[{"title":"The application of persistent homology in the analysis of heart rate variability","department":[{"_id":"HeEd"}],"article_processing_charge":"No","external_id":{"isi":["000621172600045"]},"author":[{"first_name":"Grzegorz","full_name":"Graff, Grzegorz","last_name":"Graff"},{"full_name":"Graff, Beata","last_name":"Graff","first_name":"Beata"},{"first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz","last_name":"Jablonski"},{"first_name":"Krzysztof","full_name":"Narkiewicz, Krzysztof","last_name":"Narkiewicz"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-22T09:33:34Z","citation":{"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.","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.","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.","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.","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.","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"},"status":"public","conference":{"name":"ESGCO: European Study Group on Cardiovascular Oscillations","location":"Pisa, Italy","end_date":"2020-07-15","start_date":"2020-07-15"},"type":"conference","article_number":"9158054","_id":"8580","date_created":"2020-09-28T08:59:27Z","doi":"10.1109/ESGCO49734.2020.9158054","date_published":"2020-08-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","day":"01","year":"2020","publication_status":"published","publication_identifier":{"isbn":["9781728157511"]},"isi":1,"month":"08","scopus_import":"1","publisher":"IEEE","quality_controlled":"1","oa_version":"None","abstract":[{"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.","lang":"eng"}]},{"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.","quality_controlled":"1","publisher":"Wiley","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"04","publication":"Advanced Science","date_published":"2020-11-04T00:00:00Z","doi":"10.1002/advs.202001724","date_created":"2020-10-01T09:44:13Z","article_number":"2001724","project":[{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"citation":{"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.","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","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","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).","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Tian, Anhao","last_name":"Tian","first_name":"Anhao"},{"first_name":"Bo","last_name":"Kang","full_name":"Kang, Bo"},{"full_name":"Li, Baizhou","last_name":"Li","first_name":"Baizhou"},{"last_name":"Qiu","full_name":"Qiu, Biying","first_name":"Biying"},{"full_name":"Jiang, Wenhong","last_name":"Jiang","first_name":"Wenhong"},{"last_name":"Shao","full_name":"Shao, Fangjie","first_name":"Fangjie"},{"last_name":"Gao","full_name":"Gao, Qingqing","first_name":"Qingqing"},{"last_name":"Liu","full_name":"Liu, Rui","first_name":"Rui"},{"full_name":"Cai, Chengwei","last_name":"Cai","first_name":"Chengwei"},{"first_name":"Rui","full_name":"Jing, Rui","last_name":"Jing"},{"first_name":"Wei","full_name":"Wang, Wei","last_name":"Wang"},{"last_name":"Chen","full_name":"Chen, Pengxiang","first_name":"Pengxiang"},{"full_name":"Liang, Qinghui","last_name":"Liang","first_name":"Qinghui"},{"first_name":"Lili","last_name":"Bao","full_name":"Bao, Lili"},{"full_name":"Man, Jianghong","last_name":"Man","first_name":"Jianghong"},{"last_name":"Wang","full_name":"Wang, Yan","first_name":"Yan"},{"first_name":"Yu","last_name":"Shi","full_name":"Shi, Yu"},{"first_name":"Jin","full_name":"Li, Jin","last_name":"Li"},{"full_name":"Yang, Minmin","last_name":"Yang","first_name":"Minmin"},{"first_name":"Lisha","full_name":"Wang, Lisha","last_name":"Wang"},{"first_name":"Jianmin","last_name":"Zhang","full_name":"Zhang, Jianmin"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"Zhu, Junming","last_name":"Zhu","first_name":"Junming"},{"full_name":"Bian, Xiuwu","last_name":"Bian","first_name":"Xiuwu"},{"first_name":"Ying‐Jie","last_name":"Wang","full_name":"Wang, Ying‐Jie"},{"first_name":"Chong","full_name":"Liu, Chong","last_name":"Liu"}],"article_processing_charge":"No","external_id":{"isi":["000573860700001"]},"title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","month":"11","intvolume":" 7","publication_identifier":{"issn":["2198-3844"]},"publication_status":"published","file":[{"success":1,"checksum":"92818c23ecc70e35acfa671f3cfb9909","file_id":"8938","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_AdvScience_Tian.pdf","date_created":"2020-12-10T14:07:24Z","creator":"dernst","file_size":7835833,"date_updated":"2020-12-10T14:07:24Z"}],"language":[{"iso":"eng"}],"issue":"21","volume":7,"ec_funded":1,"_id":"8592","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"date_updated":"2023-08-22T09:53:01Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2020-12-10T14:07:24Z"},{"doi":"10.1038/s41467-020-18610-6","date_published":"2020-09-24T00:00:00Z","date_created":"2020-09-25T07:23:13Z","isi":1,"has_accepted_license":"1","year":"2020","day":"24","publication":"Nature Communications","publisher":"Springer