. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x","ieee":"L. Schulte et al., “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature, 2020.","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x","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.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x.","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020, doi:10.1038/s41467-020-19372-x.","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)."},"article_type":"original","day":"04","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"oa_version":"Published Version","file":[{"file_name":"2020_NatureComm_Schulte.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1670898,"file_id":"8745","relation":"main_file","date_updated":"2020-11-09T07:56:24Z","date_created":"2020-11-09T07:56:24Z","success":1,"checksum":"b2688f0347e69e6629bba582077278c5"}],"_id":"8744","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","status":"public","ddc":["570"],"intvolume":" 11","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"}],"type":"journal_article"},{"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000581559100015"]},"language":[{"iso":"eng"}],"doi":"10.1039/D0TC02182B","month":"10","publisher":"Royal Society of Chemistry","department":[{"_id":"MaIb"}],"publication_status":"published","year":"2020","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.","volume":8,"date_created":"2020-11-09T08:37:51Z","date_updated":"2023-08-22T12:41:05Z","author":[{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","first_name":"Yu","last_name":"Liu"},{"full_name":"Calcabrini, Mariano","last_name":"Calcabrini","first_name":"Mariano"},{"last_name":"Xing","first_name":"Congcong","full_name":"Xing, Congcong"},{"full_name":"Han, Xu","last_name":"Han","first_name":"Xu"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"last_name":"Cadavid","first_name":"Doris","full_name":"Cadavid, Doris"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"ec_funded":1,"page":"14092-14099","article_type":"original","citation":{"ieee":"Y. Zhang et al., “Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks,” Journal of Materials Chemistry C, 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. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/D0TC02182B","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.","ama":"Zhang Y, Liu Y, Calcabrini M, et al. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 2020;8(40):14092-14099. doi:10.1039/D0TC02182B","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.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2020. https://doi.org/10.1039/D0TC02182B.","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.” Journal of Materials Chemistry C, vol. 8, no. 40, Royal Society of Chemistry, 2020, pp. 14092–99, doi:10.1039/D0TC02182B."},"publication":"Journal of Materials Chemistry C","date_published":"2020-10-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"28","intvolume":" 8","title":"Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks","status":"public","_id":"8747","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","type":"journal_article","issue":"40","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"}]},{"abstract":[{"text":"The Habitable Exoplanet Observatory, or HabEx, has been designed to be the Great Observatory of the 2030s. For the first time in human history, technologies have matured sufficiently to enable an affordable space-based telescope mission capable of discovering and characterizing Earthlike planets orbiting nearby bright sunlike stars in order to search for signs of habitability and biosignatures. Such a mission can also be equipped with instrumentation that will enable broad and exciting general astrophysics and planetary science not possible from current or planned facilities. HabEx is a space telescope with unique imaging and multi-object spectroscopic capabilities at wavelengths ranging from ultraviolet (UV) to near-IR. These capabilities allow for a broad suite of compelling science that cuts across the entire NASA astrophysics portfolio. HabEx has three primary science goals: (1) Seek out nearby worlds and explore their habitability; (2) Map out nearby planetary systems and understand the diversity of the worlds they contain; (3) Enable new explorations of astrophysical systems from our own solar system to external galaxies by extending our reach in the UV through near-IR. This Great Observatory science will be selected through a competed GO program, and will account for about 50% of the HabEx primary mission. The preferred HabEx architecture is a 4m, monolithic, off-axis telescope that is diffraction-limited at 0.4 microns and is in an L2 orbit. HabEx employs two starlight suppression systems: a coronagraph and a starshade, each with their own dedicated instrument.","lang":"eng"}],"extern":"1","type":"preprint","article_number":"2001.06683","author":[{"first_name":"B. Scott","last_name":"Gaudi","full_name":"Gaudi, B. Scott"},{"full_name":"Seager, Sara","first_name":"Sara","last_name":"Seager"},{"first_name":"Bertrand","last_name":"Mennesson","full_name":"Mennesson, Bertrand"},{"full_name":"Kiessling, Alina","first_name":"Alina","last_name":"Kiessling"},{"first_name":"Keith","last_name":"Warfield","full_name":"Warfield, Keith"},{"last_name":"Cahoy","first_name":"Kerri","full_name":"Cahoy, Kerri"},{"first_name":"John T.","last_name":"Clarke","full_name":"Clarke, John T."},{"full_name":"Shawn Domagal-Goldman, Shawn Domagal-Goldman","last_name":"Shawn Domagal-Goldman","first_name":"Shawn Domagal-Goldman"},{"full_name":"Feinberg, Lee","first_name":"Lee","last_name":"Feinberg"},{"last_name":"Guyon","first_name":"Olivier","full_name":"Guyon, Olivier"},{"first_name":"Jeremy","last_name":"Kasdin","full_name":"Kasdin, Jeremy"},{"last_name":"Mawet","first_name":"Dimitri","full_name":"Mawet, Dimitri"},{"full_name":"Plavchan, Peter","first_name":"Peter","last_name":"Plavchan"},{"last_name":"Robinson","first_name":"Tyler","full_name":"Robinson, Tyler"},{"full_name":"Rogers, Leslie","first_name":"Leslie","last_name":"Rogers"},{"first_name":"Paul","last_name":"Scowen","full_name":"Scowen, Paul"},{"full_name":"Somerville, Rachel","last_name":"Somerville","first_name":"Rachel"},{"full_name":"Stapelfeldt, Karl","last_name":"Stapelfeldt","first_name":"Karl"},{"last_name":"Stark","first_name":"Christopher","full_name":"Stark, Christopher"},{"full_name":"Stern, Daniel","last_name":"Stern","first_name":"Daniel"},{"full_name":"Turnbull, Margaret","first_name":"Margaret","last_name":"Turnbull"},{"first_name":"Rashied","last_name":"Amini","full_name":"Amini, Rashied"},{"full_name":"Kuan, Gary","first_name":"Gary","last_name":"Kuan"},{"first_name":"Stefan","last_name":"Martin","full_name":"Martin, Stefan"},{"last_name":"Morgan","first_name":"Rhonda","full_name":"Morgan, Rhonda"},{"full_name":"Redding, David","last_name":"Redding","first_name":"David"},{"first_name":"H. Philip","last_name":"Stahl","full_name":"Stahl, H. Philip"},{"full_name":"Webb, Ryan","first_name":"Ryan","last_name":"Webb"},{"last_name":"Oscar Alvarez-Salazar","first_name":"Oscar Alvarez-Salazar","full_name":"Oscar Alvarez-Salazar, Oscar Alvarez-Salazar"},{"first_name":"William L.","last_name":"Arnold","full_name":"Arnold, William L."},{"last_name":"Arya","first_name":"Manan","full_name":"Arya, Manan"},{"first_name":"Bala","last_name":"Balasubramanian","full_name":"Balasubramanian, Bala"},{"full_name":"Baysinger, Mike","first_name":"Mike","last_name":"Baysinger"},{"full_name":"Bell, Ray","last_name":"Bell","first_name":"Ray"},{"last_name":"Below","first_name":"Chris","full_name":"Below, Chris"},{"full_name":"Benson, Jonathan","last_name":"Benson","first_name":"Jonathan"},{"last_name":"Blais","first_name":"Lindsey","full_name":"Blais, Lindsey"},{"full_name":"Booth, Jeff","first_name":"Jeff","last_name":"Booth"},{"full_name":"Bourgeois, Robert","first_name":"Robert","last_name":"Bourgeois"},{"full_name":"Bradford, Case","first_name":"Case","last_name":"Bradford"},{"first_name":"Alden","last_name":"Brewer","full_name":"Brewer, Alden"},{"full_name":"Brooks, Thomas","last_name":"Brooks","first_name":"Thomas"},{"full_name":"Cady, Eric","first_name":"Eric","last_name":"Cady"},{"full_name":"Caldwell, Mary","first_name":"Mary","last_name":"Caldwell"},{"full_name":"Calvet, Rob","last_name":"Calvet","first_name":"Rob"},{"full_name":"Carr, Steven","first_name":"Steven","last_name":"Carr"},{"last_name":"Chan","first_name":"Derek","full_name":"Chan, Derek"},{"first_name":"Velibor","last_name":"Cormarkovic","full_name":"Cormarkovic, Velibor"},{"full_name":"Coste, Keith","first_name":"Keith","last_name":"Coste"},{"first_name":"Charlie","last_name":"Cox","full_name":"Cox, Charlie"},{"last_name":"Danner","first_name":"Rolf","full_name":"Danner, Rolf"},{"full_name":"Davis, Jacqueline","last_name":"Davis","first_name":"Jacqueline"},{"last_name":"Dewell","first_name":"Larry","full_name":"Dewell, Larry"},{"full_name":"Dorsett, Lisa","first_name":"Lisa","last_name":"Dorsett"},{"last_name":"Dunn","first_name":"Daniel","full_name":"Dunn, Daniel"},{"first_name":"Matthew","last_name":"East","full_name":"East, Matthew"},{"full_name":"Effinger, Michael","first_name":"Michael","last_name":"Effinger"},{"last_name":"Eng","first_name":"Ron","full_name":"Eng, Ron"},{"first_name":"Greg","last_name":"Freebury","full_name":"Freebury, Greg"},{"full_name":"Garcia, Jay","last_name":"Garcia","first_name":"Jay"},{"full_name":"Gaskin, Jonathan","first_name":"Jonathan","last_name":"Gaskin"},{"last_name":"Greene","first_name":"Suzan","full_name":"Greene, Suzan"},{"full_name":"Hennessy, John","first_name":"John","last_name":"Hennessy"},{"first_name":"Evan","last_name":"Hilgemann","full_name":"Hilgemann, Evan"},{"last_name":"Hood","first_name":"Brad","full_name":"Hood, Brad"},{"full_name":"Holota, Wolfgang","last_name":"Holota","first_name":"Wolfgang"},{"full_name":"Howe, Scott","first_name":"Scott","last_name":"Howe"},{"first_name":"Pei","last_name":"Huang","full_name":"Huang, Pei"},{"full_name":"Hull, Tony","first_name":"Tony","last_name":"Hull"},{"full_name":"Hunt, Ron","first_name":"Ron","last_name":"Hunt"},{"full_name":"Hurd, Kevin","first_name":"Kevin","last_name":"Hurd"},{"full_name":"Johnson, Sandra","last_name":"Johnson","first_name":"Sandra"},{"full_name":"Kissil, Andrew","last_name":"Kissil","first_name":"Andrew"},{"first_name":"Brent","last_name":"Knight","full_name":"Knight, Brent"},{"first_name":"Daniel","last_name":"Kolenz","full_name":"Kolenz, Daniel"},{"full_name":"Kraus, Oliver","last_name":"Kraus","first_name":"Oliver"},{"last_name":"Krist","first_name":"John","full_name":"Krist, John"},{"full_name":"Li, Mary","first_name":"Mary","last_name":"Li"},{"full_name":"Lisman, Doug","last_name":"Lisman","first_name":"Doug"},{"last_name":"Mandic","first_name":"Milan","full_name":"Mandic, Milan"},{"first_name":"John","last_name":"Mann","full_name":"Mann, John"},{"last_name":"Marchen","first_name":"Luis","full_name":"Marchen, Luis"},{"full_name":"Colleen Marrese-Reading, Colleen Marrese-Reading","first_name":"Colleen Marrese-Reading","last_name":"Colleen Marrese-Reading"},{"first_name":"Jonathan","last_name":"McCready","full_name":"McCready, Jonathan"},{"full_name":"McGown, Jim","last_name":"McGown","first_name":"Jim"},{"first_name":"Jessica","last_name":"Missun","full_name":"Missun, Jessica"},{"first_name":"Andrew","last_name":"Miyaguchi","full_name":"Miyaguchi, Andrew"},{"first_name":"Bradley","last_name":"Moore","full_name":"Moore, Bradley"},{"full_name":"Nemati, Bijan","last_name":"Nemati","first_name":"Bijan"},{"last_name":"Nikzad","first_name":"Shouleh","full_name":"Nikzad, Shouleh"},{"full_name":"Nissen, Joel","first_name":"Joel","last_name":"Nissen"},{"last_name":"Novicki","first_name":"Megan","full_name":"Novicki, 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J. Eldorado","full_name":"Riggs, A. J. 