[{"article_processing_charge":"No","has_accepted_license":"1","day":"17","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"date_published":"2021-11-17T00:00:00Z","citation":{"apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575","ieee":"M. J. Conde-Dusman et al., “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife, vol. 10. eLife Sciences Publications, 2021.","ista":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575.","ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 2021;10. doi:10.7554/elife.71575","chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575.","short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).","mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife, vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575."},"publication":"eLife","article_type":"original","abstract":[{"text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement.","lang":"eng"}],"type":"journal_article","file":[{"file_size":2477302,"content_type":"application/pdf","creator":"lgarciar","file_name":"elife-71575-v1.pdf","access_level":"open_access","date_created":"2021-11-18T07:02:02Z","date_updated":"2021-11-18T07:02:02Z","checksum":"59318e9e41507cec83c2f4070e6ad540","success":1,"relation":"main_file","file_id":"10302"}],"oa_version":"Published Version","_id":"10301","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 10","ddc":["570"],"status":"public","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","publication_identifier":{"issn":["2050-084X"]},"month":"11","doi":"10.7554/elife.71575","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000720945900001"]},"isi":1,"quality_controlled":"1","file_date_updated":"2021-11-18T07:02:02Z","article_number":"e71575","author":[{"last_name":"Conde-Dusman","first_name":"María J","full_name":"Conde-Dusman, María J"},{"full_name":"Dey, Partha N","first_name":"Partha N","last_name":"Dey"},{"first_name":"Óscar","last_name":"Elía-Zudaire","full_name":"Elía-Zudaire, Óscar"},{"id":"33D1B084-F248-11E8-B48F-1D18A9856A87","last_name":"Garcia Rabaneda","first_name":"Luis E","full_name":"Garcia Rabaneda, Luis E"},{"full_name":"García-Lira, Carmen","first_name":"Carmen","last_name":"García-Lira"},{"full_name":"Grand, Teddy","last_name":"Grand","first_name":"Teddy"},{"full_name":"Briz, Victor","first_name":"Victor","last_name":"Briz"},{"first_name":"Eric R","last_name":"Velasco","full_name":"Velasco, Eric R"},{"full_name":"Andero Galí, Raül","first_name":"Raül","last_name":"Andero Galí"},{"first_name":"Sergio","last_name":"Niñerola","full_name":"Niñerola, Sergio"},{"full_name":"Barco, Angel","first_name":"Angel","last_name":"Barco"},{"last_name":"Paoletti","first_name":"Pierre","full_name":"Paoletti, Pierre"},{"first_name":"John F","last_name":"Wesseling","full_name":"Wesseling, John F"},{"full_name":"Gardoni, Fabrizio","last_name":"Gardoni","first_name":"Fabrizio"},{"full_name":"Tavalin, Steven J","first_name":"Steven J","last_name":"Tavalin"},{"full_name":"Perez-Otaño, Isabel","first_name":"Isabel","last_name":"Perez-Otaño"}],"volume":10,"date_created":"2021-11-18T06:59:45Z","date_updated":"2023-08-14T11:50:50Z","year":"2021","acknowledgement":"We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723).","publisher":"eLife Sciences Publications","department":[{"_id":"GaNo"}],"publication_status":"published"},{"author":[{"last_name":"Restivo","first_name":"Leonardo","full_name":"Restivo, Leonardo"},{"full_name":"Gerlach, Björn","first_name":"Björn","last_name":"Gerlach"},{"full_name":"Tsoory, Michael","first_name":"Michael","last_name":"Tsoory"},{"first_name":"Lior","last_name":"Bikovski","full_name":"Bikovski, Lior"},{"full_name":"Badurek, Sylvia","last_name":"Badurek","first_name":"Sylvia"},{"last_name":"Pitzer","first_name":"Claudia","full_name":"Pitzer, Claudia"},{"last_name":"Kos-Braun","first_name":"Isabelle C.","full_name":"Kos-Braun, Isabelle C."},{"last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj","full_name":"Mausset-Bonnefont, Anne Laure Mj"},{"last_name":"Ward","first_name":"Jonathan","full_name":"Ward, Jonathan"},{"full_name":"Schunn, Michael","first_name":"Michael","last_name":"Schunn","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300"},{"first_name":"Lucas P.J.J.","last_name":"Noldus","full_name":"Noldus, Lucas P.J.J."},{"first_name":"Anton","last_name":"Bespalov","full_name":"Bespalov, Anton"},{"full_name":"Voikar, Vootele","last_name":"Voikar","first_name":"Vootele"}],"volume":22,"date_updated":"2023-08-14T11:47:35Z","date_created":"2021-11-14T23:01:24Z","acknowledgement":"This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","year":"2021","publisher":"EMBO Press","department":[{"_id":"PreCl"}],"publication_status":"published","file_date_updated":"2022-05-16T07:07:41Z","article_number":"e53824","doi":"10.15252/embr.202153824","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000714350000001"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"month":"11","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_EmboReports_Restivo.pdf","file_size":488583,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"11381","checksum":"74743baa6ef431ef60c3de3bc4da045a","success":1,"date_updated":"2022-05-16T07:07:41Z","date_created":"2022-05-16T07:07:41Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10283","intvolume":" 22","status":"public","title":"Towards best practices in research: Role of academic core facilities","ddc":["570"],"abstract":[{"text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.","lang":"eng"}],"type":"journal_article","date_published":"2021-11-04T00:00:00Z","citation":{"ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.","apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824","chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press, 2021. https://doi.org/10.15252/embr.202153824.","mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021)."