Nature","quality_controlled":"1","oa":1,"author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"last_name":"Fitzek","full_name":"Fitzek, Harald","first_name":"Harald"},{"first_name":"Gerald","last_name":"Kothleitner","full_name":"Kothleitner, Gerald"},{"first_name":"Volker","last_name":"Presser","full_name":"Presser, Volker"},{"first_name":"Bernhard","last_name":"Gollas","full_name":"Gollas, Bernhard"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"},{"first_name":"Qamar","last_name":"Abbas","full_name":"Abbas, Qamar"}],"external_id":{"isi":["000573756600004"]},"article_processing_charge":"No","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","citation":{"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.","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.","ieee":"C. Prehal et al., “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"4838","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-19720-x","relation":"erratum"}]},"volume":11,"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","file":[{"success":1,"file_id":"8585","checksum":"eada7bc8dd16a49390137cff882ef328","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_NatureComm_Prehal.pdf","date_created":"2020-09-28T13:16:15Z","file_size":1822469,"date_updated":"2020-09-28T13:16:15Z","creator":"dernst"}],"language":[{"iso":"eng"}],"month":"09","intvolume":" 11","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"StFr"}],"file_date_updated":"2020-09-28T13:16:15Z","date_updated":"2023-08-22T09:37:24Z","ddc":["530"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"_id":"8568"},{"author":[{"first_name":"Alfonso","last_name":"Deichler","full_name":"Deichler, Alfonso"},{"first_name":"Denisse","last_name":"Carrasco","full_name":"Carrasco, Denisse"},{"first_name":"Luciana","last_name":"Lopez-Jury","full_name":"Lopez-Jury, Luciana"},{"full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A"},{"full_name":"Marquez, Natalia","last_name":"Marquez","first_name":"Natalia"},{"last_name":"Mpodozis","full_name":"Mpodozis, Jorge","first_name":"Jorge"},{"first_name":"Gonzalo","last_name":"Marin","full_name":"Marin, Gonzalo"}],"external_id":{"isi":["000577142600032"]},"article_processing_charge":"No","title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","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.","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.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"16220","date_published":"2020-10-01T00:00:00Z","doi":"10.1038/s41598-020-72848-0","date_created":"2020-10-11T22:01:14Z","has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Scientific Reports","publisher":"Springer Nature","quality_controlled":"1","oa":1,"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.).","file_date_updated":"2020-10-12T12:39:10Z","department":[{"_id":"MaJö"}],"date_updated":"2023-08-22T09:58:21Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"8643","volume":10,"publication_identifier":{"eissn":["20452322"]},"publication_status":"published","file":[{"date_created":"2020-10-12T12:39:10Z","file_name":"2020_ScientificReport_Deichler.pdf","date_updated":"2020-10-12T12:39:10Z","file_size":3906744,"creator":"dernst","checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","file_id":"8651","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 10","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version"},{"article_processing_charge":"No","external_id":{"isi":["000538696800054"],"pmid":["31742320"]},"author":[{"first_name":"Laura A","full_name":"Esteban, Laura A","last_name":"Esteban"},{"first_name":"Lyubov R","last_name":"Lonishin","full_name":"Lonishin, Lyubov R"},{"last_name":"Bobrovskiy","full_name":"Bobrovskiy, Daniil M","first_name":"Daniil M"},{"last_name":"Leleytner","full_name":"Leleytner, Gregory","first_name":"Gregory"},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S","first_name":"Natalya S"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry N ","last_name":"Ivankov","first_name":"Dmitry N "}],"title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","citation":{"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.","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","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"1960-1962","date_created":"2020-10-11T22:01:14Z","doi":"10.1093/bioinformatics/btz841","date_published":"2020-03-15T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Bioinformatics","day":"15","oa":1,"publisher":"Oxford Academic","quality_controlled":"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). ","file_date_updated":"2020-10-12T12:02:09Z","department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T09:57:29Z","ddc":["000","570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"8645","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"6","volume":36,"publication_status":"published","publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8649","checksum":"21d6f71839deb3b83e4a356193f72767","success":1,"date_updated":"2020-10-12T12:02:09Z","file_size":308341,"creator":"dernst","date_created":"2020-10-12T12:02:09Z","file_name":"2020_Bioinformatics_Esteban.pdf"}],"scopus_import":"1","intvolume":" 36","month":"03","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version"},{"day":"23","publication":"Physical Biology","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1088/1478-3975/abb2db","date_published":"2020-09-23T00:00:00Z","date_created":"2020-10-04T22:01:35Z","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.","quality_controlled":"1","publisher":"IOP Publishing","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005.","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.","short":"J. Merrin, Physical Biology 17 (2020).","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.","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","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","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."