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Scott, Sara Seager, Bertrand Mennesson, Alina Kiessling, Keith Warfield, Kerri Cahoy, John T. Clarke, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2001.06683.","short":"B.S. Gaudi, S. Seager, B. Mennesson, A. Kiessling, K. Warfield, K. Cahoy, J.T. Clarke, S.D.-G. Shawn Domagal-Goldman, L. Feinberg, O. Guyon, J. Kasdin, D. Mawet, P. Plavchan, T. Robinson, L. Rogers, P. Scowen, R. Somerville, K. Stapelfeldt, C. Stark, D. Stern, M. Turnbull, R. Amini, G. Kuan, S. Martin, R. Morgan, D. Redding, H.P. Stahl, R. Webb, O.A.-S. Oscar Alvarez-Salazar, W.L. Arnold, M. Arya, B. Balasubramanian, M. Baysinger, R. Bell, C. Below, J. Benson, L. Blais, J. Booth, R. Bourgeois, C. Bradford, A. Brewer, T. Brooks, E. Cady, M. Caldwell, R. Calvet, S. Carr, D. Chan, V. Cormarkovic, K. Coste, C. Cox, R. Danner, J. Davis, L. Dewell, L. Dorsett, D. Dunn, M. East, M. Effinger, R. Eng, G. Freebury, J. Garcia, J. Gaskin, S. Greene, J. Hennessy, E. Hilgemann, B. Hood, W. Holota, S. Howe, P. Huang, T. Hull, R. Hunt, K. Hurd, S. Johnson, A. Kissil, B. Knight, D. Kolenz, O. Kraus, J. Krist, M. Li, D. Lisman, M. Mandic, J. Mann, L. Marchen, C.M.-R. Colleen Marrese-Reading, J. McCready, J. McGown, J. Missun, A. Miyaguchi, B. Moore, B. Nemati, S. Nikzad, J. Nissen, M. Novicki, T. Perrine, C. Pineda, O. Polanco, D. Putnam, A. Qureshi, M. Richards, A.J.E. Riggs, M. Rodgers, M. Rud, N. Saini, D. Scalisi, D. Scharf, K. Schulz, G. Serabyn, N. Sigrist, G. Sikkia, A. Singleton, S. Shaklan, S. Smith, B. Southerd, M. Stahl, J. Steeves, B. Sturges, C. Sullivan, H. Tang, N. Taras, J. Tesch, M. Therrell, H. Tseng, M. Valente, D.V. Buren, J. Villalvazo, S. Warwick, D. Webb, T. Westerhoff, R. Wofford, G. Wu, J. Woo, M. Wood, J. Ziemer, G. Arney, J. Anderson, J.M.-A. Jesús Maíz-Apellániz, J. Bartlett, R. Belikov, E. Bendek, B. Cenko, E. Douglas, S. Dulz, C. Evans, V. Faramaz, Y.K. Feng, H. Ferguson, K. Follette, S. Ford, M. García, M. Geha, D. Gelino, Y.L.L. Götberg, S. Hildebrandt, R. Hu, K. Jahnke, G. Kennedy, L. Kreidberg, A. Isella, E. Lopez, F. Marchis, L. Macri, M. Marley, W. Matzko, J. Mazoyer, S. McCandliss, T. Meshkat, C. Mordasini, P. Morris, E. Nielsen, P. Newman, E. Petigura, M. Postman, A. Reines, A. Roberge, I. Roederer, G. Ruane, E. Schwieterman, D. Sirbu, C. Spalding, H. Teplitz, J. Tumlinson, N. Turner, J. Werk, A. Wofford, M. Wyatt, A. Young, R. Zellem, ArXiv (n.d.).","mla":"Gaudi, B. Scott, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, 2001.06683, doi:10.48550/arXiv.2001.06683.","ieee":"B. S. Gaudi et al., “The habitable exoplanet observatory (HabEx) mission concept study final report,” arXiv. .","apa":"Gaudi, B. S., Seager, S., Mennesson, B., Kiessling, A., Warfield, K., Cahoy, K., … Zellem, R. (n.d.). The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. https://doi.org/10.48550/arXiv.2001.06683","ista":"Gaudi BS et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv, 2001.06683.","ama":"Gaudi BS, Seager S, Mennesson B, et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. doi:10.48550/arXiv.2001.06683"},"publication":"arXiv"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000591317200004"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pcbi.1008402","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"month":"11","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.","year":"2020","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"full_name":"Kaveh, Kamran","first_name":"Kamran","last_name":"Kaveh"},{"full_name":"McAvoy, Alex","last_name":"McAvoy","first_name":"Alex"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"volume":16,"date_updated":"2023-08-22T12:49:18Z","date_created":"2020-11-18T07:20:23Z","article_number":"e1008402","file_date_updated":"2020-11-18T07:26:10Z","citation":{"ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 2020;16(11). doi:10.1371/journal.pcbi.1008402","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” PLOS Computational Biology, vol. 16, no. 11. Public Library of Science, 2020.","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., & Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008402","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1008402.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1008402."},"publication":"PLOS Computational Biology","article_type":"original","date_published":"2020-11-05T00:00:00Z","scopus_import":"1","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"article_processing_charge":"No","has_accepted_license":"1","day":"05","_id":"8767","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 16","ddc":["000"],"status":"public","title":"The Moran process on 2-chromatic graphs","oa_version":"Published Version","file":[{"file_id":"8768","relation":"main_file","success":1,"checksum":"555456dd0e47bcf9e0994bcb95577e88","date_updated":"2020-11-18T07:26:10Z","date_created":"2020-11-18T07:26:10Z","access_level":"open_access","file_name":"2020_PlosCompBio_Kaveh.pdf","creator":"dernst","file_size":2498594,"content_type":"application/pdf"}],"type":"journal_article","issue":"11","abstract":[{"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.","lang":"eng"}]},{"date_created":"2020-11-10T07:04:57Z","date_updated":"2023-08-22T12:48:18Z","author":[{"full_name":"Forets, Marcelo","last_name":"Forets","first_name":"Marcelo"},{"first_name":"Daniel","last_name":"Freire","full_name":"Freire, Daniel"},{"first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"}],"publication_status":"published","publisher":"IEEE","department":[{"_id":"ToHe"}],"year":"2020","ec_funded":1,"article_number":"9314994","language":[{"iso":"eng"}],"conference":{"location":"Virtual Conference","start_date":"2020-12-02","end_date":"2020-12-04","name":"MEMOCODE: Conference on Formal Methods and Models for System Design"},"doi":"10.1109/MEMOCODE51338.2020.9314994","isi":1,"quality_controlled":"1","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2006.12325","open_access":"1"}],"external_id":{"arxiv":["2006.12325"],"isi":["000661920400013"]},"month":"12","publication_identifier":{"isbn":["9781728191485"]},"oa_version":"Preprint","status":"public","title":"Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8750","abstract":[{"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.","lang":"eng"}],"type":"conference","date_published":"2020-12-04T00:00:00Z","publication":"18th ACM-IEEE International Conference on Formal Methods and Models for System Design","citation":{"chicago":"Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.” In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE, 2020. https://doi.org/10.1109/MEMOCODE51338.2020.9314994.","short":"M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020.","mla":"Forets, Marcelo, et al. “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, 9314994, IEEE, 2020, doi:10.1109/MEMOCODE51338.2020.9314994.","ieee":"M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions,” in 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, Virtual Conference, 2020.","apa":"Forets, M., Freire, D., & Schilling, C. (2020). Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. Virtual Conference: IEEE. https://doi.org/10.1109/MEMOCODE51338.2020.9314994","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: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE; 2020. doi:10.1109/MEMOCODE51338.2020.9314994"},"day":"04","article_processing_charge":"No","scopus_import":"1"},{"doi":"10.1007/s10955-020-02663-4","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000587107200002"],"arxiv":["2004.02831"]},"oa":1,"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Taming Complexity in Partial Di erential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["15729613"],"issn":["00224715"]},"month":"12","author":[{"full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"last_name":"Mielke","first_name":"Alexander","full_name":"Mielke, Alexander"}],"volume":181,"date_created":"2020-11-15T23:01:18Z","date_updated":"2023-08-22T13:24:27Z","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).","year":"2020","department":[{"_id":"JaMa"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"file_date_updated":"2021-02-04T10:29:11Z","date_published":"2020-12-01T00:00:00Z","citation":{"ama":"Maas J, Mielke A. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 2020;181(6):2257-2303. doi:10.1007/s10955-020-02663-4","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.","apa":"Maas, J., & Mielke, A. (2020). Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-020-02663-4","ieee":"J. Maas and A. Mielke, “Modeling of chemical reaction systems with detailed balance using gradient structures,” Journal of Statistical Physics, vol. 181, no. 6. Springer Nature, pp. 2257–2303, 2020.","mla":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics, vol. 181, no. 6, Springer Nature, 2020, pp. 2257–303, doi:10.1007/s10955-020-02663-4.","short":"J. Maas, A. Mielke, Journal of Statistical Physics 181 (2020) 2257–2303.","chicago":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-020-02663-4."},"publication":"Journal of Statistical Physics","page":"2257-2303","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9087","checksum":"bc2b63a90197b97cbc73eccada4639f5","success":1,"date_updated":"2021-02-04T10:29:11Z","date_created":"2021-02-04T10:29:11Z","access_level":"open_access","file_name":"2020_JourStatPhysics_Maas.pdf","file_size":753596,"content_type":"application/pdf","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8758","intvolume":" 181","title":"Modeling of chemical reaction systems with detailed balance using gradient structures","status":"public","ddc":["510"],"issue":"6","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."