},"publication":"EMBO Reports","article_type":"original","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"04","scopus_import":"1"},{"article_number":"304","file_date_updated":"2021-11-19T15:09:18Z","publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Springer ","acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","year":"2021","pmid":1,"date_created":"2021-11-19T11:37:29Z","date_updated":"2023-08-14T11:51:19Z","volume":4,"author":[{"id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","orcid":"0000-0002-3219-2022","first_name":"Mehmet Orkun","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun"},{"full_name":"Frank, Anna","last_name":"Frank","first_name":"Anna"},{"full_name":"Tanaka, Hideaki","last_name":"Tanaka","first_name":"Hideaki"},{"last_name":"Kawamoto","first_name":"Akihiro","full_name":"Kawamoto, Akihiro"},{"full_name":"El-Mohsnawy, Eithar","last_name":"El-Mohsnawy","first_name":"Eithar"},{"full_name":"Kato, Takayuki","last_name":"Kato","first_name":"Takayuki"},{"last_name":"Namba","first_name":"Keiichi","full_name":"Namba, Keiichi"},{"last_name":"Gerle","first_name":"Christoph","full_name":"Gerle, Christoph"},{"first_name":"Marc M.","last_name":"Nowaczyk","full_name":"Nowaczyk, Marc M."},{"last_name":"Kurisu","first_name":"Genji","full_name":"Kurisu, Genji"}],"month":"03","publication_identifier":{"issn":["2399-3642"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["33686186"],"isi":["000627440700001"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42003-021-01808-9","type":"journal_article","abstract":[{"text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700.","lang":"eng"}],"issue":"1","ddc":["570"],"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","status":"public","intvolume":" 4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10310","file":[{"file_name":"2021_CommBio_Çoruh.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6030261,"creator":"cchlebak","relation":"main_file","file_id":"10318","date_created":"2021-11-19T15:09:18Z","date_updated":"2021-11-19T15:09:18Z","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1}],"oa_version":"Published Version","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Communications Biology","citation":{"ieee":"M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications Biology, vol. 4, no. 1. Springer , 2021.","apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9","ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304.","ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9","chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9.","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9."},"date_published":"2021-03-08T00:00:00Z"},{"type":"journal_article","abstract":[{"text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10270","intvolume":" 10","ddc":["570"],"status":"public","title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","file":[{"file_id":"11372","relation":"main_file","date_created":"2022-05-13T09:00:29Z","date_updated":"2022-05-13T09:00:29Z","success":1,"checksum":"fad13c509b53bb7a2bef9c946a7ca60a","file_name":"2021_eLife_Marconi.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":14137503}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","citation":{"chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72132.","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife, vol. 10, 72132, eLife Sciences Publications, 2021, doi:10.7554/elife.72132.","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72132","ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132.","ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132"},"publication":"eLife","article_type":"original","date_published":"2021-11-01T00:00:00Z","article_number":"72132","file_date_updated":"2022-05-13T09:00:29Z","pmid":1,"year":"2021","acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","department":[{"_id":"EvBe"}],"publisher":"eLife Sciences Publications","publication_status":"published","author":[{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi","first_name":"Marçal"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"},{"last_name":"Wabnik","first_name":"Krzysztof","full_name":"Wabnik, Krzysztof"}],"volume":10,"date_created":"2021-11-11T10:05:18Z","date_updated":"2023-08-14T11:49:23Z","publication_identifier":{"issn":["2050-084X"]},"month":"11","external_id":{"isi":["000734671200001"],"pmid":["34723798"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.7554/elife.72132","language":[{"iso":"eng"}]},{"article_number":"e2102350118","author":[{"full_name":"Choueiri, George H","last_name":"Choueiri","first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jose M","last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M"},{"full_name":"Varshney, Atul","last_name":"Varshney","first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sankar, Sarath","first_name":"Sarath","last_name":"Sankar"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"date_created":"2021-11-17T13:24:24Z","date_updated":"2023-08-14T11:50:10Z","volume":118,"acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"National Academy of Sciences","month":"11","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.2102350118","language":[{"iso":"eng"}],"external_id":{"pmid":[" 34732570"],"isi":["000720926900019"],"arxiv":["2103.00023"]},"main_file_link":[{"url":"https://arxiv.org/abs/2103.00023","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188"}],"abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"issue":"45","type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10299","status":"public","title":"Experimental observation of the origin and structure of elastoinertial turbulence","intvolume":" 118","day":"03","article_processing_charge":"No","scopus_import":"1","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"date_published":"2021-11-03T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118.","ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” Proceedings of the National Academy of Sciences, vol. 118, no. 45. National Academy of Sciences, 2021.","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 118(45), e2102350118."