},"title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide","author":[{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000575539700001"]},"article_number":"065005","file":[{"success":1,"file_id":"8609","checksum":"fec9bdd355ed349f09990faab20838a7","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_PhysBio_Merrin.pdf","date_created":"2020-10-05T13:53:59Z","file_size":1667111,"date_updated":"2020-10-05T13:53:59Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14783975"]},"publication_status":"published","volume":17,"issue":"6","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"09","intvolume":" 17","scopus_import":"1","ddc":["510","570"],"date_updated":"2023-08-22T09:53:29Z","file_date_updated":"2020-10-05T13:53:59Z","department":[{"_id":"NanoFab"}],"_id":"8597","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"intvolume":" 108","month":"12","scopus_import":"1","pmid":1,"oa_version":"Published Version","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."}],"volume":108,"issue":"5","language":[{"iso":"eng"}],"file":[{"date_created":"2020-12-10T14:42:09Z","file_name":"2020_Neuron_Henneberger.pdf","creator":"dernst","date_updated":"2020-12-10T14:42:09Z","file_size":7518960,"checksum":"054562bb50165ef9a1f46631c1c5e36b","file_id":"8939","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"8674","department":[{"_id":"HaJa"}],"file_date_updated":"2020-12-10T14:42:09Z","ddc":["570"],"date_updated":"2023-08-22T09:59:29Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","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.).","date_created":"2020-10-18T22:01:38Z","date_published":"2020-12-09T00:00:00Z","doi":"10.1016/j.neuron.2020.08.030","page":"P919-936.E11","publication":"Neuron","day":"09","year":"2020","isi":1,"has_accepted_license":"1","title":"LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia","external_id":{"pmid":["32976770"],"isi":["000603428000010"]},"article_processing_charge":"No","author":[{"first_name":"Christian","full_name":"Henneberger, Christian","last_name":"Henneberger"},{"first_name":"Lucie","full_name":"Bard, Lucie","last_name":"Bard"},{"last_name":"Panatier","full_name":"Panatier, Aude","first_name":"Aude"},{"last_name":"Reynolds","full_name":"Reynolds, James P.","first_name":"James P."},{"full_name":"Kopach, Olga","last_name":"Kopach","first_name":"Olga"},{"last_name":"Medvedev","full_name":"Medvedev, Nikolay I.","first_name":"Nikolay I."},{"last_name":"Minge","full_name":"Minge, Daniel","first_name":"Daniel"},{"first_name":"Michel K.","last_name":"Herde","full_name":"Herde, Michel K."},{"first_name":"Stefanie","full_name":"Anders, Stefanie","last_name":"Anders"},{"full_name":"Kraev, Igor","last_name":"Kraev","first_name":"Igor"},{"full_name":"Heller, Janosch P.","last_name":"Heller","first_name":"Janosch P."},{"first_name":"Sylvain","last_name":"Rama","full_name":"Rama, Sylvain"},{"full_name":"Zheng, Kaiyu","last_name":"Zheng","first_name":"Kaiyu"},{"last_name":"Jensen","full_name":"Jensen, Thomas P.","first_name":"Thomas P."},{"first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez-Romero","full_name":"Sanchez-Romero, Inmaculada"},{"first_name":"Colin J.","last_name":"Jackson","full_name":"Jackson, Colin J."},{"last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"first_name":"Ole Petter","full_name":"Ottersen, Ole Petter","last_name":"Ottersen"},{"first_name":"Erlend Arnulf","full_name":"Nagelhus, Erlend Arnulf","last_name":"Nagelhus"},{"first_name":"Stephane H.R.","full_name":"Oliet, Stephane H.R.","last_name":"Oliet"},{"first_name":"Michael G.","last_name":"Stewart","full_name":"Stewart, Michael G."},{"first_name":"U. VAlentin","last_name":"Nägerl","full_name":"Nägerl, U. VAlentin"},{"last_name":"Rusakov","full_name":"Rusakov, Dmitri A. ","first_name":"Dmitri A. "}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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","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.","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."}},{"citation":{"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).","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.","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","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","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.","ista":"Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes","external_id":{"isi":["000581681000001"]},"title":"Filtering spins by scattering from a lattice of point magnets","article_number":"178","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"09","publication":"Communications Physics","date_published":"2020-10-09T00:00:00Z","doi":"10.1038/s42005-020-00445-8","date_created":"2020-10-13T09:48:59Z","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).