}],"type":"journal_article"},{"month":"09","day":"27","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4052883","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882.","mla":"Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882.","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882"},"doi":"10.5281/ZENODO.4052882","date_published":"2020-09-27T00:00:00Z","type":"research_data_reference","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"ddc":["530"],"title":"Surpassing the resistance quantum with a geometric superinductor","status":"public","publisher":"Zenodo","department":[{"_id":"JoFi"}],"year":"2020","_id":"13070","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-22T13:23:57Z","date_created":"2023-05-23T16:42:30Z","oa_version":"Published Version","author":[{"full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea","last_name":"Trioni","full_name":"Trioni, Andrea"},{"full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid"},{"full_name":"Zemlicka, Martin","first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8755"}]}},{"ec_funded":1,"file_date_updated":"2020-11-23T13:29:49Z","article_number":"5778","volume":11,"date_created":"2020-11-22T23:01:23Z","date_updated":"2023-08-22T13:26:26Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31310-7","relation":"erratum"}]},"author":[{"first_name":"Leo","last_name":"Nicolai","full_name":"Nicolai, Leo"},{"last_name":"Schiefelbein","first_name":"Karin","full_name":"Schiefelbein, Karin"},{"full_name":"Lipsky, Silvia","last_name":"Lipsky","first_name":"Silvia"},{"last_name":"Leunig","first_name":"Alexander","full_name":"Leunig, Alexander"},{"full_name":"Hoffknecht, Marie","first_name":"Marie","last_name":"Hoffknecht"},{"full_name":"Pekayvaz, Kami","first_name":"Kami","last_name":"Pekayvaz"},{"full_name":"Raude, Ben","last_name":"Raude","first_name":"Ben"},{"full_name":"Marx, Charlotte","first_name":"Charlotte","last_name":"Marx"},{"first_name":"Andreas","last_name":"Ehrlich","full_name":"Ehrlich, Andreas"},{"full_name":"Pircher, Joachim","first_name":"Joachim","last_name":"Pircher"},{"first_name":"Zhe","last_name":"Zhang","full_name":"Zhang, Zhe"},{"full_name":"Saleh, Inas","last_name":"Saleh","first_name":"Inas"},{"full_name":"Marel, Anna-Kristina","last_name":"Marel","first_name":"Anna-Kristina"},{"first_name":"Achim","last_name":"Löf","full_name":"Löf, Achim"},{"full_name":"Petzold, Tobias","first_name":"Tobias","last_name":"Petzold"},{"full_name":"Lorenz, Michael","last_name":"Lorenz","first_name":"Michael"},{"last_name":"Stark","first_name":"Konstantin","full_name":"Stark, Konstantin"},{"last_name":"Pick","first_name":"Robert","full_name":"Pick, Robert"},{"full_name":"Rosenberger, Gerhild","last_name":"Rosenberger","first_name":"Gerhild"},{"full_name":"Weckbach, Ludwig","first_name":"Ludwig","last_name":"Weckbach"},{"first_name":"Bernd","last_name":"Uhl","full_name":"Uhl, Bernd"},{"last_name":"Xia","first_name":"Sheng","full_name":"Xia, Sheng"},{"first_name":"Christoph Andreas","last_name":"Reichel","full_name":"Reichel, Christoph Andreas"},{"last_name":"Walzog","first_name":"Barbara","full_name":"Walzog, Barbara"},{"last_name":"Schulz","first_name":"Christian","full_name":"Schulz, Christian"},{"full_name":"Zheden, Vanessa","first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783"},{"last_name":"Bender","first_name":"Markus","full_name":"Bender, Markus"},{"full_name":"Li, Rong","first_name":"Rong","last_name":"Li"},{"first_name":"Steffen","last_name":"Massberg","full_name":"Massberg, Steffen"},{"last_name":"Gärtner","first_name":"Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R"}],"department":[{"_id":"MiSi"},{"_id":"EM-Fac"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical\r\ndiscussions. This study was supported by the DFG SFB 914 (S.M. [B02 and Z01], K.Sch.\r\n[B02], B.W. [A02 and Z03], C.A.R. [B03], C.S. [A10], J.P. [Gerok position]), the DFG\r\nSFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Center for\r\nCardiovascular Research (DZHK) (Clinician Scientist Program [L.N.], MHA 1.4VD\r\n[S.M.], Postdoc Start-up Grant, 81×3600213 [F.G.]), FP7 program (project 260309,\r\nPRESTIGE [S.M.]), FöFoLe project 1015/1009 (L.N.), FöFoLe project 947 (F.G.), the\r\nFriedrich-Baur-Stiftung project 41/16 (F.G.), and LMUexcellence NFF (F.G.). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no.\r\n833440) (S.M.). F.G. received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement no.\r\n747687.","year":"2020","publication_identifier":{"eissn":["20411723"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-19515-0","project":[{"call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000594648000014"],"pmid":["33188196"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"text":"Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"8798","checksum":"485b7b6cf30198ba0ce126491a28f125","success":1,"date_created":"2020-11-23T13:29:49Z","date_updated":"2020-11-23T13:29:49Z","access_level":"open_access","file_name":"2020_NatureComm_Nicolai.pdf","file_size":7035340,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","intvolume":" 11","title":"Vascular surveillance by haptotactic blood platelets in inflammation and infection","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8787","has_accepted_license":"1","article_processing_charge":"No","day":"13","scopus_import":"1","date_published":"2020-11-13T00:00:00Z","article_type":"original","citation":{"mla":"Nicolai, Leo, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications, vol. 11, 5778, Springer Nature, 2020, doi:10.1038/s41467-020-19515-0.","short":"L. Nicolai, K. Schiefelbein, S. Lipsky, A. Leunig, M. Hoffknecht, K. Pekayvaz, B. Raude, C. Marx, A. Ehrlich, J. Pircher, Z. Zhang, I. Saleh, A.-K. Marel, A. Löf, T. Petzold, M. Lorenz, K. Stark, R. Pick, G. Rosenberger, L. Weckbach, B. Uhl, S. Xia, C.A. Reichel, B. Walzog, C. Schulz, V. Zheden, M. Bender, R. Li, S. Massberg, F.R. Gärtner, Nature Communications 11 (2020).","chicago":"Nicolai, Leo, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19515-0.","ama":"Nicolai L, Schiefelbein K, Lipsky S, et al. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 2020;11. doi:10.1038/s41467-020-19515-0","ista":"Nicolai L, Schiefelbein K, Lipsky S, Leunig A, Hoffknecht M, Pekayvaz K, Raude B, Marx C, Ehrlich A, Pircher J, Zhang Z, Saleh I, Marel A-K, Löf A, Petzold T, Lorenz M, Stark K, Pick R, Rosenberger G, Weckbach L, Uhl B, Xia S, Reichel CA, Walzog B, Schulz C, Zheden V, Bender M, Li R, Massberg S, Gärtner FR. 2020. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 11, 5778.","apa":"Nicolai, L., Schiefelbein, K., Lipsky, S., Leunig, A., Hoffknecht, M., Pekayvaz, K., … Gärtner, F. R. (2020). Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19515-0","ieee":"L. Nicolai et al., “Vascular surveillance by haptotactic blood platelets in inflammation and infection,” Nature Communications, vol. 11. Springer Nature, 2020."},"publication":"Nature Communications"},{"oa_version":"Published Version","file":[{"date_updated":"2020-11-23T13:06:30Z","date_created":"2020-11-23T13:06:30Z","success":1,"checksum":"61cfcc3b35760656ce7a9385a4ace5d2","file_id":"8797","relation":"main_file","creator":"dernst","file_size":565191,"content_type":"application/pdf","file_name":"2020_Mathematics_Kleshnina.pdf","access_level":"open_access"}],"intvolume":" 8","title":"Prioritised learning in snowdrift-type games","status":"public","ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8789","issue":"11","abstract":[{"text":"Cooperation is a ubiquitous and beneficial behavioural trait despite being prone to exploitation by free-riders. Hence, cooperative populations are prone to invasions by selfish individuals. However, a population consisting of only free-riders typically does not survive. Thus, cooperators and free-riders often coexist in some proportion. An evolutionary version of a Snowdrift Game proved its efficiency in analysing this phenomenon. However, what if the system has already reached its stable state but was perturbed due to a change in environmental conditions? Then, individuals may have to re-learn their effective strategies. To address this, we consider behavioural mistakes in strategic choice execution, which we refer to as incompetence. Parametrising the propensity to make such mistakes allows for a mathematical description of learning. We compare strategies based on their relative strategic advantage relying on both fitness and learning factors. When strategies are learned at distinct rates, allowing learning according to a prescribed order is optimal. Interestingly, the strategy with the lowest strategic advantage should be learnt first if we are to optimise fitness over the learning path. Then, the differences between strategies are balanced out in order to minimise the effect of behavioural uncertainty.","lang":"eng"}],"type":"journal_article","date_published":"2020-11-04T00:00:00Z","article_type":"original","citation":{"ama":"Kleshnina M, Streipert S, Filar J, Chatterjee K. Prioritised learning in snowdrift-type games. Mathematics. 2020;8(11). doi:10.3390/math8111945","ieee":"M. Kleshnina, S. Streipert, J. Filar, and K. Chatterjee, “Prioritised learning in snowdrift-type games,” Mathematics, vol. 8, no. 11. MDPI, 2020.","apa":"Kleshnina, M., Streipert, S., Filar, J., & Chatterjee, K. (2020). Prioritised learning in snowdrift-type games. Mathematics. MDPI. https://doi.org/10.3390/math8111945","ista":"Kleshnina M, Streipert S, Filar J, Chatterjee K. 2020. Prioritised learning in snowdrift-type games. Mathematics. 8(11), 1945.","short":"M. Kleshnina, S. Streipert, J. Filar, K. Chatterjee, Mathematics 8 (2020).","mla":"Kleshnina, Maria, et al. “Prioritised Learning in Snowdrift-Type Games.” Mathematics, vol. 8, no. 11, 1945, MDPI, 2020, doi:10.3390/math8111945.","chicago":"Kleshnina, Maria, Sabrina Streipert, Jerzy Filar, and Krishnendu Chatterjee. “Prioritised Learning in Snowdrift-Type Games.” Mathematics. MDPI, 2020. https://doi.org/10.3390/math8111945."},"publication":"Mathematics","article_processing_charge":"No","has_accepted_license":"1","day":"04","scopus_import":"1","volume":8,"date_created":"2020-11-22T23:01:24Z","date_updated":"2023-08-22T13:25:45Z","author":[{"full_name":"Kleshnina, Maria","first_name":"Maria","last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Streipert, Sabrina","first_name":"Sabrina","last_name":"Streipert"},{"full_name":"Filar, Jerzy","first_name":"Jerzy","last_name":"Filar"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"}],"publisher":"MDPI","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2020","acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411, the Australian Research Council Discovery Grants DP160101236 and DP150100618, and the European Research Council Consolidator Grant 863818 (FoRM-SMArt).\r\nAuthors would like to thank Patrick McKinlay for his work on the preliminary results for this paper.","ec_funded":1,"file_date_updated":"2020-11-23T13:06:30Z","article_number":"1945","language":[{"iso":"eng"}],"doi":"10.3390/math8111945","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000593962100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["22277390"]},"month":"11"},{"publication":"Proceedings of the International Conference on Embedded Software","citation":{"ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” in Proceedings of the International Conference on Embedded Software, Virtual , 2020.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. In Proceedings of the International Conference on Embedded Software. Virtual .","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. In: Proceedings of the International Conference on Embedded Software. ; 2020.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In Proceedings of the International Conference on Embedded Software, 2020.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” Proceedings of the International Conference on Embedded Software, 2020.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020."