},"article_type":"original"},{"_id":"10280","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["530"],"title":"Metamachines of pluripotent colloids","intvolume":" 12","file":[{"access_level":"open_access","file_name":"2021_NatComm_Aubret.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":6282703,"file_id":"10292","relation":"main_file","success":1,"checksum":"1c392b12b9b7b615d422d9fabe19cdb9","date_updated":"2021-11-15T13:25:52Z","date_created":"2021-11-15T13:25:52Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials.","lang":"eng"}],"issue":"1","publication":"Nature Communications","citation":{"ama":"Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6","apa":"Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","mla":"Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” Nature Communications, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:10.1038/s41467-021-26699-6.","chicago":"Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26699-6."},"article_type":"original","date_published":"2021-11-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"Yes","has_accepted_license":"1","year":"2021","acknowledgement":"The authors thank R. Jazzar for useful advice regarding the synthesis of heterodimers. We thank S. Sacanna for critical reading. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1554724 and Department of Army Research under grant W911NF-20-1-0112.","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JePa"}],"author":[{"first_name":"Antoine","last_name":"Aubret","full_name":"Aubret, Antoine"},{"full_name":"Martinet, Quentin","last_name":"Martinet","first_name":"Quentin","orcid":"0000-0002-2916-6632","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab"},{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","last_name":"Palacci"}],"date_updated":"2023-08-14T11:48:37Z","date_created":"2021-11-14T23:01:23Z","volume":12,"article_number":"6398","file_date_updated":"2021-11-15T13:25:52Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000714754400010"],"pmid":["34737315"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-021-26699-6","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"eissn":["2041-1723"]}},{"type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal."}],"intvolume":" 19","ddc":["570"],"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10322","file":[{"access_level":"open_access","file_name":"2021_PLoSBio_Chauve.pdf","creator":"cchlebak","file_size":4069215,"content_type":"application/pdf","file_id":"10330","relation":"main_file","success":1,"checksum":"0c61b667f814fd9435b3ac42036fc36d","date_created":"2021-11-22T09:34:03Z","date_updated":"2021-11-22T09:34:03Z"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","article_type":"original","citation":{"ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 2021;19(11). doi:10.1371/journal.pbio.3001431","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans,” PLoS Biology, vol. 19, no. 11. Public Library of Science, 2021.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H. J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001431","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 19(11), e3001431.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, PLoS Biology 19 (2021).","mla":"Chauve, Laetitia, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology, vol. 19, no. 11, e3001431, Public Library of Science, 2021, doi:10.1371/journal.pbio.3001431.","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pbio.3001431."},"publication":"PLoS Biology","date_published":"2021-11-01T00:00:00Z","article_number":"e3001431","file_date_updated":"2021-11-22T09:34:03Z","publisher":"Public Library of Science","department":[{"_id":"MaDe"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We dedicate this work to the memory of Michael J.O. Wakelam. We would like to acknowledge Michael Fasseas (Invermis, Magnitude Biosciences) for plasmid injections and Sunny Biotech for transgenics; Catalina Vallejos and John Marioni for statistical advice at the beginning of the work; Simon Walker, Imaging, Bioinformatics and Lipidomics Facilities at Babraham Institute for technical support; and Cindy Voisine, Michael Witting, Jon Houseley, Len Stephens, Carmen Nussbaum Krammer, Rebeca Aldunate, Patricija van Oosten-Hawle, Jean-Louis Bessereau, and Jane Alfred for feedback on the manuscript. We thank Andy Dillin, Atsushi Kuhara, Amy Walker, Andrew Leifer, Yun Zhang, and Michalis Barkoulas for reagents and Julie Ahringer, Anne Ferguson-Smith, and Anne Corcoran for support and helpful discussions. We also acknowledge Babraham Institute Facilities.","volume":19,"date_created":"2021-11-21T23:01:28Z","date_updated":"2023-08-14T11:53:27Z","related_material":{"record":[{"id":"13069","status":"public","relation":"research_data"}]},"author":[{"last_name":"Chauve","first_name":"Laetitia","full_name":"Chauve, Laetitia"},{"first_name":"Francesca","last_name":"Hodge","full_name":"Hodge, Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"last_name":"Masoudzadeh","first_name":"Fatemah","full_name":"Masoudzadeh, Fatemah"},{"first_name":"Harry Jack","last_name":"Mann","full_name":"Mann, Harry Jack"},{"full_name":"Lopez-Clavijo, Andrea","first_name":"Andrea","last_name":"Lopez-Clavijo"},{"full_name":"Okkenhaug, Hanneke","last_name":"Okkenhaug","first_name":"Hanneke"},{"last_name":"West","first_name":"Greg","full_name":"West, Greg"},{"first_name":"Bebiana C.","last_name":"Sousa","full_name":"Sousa, Bebiana C."