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-08-22T09:58:46Z","ddc":["530"],"department":[{"_id":"MiLe"}],"file_date_updated":"2020-10-14T15:16:28Z","_id":"8652","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["2399-3650"]},"publication_status":"published","file":[{"file_size":1462934,"date_updated":"2020-10-14T15:16:28Z","creator":"dernst","file_name":"2020_CommPhysics_Ghazaryan.pdf","date_created":"2020-10-14T15:16:28Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"60cd35b99f0780acffc7b6060e49ec8b","file_id":"8662"}],"language":[{"iso":"eng"}],"volume":3,"ec_funded":1,"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."}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 3"},{"citation":{"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.","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","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","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Magdalena K.","last_name":"Sznurkowska","full_name":"Sznurkowska, Magdalena K."},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Azzarelli","full_name":"Azzarelli, Roberta","first_name":"Roberta"},{"first_name":"Lemonia","full_name":"Chatzeli, Lemonia","last_name":"Chatzeli"},{"last_name":"Ikeda","full_name":"Ikeda, Tatsuro","first_name":"Tatsuro"},{"full_name":"Yoshida, Shosei","last_name":"Yoshida","first_name":"Shosei"},{"full_name":"Philpott, Anna","last_name":"Philpott","first_name":"Anna"},{"first_name":"Benjamin D","full_name":"Simons, Benjamin D","last_name":"Simons"}],"article_processing_charge":"No","external_id":{"isi":["000577244600003"],"pmid":["33028844"]},"title":"Tracing the cellular basis of islet specification in mouse pancreas","article_number":"5037","isi":1,"has_accepted_license":"1","year":"2020","day":"07","publication":"Nature Communications","date_published":"2020-10-07T00:00:00Z","doi":"10.1038/s41467-020-18837-3","date_created":"2020-10-18T22:01:35Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-08-22T10:18:17Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2020-10-19T11:27:46Z","_id":"8669","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"0ecc0eab72d2d50694852579611a6624","file_id":"8677","creator":"dernst","file_size":5540540,"date_updated":"2020-10-19T11:27:46Z","file_name":"2020_NatureComm_Sznurkowska.pdf","date_created":"2020-10-19T11:27:46Z"}],"language":[{"iso":"eng"}],"volume":11,"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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 11"},{"title":"Abscission couples cell division to embryonic stem cell fate","external_id":{"pmid":["32979313"],"isi":["000582501100012"]},"article_processing_charge":"No","author":[{"first_name":"Agathe","last_name":"Chaigne","full_name":"Chaigne, Agathe"},{"first_name":"Céline","full_name":"Labouesse, Céline","last_name":"Labouesse"},{"first_name":"Ian J.","last_name":"White","full_name":"White, Ian J."},{"last_name":"Agnew","full_name":"Agnew, Meghan","first_name":"Meghan"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chalut","full_name":"Chalut, Kevin J.","first_name":"Kevin J."},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","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.","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."},"date_created":"2020-10-18T22:01:37Z","date_published":"2020-10-26T00:00:00Z","doi":"10.1016/j.devcel.2020.09.001","page":"195-208","publication":"Developmental Cell","day":"26","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Elsevier","quality_controlled":"1","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).","department":[{"_id":"EdHa"}],"file_date_updated":"2021-02-04T10:20:02Z","ddc":["570"],"date_updated":"2023-08-22T10:16:58Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"8672","volume":55,"issue":"2","language":[{"iso":"eng"}],"file":[{"file_name":"2020_DevelopmCell_Chaigne.pdf","date_created":"2021-02-04T10:20:02Z","creator":"dernst","file_size":6929686,"date_updated":"2021-02-04T10:20:02Z","success":1,"file_id":"9086","checksum":"88e1a031a61689165d19a19c2f16d795","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"intvolume":" 55","month":"10","scopus_import":"1","pmid":1,"oa_version":"Published Version","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"}]},{"author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X"},{"id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0001-5645-4333","full_name":"Kniely, Michael","last_name":"Kniely"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000576492700001"],"arxiv":["1906.12245"]},"title":"Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model","citation":{"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.","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.","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.","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.","short":"J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"5733-5772","date_published":"2020-11-01T00:00:00Z","doi":"10.1088/1361-6544/ab9728","date_created":"2020-10-25T23:01:16Z","isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Nonlinearity","publisher":"IOP Publishing","quality_controlled":"1","oa":1,"department":[{"_id":"JuFi"}],"file_date_updated":"2020-10-27T12:09:57Z","date_updated":"2023-08-22T10:38:38Z","ddc":["510"],"type":"journal_article","article_type":"original","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"status":"public","_id":"8697","volume":33,"issue":"11","license":"https://creativecommons.org/licenses/by/3.0/","publication_identifier":{"issn":["09517715"],"eissn":["13616544"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8710","checksum":"ed90bc6eb5f32ee6157fef7f3aabc057","success":1,"date_updated":"2020-10-27T12:09:57Z","file_size":1223899,"creator":"cziletti","date_created":"2020-10-27T12:09:57Z","file_name":"2020_Nonlinearity_Fischer.