},"date_published":"2020-01-01T00:00:00Z","keyword":["reachability","hybrid systems","decomposition"],"has_accepted_license":"1","article_processing_charge":"No","title":"Reachability analysis of linear hybrid systems via block decomposition","status":"public","ddc":["000"],"_id":"8287","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_name":"2020EMSOFT.pdf","access_level":"open_access","creator":"cschilli","content_type":"application/pdf","file_size":696384,"file_id":"8288","relation":"main_file","date_updated":"2020-08-24T12:53:15Z","date_created":"2020-08-24T12:53:15Z","success":1,"checksum":"d19e97d0f8a3a441dc078ec812297d75"}],"oa_version":"Preprint","type":"conference","abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1905.02458"]},"language":[{"iso":"eng"}],"conference":{"name":"EMSOFT: International Conference on Embedded Software","end_date":"2020-09-25","start_date":"2020-09-20","location":"Virtual "},"publication_status":"published","department":[{"_id":"ToHe"}],"year":"2020","date_updated":"2023-08-22T13:27:32Z","date_created":"2020-08-24T12:56:20Z","author":[{"last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"full_name":"Potomkin, Kostiantyn","last_name":"Potomkin","first_name":"Kostiantyn"},{"first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"}],"related_material":{"record":[{"id":"8790","relation":"later_version","status":"public"}]},"file_date_updated":"2020-08-24T12:53:15Z","ec_funded":1},{"abstract":[{"text":"We consider a real-time setting where an environment releases sequences of firm-deadline tasks, and an online scheduler chooses on-the-fly the ones to execute on a single processor so as to maximize cumulated utility. The competitive ratio is a well-known performance measure for the scheduler: it gives the worst-case ratio, among all possible choices for the environment, of the cumulated utility of the online scheduler versus an offline scheduler that knows these choices in advance. Traditionally, competitive analysis is performed by hand, while automated techniques are rare and only handle static environments with independent tasks. We present a quantitative-verification framework for precedence-aware competitive analysis, where task releases may depend on preceding scheduling choices, i.e., the environment can respond to scheduling decisions dynamically . We consider two general classes of precedences: 1) follower precedences force the release of a dependent task upon the completion of a set of precursor tasks, while and 2) pairing precedences modify the characteristics of a dependent task provided the completion of a set of precursor tasks. Precedences make competitive analysis challenging, as the online and offline schedulers operate on diverging sequences. We make a formal presentation of our framework, and use a GPU-based implementation to analyze ten well-known schedulers on precedence-based application examples taken from the existing literature: 1) a handshake protocol (HP); 2) network packet-switching; 3) query scheduling (QS); and 4) a sporadic-interrupt setting. Our experimental results show that precedences and task parameters can vary drastically the best scheduler. Our framework thus supports application designers in choosing the best scheduler among a given set automatically.","lang":"eng"}],"issue":"11","type":"journal_article","oa_version":"None","status":"public","title":"Precedence-aware automated competitive analysis of real-time scheduling","intvolume":" 39","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8788","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2020-11-01T00:00:00Z","article_type":"original","page":"3981-3992","publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","citation":{"ieee":"A. Pavlogiannis, N. Schaumberger, U. Schmid, and K. Chatterjee, “Precedence-aware automated competitive analysis of real-time scheduling,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11. IEEE, pp. 3981–3992, 2020.","apa":"Pavlogiannis, A., Schaumberger, N., Schmid, U., & Chatterjee, K. (2020). Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE. https://doi.org/10.1109/TCAD.2020.3012803","ista":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. 2020. Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 3981–3992.","ama":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 2020;39(11):3981-3992. doi:10.1109/TCAD.2020.3012803","chicago":"Pavlogiannis, Andreas, Nico Schaumberger, Ulrich Schmid, and Krishnendu Chatterjee. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012803.","short":"A. Pavlogiannis, N. Schaumberger, U. Schmid, K. Chatterjee, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 3981–3992.","mla":"Pavlogiannis, Andreas, et al. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 3981–92, doi:10.1109/TCAD.2020.3012803."},"date_updated":"2023-08-22T13:27:05Z","date_created":"2020-11-22T23:01:24Z","volume":39,"author":[{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"},{"first_name":"Nico","last_name":"Schaumberger","full_name":"Schaumberger, Nico"},{"first_name":"Ulrich","last_name":"Schmid","full_name":"Schmid, Ulrich"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IEEE","year":"2020","acknowledgement":"This work was supported by the Austrian Science Foundation (FWF) under the NFN RiSE/SHiNE under Grant S11405 and Grant S11407. This article was presented in the International Conference on Embedded Software 2020 and appears as part of the ESWEEK-TCAD special issue. ","month":"11","publication_identifier":{"issn":["02780070"],"eissn":["19374151"]},"language":[{"iso":"eng"}],"doi":"10.1109/TCAD.2020.3012803","quality_controlled":"1","isi":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"external_id":{"isi":["000587712700069"]}},{"author":[{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"full_name":"Forets, Marcelo","first_name":"Marcelo","last_name":"Forets"},{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"first_name":"Kostiantyn","last_name":"Potomkin","full_name":"Potomkin, Kostiantyn"},{"last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"8287"}]},"date_created":"2020-11-22T23:01:25Z","date_updated":"2023-08-22T13:27:33Z","volume":39,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, and the Air Force Office of Scientific Research under award number FA2386-17-1-4065. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the United States Air Force. ","year":"2020","publication_status":"published","publisher":"IEEE","department":[{"_id":"ToHe"}],"ec_funded":1,"doi":"10.1109/TCAD.2020.3012859","language":[{"iso":"eng"}],"external_id":{"isi":["000587712700072"],"arxiv":["1905.02458"]},"main_file_link":[{"url":"https://arxiv.org/abs/1905.02458","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"month":"11","publication_identifier":{"eissn":["19374151"],"issn":["02780070"]},"oa_version":"Preprint","_id":"8790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Reachability analysis of linear hybrid systems via block decomposition","intvolume":" 39","abstract":[{"lang":"eng","text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this article, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks."}],"issue":"11","type":"journal_article","date_published":"2020-11-01T00:00:00Z","publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","citation":{"chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012859.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 4018–4029.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 4018–29, doi:10.1109/TCAD.2020.3012859.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE. https://doi.org/10.1109/TCAD.2020.3012859","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11. IEEE, pp. 4018–4029, 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 4018–4029.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 2020;39(11):4018-4029. doi:10.1109/TCAD.2020.3012859"},"article_type":"original","page":"4018-4029","day":"01","article_processing_charge":"No","scopus_import":"1"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"10","article_type":"original","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.” Frontiers in Plant Science, vol. 11, 586870, Frontiers, 2020, doi:10.3389/fpls.2020.586870.","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.” Frontiers in Plant Science. Frontiers, 2020. https://doi.org/10.3389/fpls.2020.586870.","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. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.586870","apa":"Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N., Cavallari, N., & Doonan, J. H. (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. Frontiers. https://doi.org/10.3389/fpls.2020.586870","ieee":"C. Nibau et al., “A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,” Frontiers in Plant Science, vol. 11. Frontiers, 2020.","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."},"publication":"Frontiers in Plant Science","date_published":"2020-11-10T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"intvolume":" 11","ddc":["580"],"title":"A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis","status":"public","_id":"8924","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_size":1833244,"content_type":"application/pdf","file_name":"2020_Frontiers_Nibau.pdf","access_level":"open_access","date_updated":"2020-12-09T09:14:19Z","date_created":"2020-12-09T09:14:19Z","success":1,"checksum":"1c0ee6ce9950aa665d6a5cc64aa6b752","file_id":"8929","relation":"main_file"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1664-462X"]},"month":"11","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000591637000001"]},"language":[{"iso":"eng"}],"doi":"10.3389/fpls.2020.586870","article_number":"586870","file_date_updated":"2020-12-09T09:14:19Z","department":[{"_id":"EvBe"}],"publisher":"Frontiers","publication_status":"published","year":"2020","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.","volume":11,"date_created":"2020-12-06T23:01:14Z","date_updated":"2023-08-24T10:50:00Z","author":[{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"last_name":"Dadarou","first_name":"Despoina","full_name":"Dadarou, Despoina"},{"full_name":"Kargios, Nestoras","first_name":"Nestoras","last_name":"Kargios"},{"full_name":"Mallioura, Areti","last_name":"Mallioura","first_name":"Areti"},{"last_name":"Fernandez-Fuentes","first_name":"Narcis","full_name":"Fernandez-Fuentes, Narcis"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"full_name":"Doonan, John H.","last_name":"Doonan","first_name":"John H."}]},{"_id":"8926","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 10","title":"Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction","status":"public","oa_version":"None","type":"journal_article","issue":"22","abstract":[{"text":"Bimetallic nanoparticles with tailored size and specific composition have shown promise as stable and selective catalysts for electrochemical reduction of CO2 (CO2R) in batch systems. Yet, limited effort was devoted to understand the effect of ligand coverage and postsynthesis treatments on CO2 reduction, especially under industrially applicable conditions, such as at high currents (>100 mA/cm2) using gas diffusion electrodes (GDE) and flow reactors. In this work, Cu–Ag core–shell nanoparticles (11 ± 2 nm) were prepared with three different surface modes: (i) capped with oleylamine, (ii) capped with monoisopropylamine, and (iii) surfactant-free with a reducing borohydride agent; Cu–Ag (OAm), Cu–Ag (MIPA), and Cu–Ag (NaBH4), respectively. The ligand exchange and removal was evidenced by infrared spectroscopy (ATR-FTIR) analysis, whereas high-resolution scanning transmission electron microscopy (HAADF-STEM) showed their effect on the interparticle distance and nanoparticle rearrangement. Later on, we developed a process-on-substrate method to track these effects on CO2R. Cu–Ag (OAm) gave a lower on-set potential for hydrocarbon production, whereas Cu–Ag (MIPA) and Cu–Ag (NaBH4) promoted syngas production. The electrochemical impedance and surface area analysis on the well-controlled electrodes showed gradual increases in the electrical conductivity and active surface area after each surface treatment. We found that the increasing amount of the triple phase boundaries (the meeting point for the electron–electrolyte–CO2 reactant) affect the required electrode potential and eventually the C+2e̅/C2e̅ product ratio. This study highlights the importance of the electron transfer to those active sites affected by the capping agents—particularly on larger substrates that are crucial for their industrial application.","lang":"eng"}],"citation":{"chicago":"Irtem, Erdem, Daniel Arenas Esteban, Miguel Duarte, Daniel Choukroun, Seungho Lee, Maria Ibáñez, Sara Bals, and Tom Breugelmans. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” ACS Catalysis. American Chemical Society, 2020. https://doi.org/10.1021/acscatal.0c03210.","short":"E. Irtem, D. Arenas Esteban, M. Duarte, D. Choukroun, S. Lee, M. Ibáñez, S. Bals, T. Breugelmans, ACS Catalysis 10 (2020) 13468–13478.","mla":"Irtem, Erdem, et al. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” ACS Catalysis, vol. 10, no. 22, American Chemical Society, 2020, pp. 13468–78, doi:10.1021/acscatal.0c03210.","ieee":"E. Irtem et al., “Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction,” ACS Catalysis, vol. 10, no. 22. American Chemical Society, pp. 13468–13478, 2020.","apa":"Irtem, E., Arenas Esteban, D., Duarte, M., Choukroun, D., Lee, S., Ibáñez, M., … Breugelmans, T. (2020). Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. American Chemical Society. https://doi.org/10.1021/acscatal.0c03210","ista":"Irtem E, Arenas Esteban D, Duarte M, Choukroun D, Lee S, Ibáñez M, Bals S, Breugelmans T. 2020. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 10(22), 13468–13478.","ama":"Irtem E, Arenas Esteban D, Duarte M, et al. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 2020;10(22):13468-13478. doi:10.1021/acscatal.0c03210"},"publication":"ACS Catalysis","page":"13468-13478","article_type":"original","date_published":"2020-11-20T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"20","acknowledgement":"The authors also acknowledge financial support from the University Research Fund (BOF-GOA-PS ID No. 33928). S.L. has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2020","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"publication_status":"published","author":[{"last_name":"Irtem","first_name":"Erdem","full_name":"Irtem, Erdem"},{"full_name":"Arenas Esteban, Daniel","first_name":"Daniel","last_name":"Arenas Esteban"},{"last_name":"Duarte","first_name":"Miguel","full_name":"Duarte, Miguel"},{"first_name":"Daniel","last_name":"Choukroun","full_name":"Choukroun, Daniel"},{"last_name":"Lee","first_name":"Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"full_name":"Bals, Sara","first_name":"Sara","last_name":"Bals"},{"full_name":"Breugelmans, Tom","last_name":"Breugelmans","first_name":"Tom"}],"volume":10,"date_updated":"2023-08-24T10:52:32Z","date_created":"2020-12-06T23:01:15Z","ec_funded":1,"external_id":{"isi":["000592978900031"]},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1021/acscatal.0c03210","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["21555435"]},"month":"11"},{"issue":"18","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."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 102","title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","status":"public","_id":"8944","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-11-01T00:00:00Z","article_type":"original","citation":{"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 et al., “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” Physical Review B, 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. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.102.180508","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. Physical Review B. 2020;102(18). doi:10.1103/PhysRevB.102.180508","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.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.102.180508.","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.” Physical Review B, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:10.1103/PhysRevB.102.180508.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020)."},"publication":"Physical Review B","article_number":"180508","volume":102,"date_updated":"2023-08-24T10:53:36Z","date_created":"2020-12-13T23:01:21Z","author":[{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin","full_name":"Zemlicka, Martin"},{"last_name":"Kopčík","first_name":"M.","full_name":"Kopčík, M."},{"last_name":"Szabó","first_name":"P.","full_name":"Szabó, P."},{"full_name":"Samuely, T.","first_name":"T.","last_name":"Samuely"},{"full_name":"Kačmarčík, J.","first_name":"J.","last_name":"Kačmarčík"},{"full_name":"Neilinger, P.","last_name":"Neilinger","first_name":"P."},{"full_name":"Grajcar, M.","last_name":"Grajcar","first_name":"M."},{"full_name":"Samuely, P.","first_name":"P.","last_name":"Samuely"}],"publisher":"American Physical Society","department":[{"_id":"JoFi"}],"publication_status":"published","year":"2020","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. ","publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.102.180508","quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["2011.04329"],"isi":["000591509900003"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.04329"}]},{"doi":"10.3389/fphys.2020.558070","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000596849400001"],"pmid":["33324233"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"month":"11","publication_identifier":{"eissn":["1664042X"]},"author":[{"last_name":"Rizzo","first_name":"Rossella","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"},{"full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249"},{"full_name":"Ivanov, Plamen Ch","first_name":"Plamen Ch","last_name":"Ivanov"}],"date_created":"2020-12-20T23:01:18Z","date_updated":"2023-08-24T11:00:45Z","volume":11,"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.","year":"2020","pmid":1,"publication_status":"published","publisher":"Frontiers","department":[{"_id":"GaTk"}],"file_date_updated":"2020-12-21T10:37:50Z","ec_funded":1,"article_number":"558070","date_published":"2020-11-26T00:00:00Z","publication":"Frontiers in Physiology","citation":{"short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology, vol. 11, 558070, Frontiers, 2020, doi:10.3389/fphys.2020.558070.","chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology. Frontiers, 2020. https://doi.org/10.3389/fphys.2020.558070.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 2020;11. doi:10.3389/fphys.2020.558070","apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., & Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. Frontiers in Physiology. Frontiers. https://doi.org/10.3389/fphys.2020.558070","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” Frontiers in Physiology, vol. 11. Frontiers, 2020.","ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070."},"article_type":"original","day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"8961","relation":"main_file","success":1,"checksum":"ef9515b28c5619b7126c0f347958bcb3","date_updated":"2020-12-21T10:37:50Z","date_created":"2020-12-21T10:37:50Z","access_level":"open_access","file_name":"2020_Frontiers_Rizzo.pdf","creator":"dernst","file_size":13380030,"content_type":"application/pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8955","ddc":["570"],"title":"Network physiology of cortico–muscular interactions","status":"public","intvolume":" 11","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"}],"type":"journal_article"},{"isi":1,"quality_controlled":"1","project":[{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000601787300001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/cells9122662","month":"12","publication_identifier":{"issn":["2073-4409"]},"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"MDPI","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.","year":"2020","date_created":"2020-12-14T08:04:03Z","date_updated":"2023-08-24T10:57:48Z","volume":9,"author":[{"full_name":"Zhang, Xuying","first_name":"Xuying","last_name":"Zhang"},{"full_name":"Mennicke, Christine V.","first_name":"Christine V.","last_name":"Mennicke"},{"full_name":"Xiao, Guanxi","last_name":"Xiao","first_name":"Guanxi"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","first_name":"Robert J","last_name":"Beattie","full_name":"Beattie, Robert J"},{"last_name":"Haider","first_name":"Mansoor","full_name":"Haider, Mansoor"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ghashghaei","first_name":"H. Troy","full_name":"Ghashghaei, H. Troy"}],"article_number":"2662","file_date_updated":"2020-12-14T08:09:43Z","ec_funded":1,"article_type":"original","publication":"Cells","citation":{"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.","ieee":"X. Zhang et al., “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” Cells, vol. 9, no. 12. MDPI, 2020.","apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., & Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. MDPI. https://doi.org/10.3390/cells9122662","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. Cells. 2020;9(12). doi:10.3390/cells9122662","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.” Cells. MDPI, 2020. https://doi.org/10.3390/cells9122662.","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.” Cells, vol. 9, no. 12, 2662, MDPI, 2020, doi:10.3390/cells9122662.","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020)."},"date_published":"2020-12-11T00:00:00Z","day":"11","has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","status":"public","intvolume":" 9","_id":"8949","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_id":"8950","relation":"main_file","success":1,"checksum":"5095cbdc728c9a510c5761cf60a8861c","date_created":"2020-12-14T08:09:43Z","date_updated":"2020-12-14T08:09:43Z","access_level":"open_access","file_name":"2020_Cells_Zhang.pdf","creator":"dernst","content_type":"application/pdf","file_size":3504525}],"type":"journal_article","abstract":[{"text":"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.","lang":"eng"}],"issue":"12"},{"file_date_updated":"2020-12-28T08:16:10Z","article_number":"6437","date_created":"2020-12-23T08:25:45Z","date_updated":"2023-08-24T11:01:50Z","volume":11,"author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"full_name":"Wan, William","last_name":"Wan","first_name":"William"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"year":"2020","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","month":"12","publication_identifier":{"issn":["2041-1723"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-20286-x","quality_controlled":"1","isi":1,"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","grant_number":"M02495","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000603078000003"]},"abstract":[{"lang":"eng","text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation."}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"55d43ea0061cc4027ba45e966e1db8cc","success":1,"date_created":"2020-12-28T08:16:10Z","date_updated":"2020-12-28T08:16:10Z","relation":"main_file","file_id":"8975","content_type":"application/pdf","file_size":3958727,"creator":"dernst","access_level":"open_access","file_name":"2020_NatureComm_Faessler.pdf"}],"status":"public","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","ddc":["570"],"intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8971","day":"22","article_processing_charge":"No","has_accepted_license":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"scopus_import":"1","date_published":"2020-12-22T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications, vol. 11, 6437, Springer Nature, 2020, doi:10.1038/s41467-020-20286-x.","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-20286-x.