},{"first_name":"Anne","last_name":"Segonds-Pichon","full_name":"Segonds-Pichon, Anne"},{"first_name":"Cheryl","last_name":"Li","full_name":"Li, Cheryl"},{"last_name":"Wingett","first_name":"Steven","full_name":"Wingett, Steven"},{"full_name":"Kienberger, Hermine","last_name":"Kienberger","first_name":"Hermine"},{"full_name":"Kleigrewe, Karin","last_name":"Kleigrewe","first_name":"Karin"},{"full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","first_name":"Mario"},{"last_name":"Wakelam","first_name":"Michael","full_name":"Wakelam, Michael"},{"full_name":"Casanueva, Olivia","last_name":"Casanueva","first_name":"Olivia"}],"publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"month":"11","quality_controlled":"1","isi":1,"external_id":{"pmid":["34723964"],"isi":["000715818400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.3001431"},{"publication_identifier":{"issn":["1058-6458"],"eissn":["1944-950X"]},"month":"10","doi":"10.1080/10586458.2021.1980459","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000710893500001"],"arxiv":["2007.07783"]},"project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"Discretization in Geometry and Dynamics","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-08-14T11:55:10Z","author":[{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","first_name":"Anton"}],"date_created":"2021-11-07T23:01:25Z","date_updated":"2023-08-14T11:57:07Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and for directing us to relevant references. We also thank to Anton Mellit for a useful discussion on Bessel functions.","year":"2021","publisher":"Taylor and Francis","department":[{"_id":"HeEd"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"25","scopus_import":"1","date_published":"2021-10-25T00:00:00Z","citation":{"ieee":"A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis, pp. 1–15, 2021.","apa":"Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2021.1980459","ista":"Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics., 1–15.","ama":"Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459","chicago":"Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics. Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459.","short":"A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021) 1–15.","mla":"Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459."},"publication":"Experimental Mathematics","page":"1-15","article_type":"original","abstract":[{"lang":"eng","text":"Consider a random set of points on the unit sphere in ℝd, which can be either uniformly sampled or a Poisson point process. Its convex hull is a random inscribed polytope, whose boundary approximates the sphere. We focus on the case d = 3, for which there are elementary proofs and fascinating formulas for metric properties. In particular, we study the fraction of acute facets, the expected intrinsic volumes, the total edge length, and the distance to a fixed point. Finally we generalize the results to the ellipsoid with homeoid density."}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"3514382e3a1eb87fa6c61ad622874415","date_created":"2023-08-14T11:55:10Z","date_updated":"2023-08-14T11:55:10Z","file_id":"14053","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1966019,"access_level":"open_access","file_name":"2023_ExperimentalMath_Akopyan.pdf"}],"_id":"10222","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["510"],"title":"The beauty of random polytopes inscribed in the 2-sphere"},{"year":"2021","acknowledgement":"We thank Juan C. Fontecilla-Camps for insightful discussions related to ATP-driven machineries, and Elif Karagöz for providing the structural model of the Hsp90-Tau complex. This study was supported by the European Research Council (StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp).","pmid":1,"publication_status":"published","publisher":"Frontiers","department":[{"_id":"PaSc"}],"author":[{"first_name":"Iva","last_name":"Sučec","full_name":"Sučec, Iva"},{"last_name":"Bersch","first_name":"Beate","full_name":"Bersch, Beate"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"}],"date_created":"2021-11-21T23:01:29Z","date_updated":"2023-08-14T11:55:04Z","volume":8,"article_number":"762005","file_date_updated":"2021-11-23T15:06:58Z","external_id":{"isi":["000717241700001"],"pmid":["34760928"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.3389/fmolb.2021.762005","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["2296-889X"]},"_id":"10323","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"How do chaperones bind (partly) unfolded client proteins?","status":"public","ddc":["547"],"intvolume":" 8","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":4700798,"access_level":"open_access","file_name":"2021_FrontiersMolBioSc_Sučec.pdf","success":1,"checksum":"a5c9dbf80dc2c5aaa737f456c941d964","date_created":"2021-11-23T15:06:58Z","date_updated":"2021-11-23T15:06:58Z","file_id":"10333","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity."}],"publication":"Frontiers in Molecular Biosciences","citation":{"chicago":"Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences. Frontiers, 2021. https://doi.org/10.3389/fmolb.2021.762005.","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021).","mla":"Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences, vol. 8, 762005, Frontiers, 2021, doi:10.3389/fmolb.2021.762005.","ieee":"I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021.","apa":"Sučec, I., Bersch, B., & Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. Frontiers. https://doi.org/10.3389/fmolb.2021.762005","ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005.","ama":"Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 