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"11","intvolume":" 33","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"}],"oa_version":"Published Version"},{"month":"10","intvolume":" 370","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/803635v1","open_access":"1"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"issue":"6512","related_material":{"link":[{"url":"https://ist.ac.at/en/news/sticking-together/","relation":"press_release","description":"News on IST Homepage"}]},"volume":370,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","status":"public","keyword":["Multidisciplinary"],"type":"journal_article","article_type":"original","_id":"8680","department":[{"_id":"CaHe"}],"date_updated":"2023-08-22T10:36:35Z","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"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.).","doi":"10.1126/science.aba6637","date_published":"2020-10-02T00:00:00Z","date_created":"2020-10-19T14:09:38Z","page":"113-116","day":"02","publication":"Science","isi":1,"year":"2020","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","author":[{"first_name":"Tony Y.-C.","last_name":"Tsai","full_name":"Tsai, Tony Y.-C."},{"first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"full_name":"Xia, Peng","orcid":"0000-0002-5419-7756","last_name":"Xia","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","first_name":"Peng"},{"first_name":"Tugba","full_name":"Colak-Champollion, Tugba","last_name":"Colak-Champollion"},{"full_name":"Knaut, Holger","last_name":"Knaut","first_name":"Holger"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Megason","full_name":"Megason, Sean G.","first_name":"Sean G."}],"article_processing_charge":"No","external_id":{"isi":["000579169000053"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","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.","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."}},{"citation":{"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.","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.","short":"S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000579693500004"],"pmid":["33077914"]},"article_processing_charge":"No","author":[{"first_name":"Silvia","last_name":" Galan","full_name":" Galan, Silvia"},{"first_name":"Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","last_name":"Machnik","full_name":"Machnik, Nick N","orcid":"0000-0001-6617-9742"},{"first_name":"Kai","last_name":"Kruse","full_name":"Kruse, Kai"},{"first_name":"Noelia","full_name":"Díaz, Noelia","last_name":"Díaz"},{"last_name":"Marti-Renom","full_name":"Marti-Renom, Marc A","first_name":"Marc A"},{"last_name":"Vaquerizas","full_name":"Vaquerizas, Juan M","first_name":"Juan M"}],"title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","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.","quality_controlled":"1","publisher":"Springer Nature","year":"2020","isi":1,"publication":"Nature Genetics","day":"19","page":"1247-1255","date_created":"2020-10-25T23:01:20Z","doi":"10.1038/s41588-020-00712-y","date_published":"2020-10-19T00:00:00Z","_id":"8707","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-22T10:37:10Z","department":[{"_id":"FyKo"}],"abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"None","scopus_import":"1","intvolume":" 52","month":"10","publication_status":"published","publication_identifier":{"issn":["10614036"],"eissn":["15461718"]},"language":[{"iso":"eng"}],"volume":52},{"oa_version":"None","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"}],"intvolume":" 2","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2522-5839"]},"volume":2,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-deep-learning-models/"}]},"_id":"8679","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-22T10:36:06Z","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature Machine Intelligence","day":"01","year":"2020","isi":1,"date_created":"2020-10-19T13:46:06Z","date_published":"2020-10-01T00:00:00Z","doi":"10.1038/s42256-020-00237-3","page":"642-652","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 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","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","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.","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."