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 2020;11. doi:10.1038/s41467-020-20286-x","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., & Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20286-x","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437."}},{"author":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"volume":12578,"date_created":"2021-01-03T23:01:23Z","date_updated":"2023-08-24T11:08:58Z","year":"2020","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"publication_status":"published","ec_funded":1,"doi":"10.1007/978-3-030-65277-7_1","conference":{"name":"INDOCRYPT: International Conference on Cryptology in India","end_date":"2020-12-16","start_date":"2020-12-13","location":"Bangalore, India"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/418"}],"external_id":{"isi":["000927592800001"]},"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["03029743"],"isbn":["9783030652760"],"eissn":["16113349"]},"month":"12","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8987","intvolume":" 12578","status":"public","title":"Delayed authentication: Preventing replay and relay attacks in private contact tracing","abstract":[{"lang":"eng","text":"Currently several projects aim at designing and implementing protocols for privacy preserving automated contact tracing to help fight the current pandemic. Those proposal are quite similar, and in their most basic form basically propose an app for mobile phones which broadcasts frequently changing pseudorandom identifiers via (low energy) Bluetooth, and at the same time, the app stores IDs broadcast by phones in its proximity. Only if a user is tested positive, they upload either the beacons they did broadcast (which is the case in decentralized proposals as DP-3T, east and west coast PACT or Covid watch) or received (as in Popp-PT or ROBERT) during the last two weeks or so.\r\n\r\nVaudenay [eprint 2020/399] observes that this basic scheme (he considers the DP-3T proposal) succumbs to relay and even replay attacks, and proposes more complex interactive schemes which prevent those attacks without giving up too many privacy aspects. Unfortunately interaction is problematic for this application for efficiency and security reasons. The countermeasures that have been suggested so far are either not practical or give up on key privacy aspects. We propose a simple non-interactive variant of the basic protocol that\r\n(security) Provably prevents replay and (if location data is available) relay attacks.\r\n(privacy) The data of all parties (even jointly) reveals no information on the location or time where encounters happened.\r\n(efficiency) The broadcasted message can fit into 128 bits and uses only basic crypto (commitments and secret key authentication).\r\n\r\nTowards this end we introduce the concept of “delayed authentication”, which basically is a message authentication code where verification can be done in two steps, where the first doesn’t require the key, and the second doesn’t require the message."}],"type":"conference","date_published":"2020-12-08T00:00:00Z","citation":{"short":"K.Z. Pietrzak, in:, Progress in Cryptology, Springer Nature, 2020, pp. 3–15.","mla":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” Progress in Cryptology, vol. 12578, Springer Nature, 2020, pp. 3–15, doi:10.1007/978-3-030-65277-7_1.","chicago":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” In Progress in Cryptology, 12578:3–15. LNCS. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-65277-7_1.","ama":"Pietrzak KZ. Delayed authentication: Preventing replay and relay attacks in private contact tracing. In: Progress in Cryptology. Vol 12578. LNCS. Springer Nature; 2020:3-15. doi:10.1007/978-3-030-65277-7_1","ieee":"K. Z. Pietrzak, “Delayed authentication: Preventing replay and relay attacks in private contact tracing,” in Progress in Cryptology, Bangalore, India, 2020, vol. 12578, pp. 3–15.","apa":"Pietrzak, K. Z. (2020). Delayed authentication: Preventing replay and relay attacks in private contact tracing. In Progress in Cryptology (Vol. 12578, pp. 3–15). Bangalore, India: Springer Nature. https://doi.org/10.1007/978-3-030-65277-7_1","ista":"Pietrzak KZ. 2020. Delayed authentication: Preventing replay and relay attacks in private contact tracing. Progress in Cryptology. INDOCRYPT: International Conference on Cryptology in IndiaLNCS vol. 12578, 3–15."},"publication":"Progress in Cryptology","page":"3-15","article_processing_charge":"No","day":"08","scopus_import":"1","series_title":"LNCS"},{"external_id":{"isi":["000600665700008"],"pmid":["33207225"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.devcel.2020.10.016","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"month":"12","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion, Hitoyoshi Yasuo for sharing lab equipment, Lucas Leclère and Hitoyoshi Yasuo for their comments on a preliminary version of the manuscript, and Philippe Dru for the Rose plots. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a grant from the French Government funding agency Agence National de la Recherche (ANR “MorCell”: ANR-17-CE 13-002 8).","year":"2020","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"CaHe"}],"author":[{"full_name":"Godard, Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G","last_name":"Godard"},{"last_name":"Dumollard","first_name":"Rémi","full_name":"Dumollard, Rémi"},{"last_name":"Munro","first_name":"Edwin","full_name":"Munro, Edwin"},{"full_name":"Chenevert, Janet","last_name":"Chenevert","first_name":"Janet"},{"first_name":"Céline","last_name":"Hebras","full_name":"Hebras, Céline"},{"first_name":"Alex","last_name":"Mcdougall","full_name":"Mcdougall, Alex"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/relaxing-cell-divisions/","description":"News on IST Homepage","relation":"press_release"}]},"date_created":"2020-12-20T23:01:19Z","date_updated":"2023-08-24T11:01:22Z","volume":55,"publication":"Developmental Cell","citation":{"chicago":"Godard, Benoit G, Rémi Dumollard, Edwin Munro, Janet Chenevert, Céline Hebras, Alex Mcdougall, and Carl-Philipp J Heisenberg. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.10.016.","short":"B.G. Godard, R. Dumollard, E. Munro, J. Chenevert, C. Hebras, A. Mcdougall, C.-P.J. Heisenberg, Developmental Cell 55 (2020) 695–706.","mla":"Godard, Benoit G., et al. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell, vol. 55, no. 6, Elsevier, 2020, pp. 695–706, doi:10.1016/j.devcel.2020.10.016.","apa":"Godard, B. G., Dumollard, R., Munro, E., Chenevert, J., Hebras, C., Mcdougall, A., & Heisenberg, C.-P. J. (2020). Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.10.016","ieee":"B. G. Godard et al., “Apical relaxation during mitotic rounding promotes tension-oriented cell division,” Developmental Cell, vol. 55, no. 6. Elsevier, pp. 695–706, 2020.","ista":"Godard BG, Dumollard R, Munro E, Chenevert J, Hebras C, Mcdougall A, Heisenberg C-PJ. 2020. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 55(6), 695–706.","ama":"Godard BG, Dumollard R, Munro E, et al. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 2020;55(6):695-706. doi:10.1016/j.devcel.2020.10.016"},"article_type":"original","page":"695-706","date_published":"2020-12-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","_id":"8957","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Apical relaxation during mitotic rounding promotes tension-oriented cell division","intvolume":" 55","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Global tissue tension anisotropy has been shown to trigger stereotypical cell division orientation by elongating mitotic cells along the main tension axis. Yet, how tissue tension elongates mitotic cells despite those cells undergoing mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains unclear. We addressed this question by taking advantage of ascidian embryos, consisting of a small number of interphasic and mitotic blastomeres and displaying an invariant division pattern. We found that blastomeres undergo MR by locally relaxing cortical tension at their apex, thereby allowing extrinsic pulling forces from neighboring interphasic blastomeres to polarize their shape and thus division orientation. Consistently, interfering with extrinsic forces by reducing the contractility of interphasic blastomeres or disrupting the establishment of asynchronous mitotic domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation during MR constitutes a key mechanism by which tissue tension anisotropy controls stereotypical cell division orientation."}],"issue":"6"},{"issue":"50","abstract":[{"lang":"eng","text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1199247,"creator":"dernst","access_level":"open_access","file_name":"2020_PNAS_Grah.pdf","checksum":"69039cd402a571983aa6cb4815ffa863","success":1,"date_updated":"2021-01-11T08:37:31Z","date_created":"2021-01-11T08:37:31Z","relation":"main_file","file_id":"9004"}],"_id":"9000","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 117","ddc":["570"],"title":"Nonequilibrium models of optimal enhancer function","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2020-12-15T00:00:00Z","citation":{"short":"R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.","mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006731117.","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. PNAS. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” PNAS, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2006731117","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. PNAS. 117(50), 31614–31622."},"publication":"PNAS","page":"31614-31622","article_type":"original","file_date_updated":"2021-01-11T08:37:31Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/"}]},"author":[{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","first_name":"Rok"},{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"volume":117,"date_created":"2021-01-10T23:01:17Z","date_updated":"2023-08-24T11:10:22Z","pmid":1,"year":"2020","acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"publication_status":"published","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"month":"12","doi":"10.1073/pnas.2006731117","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000600608300015"],"pmid":["33268497"]},"oa":1,"project":[{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"type":"journal_article","abstract":[{"text":"Quantum illumination uses entangled signal-idler photon pairs to boost the detection efficiency of low-reflectivity objects in environments with bright thermal noise. Its advantage is particularly evident at low signal powers, a promising feature for applications such as noninvasive biomedical scanning or low-power short-range radar. Here, we experimentally investigate the concept of quantum illumination at microwave frequencies. We generate entangled fields to illuminate a room-temperature object at a distance of 1 m in a free-space detection setup. We implement a digital phase-conjugate receiver based on linear quadrature measurements that outperforms a symmetric classical noise radar in the same conditions, despite the entanglement-breaking signal path. Starting from experimental data, we also simulate the case of perfect idler photon number detection, which results in a quantum advantage compared with the relative classical benchmark. Our results highlight the opportunities and challenges in the way toward a first room-temperature application of microwave quantum circuits.","lang":"eng"}],"issue":"19","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7910","title":"Microwave quantum illumination using a digital receiver","ddc":["530"],"status":"public","intvolume":" 6","file":[{"creator":"dernst","content_type":"application/pdf","file_size":795822,"access_level":"open_access","file_name":"2020_ScienceAdvances_Barzanjeh.pdf","checksum":"16fa61cc1951b444ee74c07188cda9da","date_updated":"2020-07-14T12:48:05Z","date_created":"2020-06-02T09:18:36Z","file_id":"7913","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","day":"06","article_processing_charge":"No","has_accepted_license":"1","publication":"Science Advances","citation":{"mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination Using a Digital Receiver.” Science Advances, vol. 6, no. 19, eabb0451, AAAS, 2020, doi:10.1126/sciadv.abb0451.","short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, Science Advances 6 (2020).","chicago":"Barzanjeh, Shabir, S. Pirandola, D Vitali, and Johannes M Fink. “Microwave Quantum Illumination Using a Digital Receiver.” Science Advances. AAAS, 2020. https://doi.org/10.1126/sciadv.abb0451.","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination using a digital receiver. Science Advances. 