2021;8. doi:10.3389/fmolb.2021.762005"},"article_type":"original","date_published":"2021-10-25T00:00:00Z","scopus_import":"1","day":"25","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"department":[{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).","year":"2021","volume":7,"date_created":"2021-11-21T23:01:30Z","date_updated":"2023-08-14T11:54:02Z","author":[{"first_name":"Enjun","last_name":"Xu","full_name":"Xu, Enjun"},{"last_name":"Chai","first_name":"Liang","full_name":"Chai, Liang"},{"full_name":"Zhang, Shiqi","last_name":"Zhang","first_name":"Shiqi"},{"full_name":"Yu, Ruixue","first_name":"Ruixue","last_name":"Yu"},{"orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","first_name":"Xixi","full_name":"Zhang, Xixi"},{"first_name":"Chongyi","last_name":"Xu","full_name":"Xu, Chongyi"},{"last_name":"Hu","first_name":"Yuxin","full_name":"Hu, Yuxin"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41477-021-01011-y","publication_identifier":{"eissn":["2055-0278"]},"month":"11","intvolume":" 7","title":"Catabolism of strigolactones by a carboxylesterase","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10326","oa_version":"None","type":"journal_article","abstract":[{"text":"Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants.","lang":"eng"}],"page":"1495–1504 ","article_type":"original","citation":{"apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-021-01011-y","ieee":"E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,” Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021.","ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y","chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y.","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y."},"publication":"Nature Plants","date_published":"2021-11-11T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"11"},{"month":"12","day":"25","article_processing_charge":"No","doi":"10.5281/ZENODO.5519410","date_published":"2021-12-25T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"mla":"Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans. Zenodo, 2021, doi:10.5281/ZENODO.5519410.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410.","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. 2021. doi:10.5281/ZENODO.5519410","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans, Zenodo, 10.5281/ZENODO.5519410.","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans.” Zenodo, 2021.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. Zenodo. https://doi.org/10.5281/ZENODO.5519410"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5547464"}],"abstract":[{"text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.","lang":"eng"}],"type":"research_data_reference","date_updated":"2023-08-14T11:53:26Z","date_created":"2023-05-23T16:40:56Z","oa_version":"Published Version","author":[{"full_name":"Chauve, Laetitia","last_name":"Chauve","first_name":"Laetitia"},{"last_name":"Hodge","first_name":"Francesca","full_name":"Hodge, Francesca"},{"full_name":"Murdoch, Sharlene","first_name":"Sharlene","last_name":"Murdoch"},{"full_name":"Masoudzadeh, Fatemah","first_name":"Fatemah","last_name":"Masoudzadeh"},{"full_name":"Mann, Harry-Jack","first_name":"Harry-Jack","last_name":"Mann"},{"full_name":"Lopez-Clavijo, Andrea","first_name":"Andrea","last_name":"Lopez-Clavijo"},{"first_name":"Hanneke","last_name":"Okkenhaug","full_name":"Okkenhaug, Hanneke"},{"last_name":"West","first_name":"Greg","full_name":"West, Greg"},{"last_name":"Sousa","first_name":"Bebiana C.","full_name":"Sousa, Bebiana C."},{"last_name":"Segonds-Pichon","first_name":"Anne","full_name":"Segonds-Pichon, Anne"},{"full_name":"Li, Cheryl","last_name":"Li","first_name":"Cheryl"},{"full_name":"Wingett, Steven","last_name":"Wingett","first_name":"Steven"},{"last_name":"Kienberger","first_name":"Hermine","full_name":"Kienberger, Hermine"},{"full_name":"Kleigrewe, Karin","first_name":"Karin","last_name":"Kleigrewe"},{"full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Wakelam","full_name":"Wakelam, Michael"},{"last_name":"Casanueva","first_name":"Olivia","full_name":"Casanueva, Olivia"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10322"}]},"status":"public","title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","ddc":["570"],"department":[{"_id":"MaDe"}],"publisher":"Zenodo","year":"2021","_id":"13069","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"page":"3-36","publication":"25th International Conference on Financial Cryptography and Data Security","citation":{"chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” In 25th International Conference on Financial Cryptography and Data Security, 12675:3–36. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_1.","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 3–36.","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 3–36, doi:10.1007/978-3-662-64331-0_1.","ieee":"A. Zamyatin et al., “SoK: Communication across distributed ledgers,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 3–36.","apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (2021). SoK: Communication across distributed ledgers. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 3–36). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_1","ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. 2021. SoK: Communication across distributed ledgers. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 3–36.","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:3-36. doi:10.1007/978-3-662-64331-0_1"},"date_published":"2021-10-23T00:00:00Z","scopus_import":"1","day":"23","article_processing_charge":"No","title":"SoK: Communication across distributed ledgers","status":"public","_id":"10325","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Since the inception of Bitcoin, a plethora of distributed ledgers differing in design and purpose has been created. While by design, blockchains provide no means to securely communicate with external systems, numerous attempts towards trustless cross-chain communication have been proposed over the years. Today, cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges, scalability efforts via sharding, extension of existing systems through sidechains, and bootstrapping of new blockchains. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence in their correctness and composability. We provide the first systematic exposition of cross-chain communication protocols. We formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. With this result in mind, we develop a framework to design new and evaluate existing CCC protocols, focusing on the inherent trust assumptions thereof, and derive a classification covering the field of cross-chain communication to date. We conclude by discussing open challenges for CCC research and the implications of interoperability on the security and privacy of blockchains."}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000712016200001"]},"main_file_link":[{"url":"https://eprint.iacr.org/2019/1128","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"name":"FC: Financial Cryptography","start_date":"2021-03-01","location":"Virtual","end_date":"2021-03-05"},"doi":"10.1007/978-3-662-64331-0_1","month":"10","publication_identifier":{"isbn":["9-783-6626-4330-3"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-662-64331-0"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ElKo"}],"year":"2021","acknowledgement":"We would like express our gratitude to Georgia Avarikioti, Daniel Perez and Dominik Harz for helpful comments and feedback on earlier versions of this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler, Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages of this research. We also wish to thank the anonymous reviewers for their valuable comments that helped improve the presentation of our results. This research was funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian Doppler Laboratory for Security and Quality Improvement in the Production System Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs through the project SLN: Scalability for the Lightning Network; and by the Austrian Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted the early stages of this work during his time at SBA Research, and was supported by a Binance Research Fellowship.","date_created":"2021-11-21T23:01:29Z","date_updated":"2023-08-14T12:59:26Z","volume":"12675 ","author":[{"full_name":"Zamyatin, Alexei","first_name":"Alexei","last_name":"Zamyatin"},{"full_name":"Al-Bassam, Mustafa","last_name":"Al-Bassam","first_name":"Mustafa"},{"full_name":"Zindros, Dionysis","last_name":"Zindros","first_name":"Dionysis"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios"},{"first_name":"Pedro","last_name":"Moreno-Sanchez","full_name":"Moreno-Sanchez, Pedro"},{"last_name":"Kiayias","first_name":"Aggelos","full_name":"Kiayias, Aggelos"},{"last_name":"Knottenbelt","first_name":"William J.","full_name":"Knottenbelt, William J."}]},{"publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-662-64331-0"],"eissn":["1611-3349"],"isbn":["9-783-6626-4330-3"]},"month":"10","doi":"10.1007/978-3-662-64331-0_11","conference":{"end_date":"2021-03-05","start_date":"2021-03-01","location":"Virtual","name":"FC: Financial Cryptography"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.11360"}],"oa":1,"external_id":{"arxiv":["1905.11360"],"isi":["000712016200011"]},"isi":1,"quality_controlled":"1","author":[{"full_name":"Avarikioti, Zeta","last_name":"Avarikioti","first_name":"Zeta"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"full_name":"Wattenhofer, Roger","last_name":"Wattenhofer","first_name":"Roger"},{"first_name":"Dionysis","last_name":"Zindros","full_name":"Zindros, Dionysis"}],"volume":"12675 ","date_updated":"2023-08-14T12:59:58Z","date_created":"2021-11-21T23:01:29Z","acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","year":"2021","department":[{"_id":"ElKo"}],"publisher":"Springer Nature","publication_status":"published","article_processing_charge":"No","day":"23","scopus_import":"1","date_published":"2021-10-23T00:00:00Z","citation":{"ista":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. 2021. Brick: Asynchronous incentive-compatible payment channels. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 209–230.","apa":"Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (2021). Brick: Asynchronous incentive-compatible payment channels. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 209–230). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_11","ieee":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous incentive-compatible payment channels,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 209–230.","ama":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous incentive-compatible payment channels. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:209-230. doi:10.1007/978-3-662-64331-0_11","chicago":"Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In 25th International Conference on Financial Cryptography and Data Security, 12675:209–30. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_11.","mla":"Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment Channels.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:10.1007/978-3-662-64331-0_11.","short":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 209–230."},"publication":"25th International Conference on Financial Cryptography and Data Security","page":"209-230","abstract":[{"text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"10324","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Brick: Asynchronous incentive-compatible payment channels","status":"public"},{"publication_identifier":{"eissn":["1741-0134"],"issn":["1741-0126"]},"month":"11","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/protein/gzab025"}],"external_id":{"pmid":["34725710"],"isi":["000746596900001"]},"language":[{"iso":"eng"}],"doi":"10.1093/protein/gzab025","article_number":"gzab025","department":[{"_id":"CaGu"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support.","volume":34,"date_created":"2021-11-28T23:01:28Z","date_updated":"2023-08-14T13:01:38Z","author":[{"full_name":"Lee, Jungmin","last_name":"Lee","first_name":"Jungmin"},{"full_name":"Vernet, Andyna","first_name":"Andyna","last_name":"Vernet"},{"full_name":"Gruber, Nathalie","last_name":"Gruber","first_name":"Nathalie","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425"},{"full_name":"Kready, Kasia M.","last_name":"Kready","first_name":"Kasia M."