},"title":"Neural circuit policies enabling auditable autonomy","external_id":{"isi":["000583337200011"]},"article_processing_charge":"No","author":[{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ramin","full_name":"Hasani, Ramin","last_name":"Hasani"},{"first_name":"Alexander","full_name":"Amini, Alexander","last_name":"Amini"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"},{"first_name":"Radu","full_name":"Grosu, Radu","last_name":"Grosu"}]},{"department":[{"_id":"JaMa"}],"date_updated":"2023-08-22T10:32:29Z","status":"public","type":"journal_article","article_type":"original","_id":"8670","ec_funded":1,"issue":"10","volume":61,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00222488"]},"intvolume":" 61","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/2007.06644","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","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"}],"title":"Equality conditions of data processing inequality for α-z Rényi relative entropies","external_id":{"arxiv":["2007.06644"],"isi":["000578529200001"]},"article_processing_charge":"No","author":[{"last_name":"Zhang","full_name":"Zhang, Haonan","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","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","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","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.","ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201.","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."},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"102201","date_created":"2020-10-18T22:01:36Z","doi":"10.1063/5.0022787","date_published":"2020-10-01T00:00:00Z","publication":"Journal of Mathematical Physics","day":"01","year":"2020","isi":1,"oa":1,"quality_controlled":"1","publisher":"AIP Publishing","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."},{"citation":{"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.","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.","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.","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Ori","full_name":"Maoz, Ori","last_name":"Maoz"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"first_name":"Mohamad Saleh","full_name":"Esteki, Mohamad Saleh","last_name":"Esteki"},{"last_name":"Kiani","full_name":"Kiani, Roozbeh","first_name":"Roozbeh"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"}],"article_processing_charge":"No","external_id":{"pmid":["32948691"],"isi":["000579045200012"]},"title":"Learning probabilistic neural representations with randomly connected circuits","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.).","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"06","publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"25066-25073","doi":"10.1073/pnas.1912804117","date_published":"2020-10-06T00:00:00Z","date_created":"2020-10-25T23:01:16Z","_id":"8698","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","date_updated":"2023-08-22T12:11:23Z","ddc":["570"],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-10-27T14:57:50Z","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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 117","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"publication_status":"published","file":[{"file_name":"2020_PNAS_Maoz.pdf","date_created":"2020-10-27T14:57:50Z","file_size":1755359,"date_updated":"2020-10-27T14:57:50Z","creator":"cziletti","success":1,"checksum":"c6a24fdecf3f28faf447078e7a274a88","file_id":"8713","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":117,"issue":"40","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"author":[{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"article_processing_charge":"No","external_id":{"isi":["000712319503110"]},"title":"Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme","citation":{"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.","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","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","short":"M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"IEEE","quality_controlled":"1","oa":1,"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.","page":"5446-5452","date_published":"2020-05-01T00:00:00Z","doi":"10.1109/ICRA40945.2020.9196608","date_created":"2020-10-25T23:01:19Z","isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Proceedings - IEEE International Conference on Robotics and Automation","type":"conference","conference":{"name":"ICRA: International Conference on Robotics and Automation","start_date":"2020-05-31","end_date":"2020-08-31","location":"Paris, France"},"status":"public","_id":"8704","file_date_updated":"2020-11-06T10:58:49Z","department":[{"_id":"ToHe"}],"date_updated":"2023-08-22T10:40:15Z","ddc":["000"],"alternative_title":["ICRA"],"scopus_import":"1","month":"05","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"}],"oa_version":"Submitted Version","publication_identifier":{"issn":["10504729"],"isbn":["9781728173955"]},"publication_status":"published","file":[{"creator":"dernst","file_size":1070010,"date_updated":"2020-11-06T10:58:49Z","file_name":"2020_ICRA_Lechner.pdf","date_created":"2020-11-06T10:58:49Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8733","checksum":"fccf7b986ac78046918a298cc6849a50"}],"language":[{"iso":"eng"}]},{"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.","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.","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.","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","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","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Sokolova","full_name":"Sokolova, E. E.","first_name":"E. E."