2020;6(19). doi:10.1126/sciadv.abb0451","ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination using a digital receiver. Science Advances. 6(19), eabb0451.","ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination using a digital receiver,” Science Advances, vol. 6, no. 19. AAAS, 2020.","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., & Fink, J. M. (2020). Microwave quantum illumination using a digital receiver. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abb0451"},"article_type":"original","date_published":"2020-05-06T00:00:00Z","article_number":"eabb0451","file_date_updated":"2020-07-14T12:48:05Z","ec_funded":1,"year":"2020","publication_status":"published","publisher":"AAAS","department":[{"_id":"JoFi"}],"author":[{"last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"first_name":"S.","last_name":"Pirandola","full_name":"Pirandola, S."},{"full_name":"Vitali, D","first_name":"D","last_name":"Vitali"},{"last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/scientists-demonstrate-quantum-radar-prototype/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"relation":"later_version","status":"public","id":"9001"}]},"date_updated":"2023-08-24T11:10:49Z","date_created":"2020-05-31T22:00:49Z","volume":6,"month":"05","publication_identifier":{"eissn":["23752548"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000531171100045"],"arxiv":["1908.03058"]},"quality_controlled":"1","isi":1,"project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"},{"call_identifier":"H2020","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894"},{"_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"}],"doi":"10.1126/sciadv.abb0451","language":[{"iso":"eng"}]},{"publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"IEEE","acknowledgement":"This work was supported by the Institute of Science and Technology Austria (IST Austria), the European Research Council under grant agreement number 758053 (ERC StG QUNNECT) and the EU’s Horizon 2020 research and innovation programme under grant agreement number 862644 (FET Open QUARTET). S.B. acknowledges support from the Marie Skłodowska Curie\r\nfellowship number 707438 (MSC-IF SUPEREOM), DV acknowledge support from EU’s Horizon 2020 research and innovation programme under grant agreement number 732894 (FET Proactive HOT) and the Project QuaSeRT funded by the QuantERA ERANET Cofund in Quantum Technologies, and J.M.F from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and\r\ninnovation programme under grant agreement number 732894 (FET Proactive\r\nHOT).","year":"2020","date_updated":"2023-08-24T11:10:49Z","date_created":"2021-01-10T23:01:17Z","volume":2020,"author":[{"last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"last_name":"Pirandola","first_name":"Stefano","full_name":"Pirandola, Stefano"},{"last_name":"Vitali","first_name":"David","full_name":"Vitali, David"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"related_material":{"record":[{"id":"7910","relation":"earlier_version","status":"public"}]},"article_number":"9266397","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644"},{"call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438"},{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"}],"external_id":{"isi":["000612224900089"],"arxiv":["1908.03058"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.03058"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"RadarConf: National Conference on Radar","end_date":"2020-09-25","start_date":"2020-09-21","location":"Florence, Italy"},"doi":"10.1109/RadarConf2043947.2020.9266397","month":"09","publication_identifier":{"issn":["1097-5659"],"isbn":["9781728189420"]},"title":"Microwave quantum illumination with a digital phase-conjugated receiver","status":"public","intvolume":" 2020","_id":"9001","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"conference","abstract":[{"text":"Quantum illumination is a sensing technique that employs entangled signal-idler beams to improve the detection efficiency of low-reflectivity objects in environments with large thermal noise. The advantage over classical strategies is evident at low signal brightness, a feature which could make the protocol an ideal prototype for non-invasive scanning or low-power short-range radar. Here we experimentally investigate the concept of quantum illumination at microwave frequencies, by generating entangled fields using a Josephson parametric converter which are then amplified to illuminate a room-temperature object at a distance of 1 meter. Starting from experimental data, we simulate the case of perfect idler photon number detection, which results in a quantum advantage compared to the relative classical benchmark. Our results highlight the opportunities and challenges on the way towards a first room-temperature application of microwave quantum circuits.","lang":"eng"}],"issue":"9","publication":"IEEE National Radar Conference - Proceedings","citation":{"chicago":"Barzanjeh, Shabir, Stefano Pirandola, David Vitali, and Johannes M Fink. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” In IEEE National Radar Conference - Proceedings, Vol. 2020. IEEE, 2020. https://doi.org/10.1109/RadarConf2043947.2020.9266397.","mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” IEEE National Radar Conference - Proceedings, vol. 2020, no. 9, 9266397, IEEE, 2020, doi:10.1109/RadarConf2043947.2020.9266397.","short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, in:, IEEE National Radar Conference - Proceedings, IEEE, 2020.","ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination with a digital phase-conjugated receiver. IEEE National Radar Conference - Proceedings. RadarConf: National Conference on Radar vol. 2020, 9266397.","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., & Fink, J. M. (2020). Microwave quantum illumination with a digital phase-conjugated receiver. In IEEE National Radar Conference - Proceedings (Vol. 2020). Florence, Italy: IEEE. https://doi.org/10.1109/RadarConf2043947.2020.9266397","ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination with a digital phase-conjugated receiver,” in IEEE National Radar Conference - Proceedings, Florence, Italy, 2020, vol. 2020, no. 9.","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination with a digital phase-conjugated receiver. In: IEEE National Radar Conference - Proceedings. Vol 2020. IEEE; 2020. doi:10.1109/RadarConf2043947.2020.9266397"},"date_published":"2020-09-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No"},{"page":"635-659","article_type":"original","citation":{"chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” Commentarii Mathematici Helvetici. European Mathematical Society, 2020. https://doi.org/10.4171/CMH/499.","mla":"Browning, Timothy D., and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” Commentarii Mathematici Helvetici, vol. 95, no. 4, European Mathematical Society, 2020, pp. 635–59, doi:10.4171/CMH/499.","short":"T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659.","ista":"Browning TD, Sawin W. 2020. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 95(4), 635–659.","ieee":"T. D. Browning and W. Sawin, “Free rational points on smooth hypersurfaces,” Commentarii Mathematici Helvetici, vol. 95, no. 4. European Mathematical Society, pp. 635–659, 2020.","apa":"Browning, T. D., & Sawin, W. (2020). Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. European Mathematical Society. https://doi.org/10.4171/CMH/499","ama":"Browning TD, Sawin W. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 2020;95(4):635-659. doi:10.4171/CMH/499"},"publication":"Commentarii Mathematici Helvetici","date_published":"2020-12-07T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"07","intvolume":" 95","title":"Free rational points on smooth hypersurfaces","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9007","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"text":"Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals.","lang":"eng"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.08463"}],"external_id":{"arxiv":["1906.08463"],"isi":["000596833300001"]},"language":[{"iso":"eng"}],"doi":"10.4171/CMH/499","publication_identifier":{"issn":["00102571"],"eissn":["14208946"]},"month":"12","department":[{"_id":"TiBr"}],"publisher":"European Mathematical Society","publication_status":"published","year":"2020","volume":95,"date_created":"2021-01-17T23:01:11Z","date_updated":"2023-08-24T11:11:36Z","author":[{"first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"},{"first_name":"Will","last_name":"Sawin","full_name":"Sawin, Will"}]},{"date_published":"2020-11-23T00:00:00Z","publication":"PRX Quantum","citation":{"ieee":"W. J. Hease et al., “Bidirectional electro-optic wavelength conversion in the quantum ground state,” PRX Quantum, vol. 1, no. 2. American Physical Society, 2020.","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H. G. L., & Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.1.020315","ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel HGL, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state. PRX Quantum. 1(2), 020315.","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. PRX Quantum. 2020;1(2). doi:10.1103/prxquantum.1.020315","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald G.L. Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” PRX Quantum. American Physical Society, 2020. https://doi.org/10.1103/prxquantum.1.020315.","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H.G.L. Schwefel, J.M. Fink, PRX Quantum 1 (2020).","mla":"Hease, William J., et al. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” PRX Quantum, vol. 1, no. 2, 020315, American Physical Society, 2020, doi:10.1103/prxquantum.1.020315."