},{"first_name":"Devin R.","last_name":"Burrill","full_name":"Burrill, Devin R."},{"full_name":"Way, Jeffrey C.","first_name":"Jeffrey C.","last_name":"Way"},{"last_name":"Silver","first_name":"Pamela A.","full_name":"Silver, Pamela A."}],"scopus_import":"1","article_processing_charge":"No","day":"01","article_type":"original","citation":{"mla":"Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection, vol. 34, gzab025, Oxford University Press, 2021, doi:10.1093/protein/gzab025.","short":"J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021).","chicago":"Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection. Oxford University Press, 2021. https://doi.org/10.1093/protein/gzab025.","ama":"Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 2021;34. doi:10.1093/protein/gzab025","ista":"Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025.","apa":"Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., & Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. Oxford University Press. https://doi.org/10.1093/protein/gzab025","ieee":"J. Lee et al., “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” Protein Engineering, Design and Selection, vol. 34. Oxford University Press, 2021."},"publication":"Protein Engineering, Design and Selection","date_published":"2021-11-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia.","lang":"eng"}],"intvolume":" 34","title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10363","oa_version":"Published Version"},{"citation":{"mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development, vol. 168, no. 12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758.","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758.","ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. 2021;168(12). doi:10.1016/j.cdev.2021.203758","ista":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.","apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” Cells and Development, vol. 168, no. 12. Elsevier, 2021."},"publication":"Cells and Development","article_type":"letter_note","date_published":"2021-11-17T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"17","_id":"10366","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 168","title":"Special rebranding issue: “Quantitative cell and developmental biology”","status":"public","oa_version":"Published Version","type":"journal_article","issue":"12","external_id":{"pmid":["34800748"],"isi":["000974771600028"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cdev.2021.203758","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1016/j.cdev.2021.203758","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2667-2901"]},"month":"11","pmid":1,"year":"2021","department":[{"_id":"CaHe"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"last_name":"Lennon","first_name":"Ana Maria","full_name":"Lennon, Ana Maria"},{"last_name":"Mayor","first_name":"Roberto","full_name":"Mayor, Roberto"},{"full_name":"Salbreux, Guillaume","first_name":"Guillaume","last_name":"Salbreux"}],"volume":168,"date_created":"2021-11-28T23:01:30Z","date_updated":"2023-08-14T13:02:40Z","article_number":"203758"},{"article_number":"6830","ec_funded":1,"file_date_updated":"2021-12-10T08:54:09Z","pmid":1,"year":"2021","acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"record":[{"id":"13058","relation":"research_data","status":"public"}]},"author":[{"full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C"},{"last_name":"Kamenev","first_name":"Dmitrii","full_name":"Kamenev, Dmitrii"},{"full_name":"Sunadome, Kazunori","first_name":"Kazunori","last_name":"Sunadome"},{"first_name":"Dominik C","last_name":"Fachet","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","full_name":"Fachet, Dominik C"},{"full_name":"Lallemend, Francois","last_name":"Lallemend","first_name":"Francois"},{"last_name":"Adameyko","first_name":"Igor","full_name":"Adameyko, Igor"},{"last_name":"Hadjab","first_name":"Saida","full_name":"Hadjab, Saida"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}],"volume":12,"date_created":"2021-12-05T23:01:40Z","date_updated":"2023-08-14T13:18:46Z","publication_identifier":{"eissn":["2041-1723"]},"month":"11","external_id":{"isi":["000722322900020"],"pmid":["34819507"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-021-27135-5","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales."}],"_id":"10402","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","ddc":["573"],"status":"public","title":"Theory of branching morphogenesis by local interactions and global guidance","file":[{"file_id":"10529","relation":"main_file","date_updated":"2021-12-10T08:54:09Z","date_created":"2021-12-10T08:54:09Z","success":1,"checksum":"63c56ec75314a71e63e7dd2920b3c5b5","file_name":"2021_NatComm_Ucar.pdf","access_level":"open_access","creator":"cchlebak","file_size":2303405,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"24","citation":{"ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5","ista":"Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830.","ieee":"M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021.","apa":"Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature, 2021, doi:10.1038/s41467-021-27135-5.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","chicago":"Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5."