},{"last_name":"Vlasov","full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"full_name":"Egorova, T. V.","last_name":"Egorova","first_name":"T. V."},{"last_name":"Shuvalov","full_name":"Shuvalov, A. V.","first_name":"A. V."},{"last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z.","first_name":"E. Z."}],"article_processing_charge":"No","external_id":{"isi":["000579441200009"]},"title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","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.","publisher":"Springer Nature","quality_controlled":"1","isi":1,"year":"2020","day":"01","publication":"Molecular Biology","page":"739-748","doi":"10.1134/S0026893320050088","date_published":"2020-09-01T00:00:00Z","date_created":"2020-10-25T23:01:17Z","_id":"8700","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-22T10:39:38Z","department":[{"_id":"FyKo"}],"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."}],"oa_version":"None","scopus_import":"1","month":"09","intvolume":" 54","publication_identifier":{"eissn":["16083245"],"issn":["00268933"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"5","related_material":{"record":[{"relation":"original","status":"public","id":"8701"}]},"volume":54},{"title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","author":[{"full_name":"Sokolova, E. E.","last_name":"Sokolova","first_name":"E. E."},{"first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","full_name":"Vlasov, Petr","last_name":"Vlasov"},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"first_name":"A. V.","full_name":"Shuvalov, A. V.","last_name":"Shuvalov"},{"first_name":"E. Z.","last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z."}],"article_processing_charge":"No","external_id":{"pmid":["33009793"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","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","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","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848.","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.","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.","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.","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."},"publisher":"Russian Academy of Sciences","quality_controlled":"1","doi":"10.31857/S0026898420050080","date_published":"2020-09-01T00:00:00Z","date_created":"2020-10-25T23:01:17Z","page":"837-848","day":"01","publication":"Molekuliarnaia biologiia","year":"2020","status":"public","article_type":"original","type":"journal_article","_id":"8701","department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T10:39:37Z","month":"09","intvolume":" 54","scopus_import":"1","pmid":1,"oa_version":"None","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."}],"volume":54,"issue":"5","related_material":{"record":[{"status":"public","id":"8700","relation":"translation"}]},"language":[{"iso":"rus"}],"publication_identifier":{"issn":["00268984"]},"publication_status":"published"},{"title":"Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics","author":[{"first_name":"Jamie A. P. Law-Smith","last_name":"Jamie A. P. Law-Smith","full_name":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith"},{"first_name":"Rosa Wallace","full_name":"Everson, Rosa Wallace","last_name":"Everson"},{"last_name":"Enrico Ramirez-Ruiz","full_name":"Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz","first_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"},{"orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"full_name":"Zellmann, Stefan","last_name":"Zellmann","first_name":"Stefan"},{"first_name":"Alejandro Vigna-Gómez","full_name":"Alejandro Vigna-Gómez, Alejandro Vigna-Gómez","last_name":"Alejandro Vigna-Gómez"},{"first_name":"Mathieu","last_name":"Renzo","full_name":"Renzo, Mathieu"},{"first_name":"Samantha","last_name":"Wu","full_name":"Wu, Samantha"},{"first_name":"Sophie L.","last_name":"Schrøder","full_name":"Schrøder, Sophie L."},{"first_name":"Ryan J.","last_name":"Foley","full_name":"Foley, Ryan J."},{"first_name":"Tenley Hutchinson-Smith","last_name":"Tenley Hutchinson-Smith","full_name":"Tenley Hutchinson-Smith, Tenley Hutchinson-Smith"}],"external_id":{"arxiv":["2011.06630"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-22T11:03:00Z","citation":{"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.","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.","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.","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","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.).","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. ."},"status":"public","type":"preprint","article_number":"2011.06630","_id":"14096","doi":"10.48550/arXiv.2011.06630","date_published":"2020-11-12T00:00:00Z","date_created":"2023-08-21T10:10:41Z","day":"12","publication":"arXiv","language":[{"iso":"eng"}],"publication_status":"submitted","year":"2020","month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2011.06630"}],"oa_version":"Preprint","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."}]}]