},"article_type":"original","day":"23","has_accepted_license":"1","article_processing_charge":"No","file":[{"relation":"main_file","file_id":"9115","checksum":"b70b12ded6d7660d4c9037eb09bfed0c","success":1,"date_updated":"2021-02-12T11:16:16Z","date_created":"2021-02-12T11:16:16Z","access_level":"open_access","file_name":"2020_PRXQuantum_Hease.pdf","file_size":2146924,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9114","status":"public","title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","ddc":["530"],"intvolume":" 1","abstract":[{"text":"Microwave photonics lends the advantages of fiber optics to electronic sensing and communication systems. In contrast to nonlinear optics, electro-optic devices so far require classical modulation fields whose variance is dominated by electronic or thermal noise rather than quantum fluctuations. Here we demonstrate bidirectional single-sideband conversion of X band microwave to C band telecom light with a microwave mode occupancy as low as 0.025 ± 0.005 and an added output noise of less than or equal to 0.074 photons. This is facilitated by radiative cooling and a triply resonant ultra-low-loss transducer operating at millikelvin temperatures. The high bandwidth of 10.7 MHz and total (internal) photon conversion\r\nefficiency of 0.03% (0.67%) combined with the extremely slow heating rate of 1.1 added output noise photons per second for the highest available pump power of 1.48 mW puts near-unity efficiency pulsed quantum transduction within reach. Together with the non-Gaussian resources of superconducting qubits this might provide the practical foundation to extend the range and scope of current quantum networks in analogy to electrical repeaters in classical fiber optic communication.","lang":"eng"}],"issue":"2","type":"journal_article","doi":"10.1103/prxquantum.1.020315","acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000674680100001"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"name":"Integrating superconducting quantum circuits","call_identifier":"FWF","grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"month":"11","publication_identifier":{"issn":["2691-3399"]},"author":[{"full_name":"Hease, William J","orcid":"0000-0001-9868-2166","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","first_name":"William J"},{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R"},{"last_name":"Sahu","first_name":"Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh"},{"full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","first_name":"Matthias"},{"orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","first_name":"Georg M","full_name":"Arnold, Georg M"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."},{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/"}],"record":[{"id":"13071","status":"public","relation":"research_data"},{"id":"12900","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"13175"}]},"date_updated":"2023-08-24T11:16:36Z","date_created":"2021-02-12T10:41:28Z","volume":1,"year":"2020","acknowledgement":"The authors acknowledge the support of T. Menner, A. Arslani, and T. Asenov from the Miba machine shop for machining the microwave cavity, and thank S. Barzanjeh, F. Sedlmeir, and C. Marquardt for fruitful discussions. This work is supported by IST Austria and the European Research Council under Grant No. 758053 (ERC StG QUNNECT). W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411.\r\nG.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71) and the European Union’s Horizon 2020 research and innovation program under Grant No. 899354 (FET Open SuperQuLAN). H.G.L.S. acknowledges support from the Aotearoa/New Zealand’s MBIE Endeavour Smart Ideas Grant No UOOX1805.","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","file_date_updated":"2021-02-12T11:16:16Z","ec_funded":1,"article_number":"020315"},{"date_published":"2020-03-01T00:00:00Z","article_type":"review","publication":"Quantum Science and Technology","citation":{"mla":"Lauk, Nikolai, et al. “Perspectives on Quantum Transduction.” Quantum Science and Technology, vol. 5, no. 2, 020501, IOP Publishing, 2020, doi:10.1088/2058-9565/ab788a.","short":"N. Lauk, N. Sinclair, S. Barzanjeh, J.P. Covey, M. Saffman, M. Spiropulu, C. Simon, Quantum Science and Technology 5 (2020).","chicago":"Lauk, Nikolai, Neil Sinclair, Shabir Barzanjeh, Jacob P Covey, Mark Saffman, Maria Spiropulu, and Christoph Simon. “Perspectives on Quantum Transduction.” Quantum Science and Technology. IOP Publishing, 2020. https://doi.org/10.1088/2058-9565/ab788a.","ama":"Lauk N, Sinclair N, Barzanjeh S, et al. Perspectives on quantum transduction. Quantum Science and Technology. 2020;5(2). doi:10.1088/2058-9565/ab788a","ista":"Lauk N, Sinclair N, Barzanjeh S, Covey JP, Saffman M, Spiropulu M, Simon C. 2020. Perspectives on quantum transduction. Quantum Science and Technology. 5(2), 020501.","apa":"Lauk, N., Sinclair, N., Barzanjeh, S., Covey, J. P., Saffman, M., Spiropulu, M., & Simon, C. (2020). Perspectives on quantum transduction. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ab788a","ieee":"N. Lauk et al., “Perspectives on quantum transduction,” Quantum Science and Technology, vol. 5, no. 2. IOP Publishing, 2020."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"file_id":"9215","relation":"main_file","success":1,"checksum":"a8562c42124a66b86836fe2489eb5f4f","date_created":"2021-03-02T09:47:13Z","date_updated":"2021-03-02T09:47:13Z","access_level":"open_access","file_name":"2020_QuantumScience_Lauk.pdf","creator":"dernst","file_size":974399,"content_type":"application/pdf"}],"oa_version":"Published Version","ddc":["530"],"status":"public","title":"Perspectives on quantum transduction","intvolume":" 5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9194","abstract":[{"text":"Quantum transduction, the process of converting quantum signals from one form of energy to another, is an important area of quantum science and technology. The present perspective article reviews quantum transduction between microwave and optical photons, an area that has recently seen a lot of activity and progress because of its relevance for connecting superconducting quantum processors over long distances, among other applications. Our review covers the leading approaches to achieving such transduction, with an emphasis on those based on atomic ensembles, opto-electro-mechanics, and electro-optics. We briefly discuss relevant metrics from the point of view of different applications, as well as challenges for the future.","lang":"eng"}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1088/2058-9565/ab788a","quality_controlled":"1","isi":1,"project":[{"_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000521449500001"]},"month":"03","publication_identifier":{"issn":["2058-9565"]},"date_created":"2021-02-25T08:32:29Z","date_updated":"2023-08-24T11:17:48Z","volume":5,"author":[{"full_name":"Lauk, Nikolai","last_name":"Lauk","first_name":"Nikolai"},{"full_name":"Sinclair, Neil","last_name":"Sinclair","first_name":"Neil"},{"full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Covey, Jacob P","last_name":"Covey","first_name":"Jacob P"},{"full_name":"Saffman, Mark","last_name":"Saffman","first_name":"Mark"},{"full_name":"Spiropulu, Maria","first_name":"Maria","last_name":"Spiropulu"},{"first_name":"Christoph","last_name":"Simon","full_name":"Simon, Christoph"}],"publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"IOP Publishing","acknowledgement":"During the writing of this article we became aware of another review of quantum transduction with somewhat different emphasis [99].\r\nWe would like to thank the participants of the transduction workshop at Caltech in September 2018 for helpful and stimulating discussions. We particularly thank John Bartholomew, Andrei Faraon, Johannes Fink, Jeff Holzgrafe, Linbo Shao, Marko Lončar, Daniel Oblak, and Oskar Painter.\r\nN L and N S acknowledge support from the Alliance for Quantum Technologies' (AQT) Intelligent Quantum Networks and Technologies (INQNET) research program and by DOE/HEP QuantISED program grant, QCCFP (Quantum Communication Channels for Fundamental Physics), award number DE-SC0019219. NS further acknowledges support by the Natural Sciences and Engineering Research Council of Canada (NSERC). SB acknowledges support from the Marie Skłodowska Curie fellowship number 707 438 (MSC-IF SUPEREOM). JPC acknowledges support from the Caltech PMA prize postdoctoral fellowship. MS acknowledges support from the ARL-CDQI and the National Science Foundation. CS acknowledges NSERC, Quantum Alberta, and the Alberta Major Innovation Fund.","year":"2020","file_date_updated":"2021-03-02T09:47:13Z","ec_funded":1,"article_number":"020501"},{"scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"No","publication":"SIAM Journal on Mathematical Analysis","citation":{"chicago":"Fischer, Julian L, Tim Laux, and Theresa M. Simon. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/20M1322182.","mla":"Fischer, Julian L., et al. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” SIAM Journal on Mathematical Analysis, vol. 52, no. 6, Society for Industrial and Applied Mathematics, 2020, pp. 6222–33, doi:10.1137/20M1322182.","short":"J.L. Fischer, T. Laux, T.M. Simon, SIAM Journal on Mathematical Analysis 52 (2020) 6222–6233.","ista":"Fischer JL, Laux T, Simon TM. 2020. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 52(6), 6222–6233.","ieee":"J. L. Fischer, T. Laux, and T. M. Simon, “Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies,” SIAM Journal on Mathematical Analysis, vol. 52, no. 6. Society for Industrial and Applied Mathematics, pp. 6222–6233, 2020.","apa":"Fischer, J. L., Laux, T., & Simon, T. M. (2020). Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1322182","ama":"Fischer JL, Laux T, Simon TM. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 2020;52(6):6222-6233. doi:10.1137/20M1322182"},"article_type":"original","page":"6222-6233","date_published":"2020-12-15T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We give a short and self-contained proof for rates of convergence of the Allen--Cahn equation towards mean curvature flow, assuming that a classical (smooth) solution to the latter exists and starting from well-prepared initial data. Our approach is based on a relative entropy technique. In particular, it does not require a stability analysis for the linearized Allen--Cahn operator. As our analysis also does not rely on the comparison principle, we expect it to be applicable to more complex equations and systems."}],"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9039","title":"Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies","status":"public","ddc":["510"],"intvolume":" 52","oa_version":"Published Version","file":[{"file_id":"9041","relation":"main_file","date_updated":"2021-01-25T07:48:39Z","date_created":"2021-01-25T07:48:39Z","success":1,"checksum":"21aa1cf4c30a86a00cae15a984819b5d","file_name":"2020_SIAM_Fischer.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":310655}],"month":"12","publication_identifier":{"issn":["00361410"],"eissn":["10957154"]},"external_id":{"isi":["000600695200027"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"doi":"10.1137/20M1322182","language":[{"iso":"eng"}],"file_date_updated":"2021-01-25T07:48:39Z","ec_funded":1,"year":"2020","acknowledgement":"This work was supported by the European Union's Horizon 2020 Research and Innovation\r\nProgramme under Marie Sklodowska-Curie grant agreement 665385 and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy, EXC-2047/1--390685813.","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"Society for Industrial and Applied Mathematics","author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"},{"first_name":"Tim","last_name":"Laux","full_name":"Laux, Tim"},{"first_name":"Theresa M.","last_name":"Simon","full_name":"Simon, Theresa M."}],"date_updated":"2023-08-24T11:15:16Z","date_created":"2021-01-24T23:01:09Z","volume":52}]