},"publication":"Nature Communications","article_type":"original","date_published":"2021-11-24T00:00:00Z"},{"volume":13043,"date_updated":"2023-08-14T13:07:46Z","date_created":"2021-12-05T23:01:42Z","author":[{"full_name":"Chakraborty, Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","last_name":"Chakraborty","first_name":"Suvradip"},{"first_name":"Stefan","last_name":"Dziembowski","full_name":"Dziembowski, Stefan"},{"last_name":"Gałązka","first_name":"Małgorzata","full_name":"Gałązka, Małgorzata"},{"full_name":"Lizurej, Tomasz","first_name":"Tomasz","last_name":"Lizurej"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","last_name":"Yeo"}],"department":[{"_id":"KrPi"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-90453-1_14","conference":{"name":"TCC: Theory of Cryptography Conference","location":"Raleigh, NC, United States","start_date":"2021-11-08","end_date":"2021-11-11"},"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000728364000014"]},"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2021/1224","open_access":"1"}],"publication_identifier":{"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"11","oa_version":"Preprint","intvolume":" 13043","status":"public","title":"Trojan-resilience without cryptography","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10407","abstract":[{"text":"Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification F one has more sophisticated circuits F⋄ manufactured (where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to F . Those solutions impose a significant overhead as F⋄ is much more complex than F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where F has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of F need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2021-11-04T00:00:00Z","page":"397-428","citation":{"chicago":"Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14.","short":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428.","mla":"Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14.","ieee":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.","apa":"Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., & Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14","ista":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.","ama":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14"},"article_processing_charge":"No","day":"04","scopus_import":"1"},{"article_number":"e65954","file_date_updated":"2021-12-10T08:31:41Z","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"eLife Sciences Publications","acknowledgement":"This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript.","year":"2021","date_updated":"2023-08-14T13:12:07Z","date_created":"2021-12-05T23:01:40Z","volume":10,"author":[{"full_name":"Biane, Celia","last_name":"Biane","first_name":"Celia"},{"last_name":"Rückerl","first_name":"Florian","full_name":"Rückerl, Florian"},{"last_name":"Abrahamsson","first_name":"Therese","full_name":"Abrahamsson, Therese"},{"full_name":"Saint-Cloment, Cécile","last_name":"Saint-Cloment","first_name":"Cécile"},{"first_name":"Jean","last_name":"Mariani","full_name":"Mariani, Jean"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Digregorio, David A.","first_name":"David A.","last_name":"Digregorio"},{"first_name":"Rachel M.","last_name":"Sherrard","full_name":"Sherrard, Rachel M."},{"first_name":"Laurence","last_name":"Cathala","full_name":"Cathala, Laurence"}],"month":"11","publication_identifier":{"eissn":["2050-084X"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000715789500001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.65954","type":"journal_article","abstract":[{"text":"Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits.","lang":"eng"}],"title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","status":"public","ddc":["570"],"intvolume":" 10","_id":"10403","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_id":"10528","relation":"main_file","success":1,"checksum":"c7c33c3319428d56e332e22349c50ed3","date_updated":"2021-12-10T08:31:41Z","date_created":"2021-12-10T08:31:41Z","access_level":"open_access","file_name":"2021_eLife_Biane.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":13131322}],"scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"eLife","citation":{"chicago":"Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.65954.","mla":"Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife Sciences Publications, 2021, doi:10.7554/eLife.65954.","short":"C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).","ista":"Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954.","apa":"Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.65954","ieee":"C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences Publications, 2021.","ama":"Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10. doi:10.7554/eLife.65954"},"date_published":"2021-11-03T00:00:00Z"},{"volume":4,"date_created":"2021-12-05T23:01:39Z","date_updated":"2023-08-14T13:04:34Z","author":[{"first_name":"Rafael E.","last_name":"Barfknecht","full_name":"Barfknecht, Rafael E."},{"full_name":"Foerster, Angela","last_name":"Foerster","first_name":"Angela"},{"first_name":"Nikolaj T.","last_name":"Zinner","full_name":"Zinner, Nikolaj T."},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem"}],"department":[{"_id":"MiLe"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"The authors acknowledge support from the European QuantERA ERA-NET Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under the Jens Christian Skou fellowship program (N.T.Z).","year":"2021","ec_funded":1,"file_date_updated":"2021-12-06T14:53:41Z","article_number":"252","language":[{"iso":"eng"}],"doi":"10.1038/s42005-021-00753-7","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2101.02020"],"isi":["10.1038/s42005-021-00753-7"]},"publication_identifier":{"eissn":["23993650"]},"month":"11","file":[{"access_level":"open_access","file_name":"2021_NatComm_Barfknecht.pdf","creator":"alisjak","file_size":1068984,"content_type":"application/pdf","file_id":"10420","relation":"main_file","success":1,"checksum":"9097319952cb9a3d96e7fd3aa9813a03","date_created":"2021-12-06T14:53:41Z","date_updated":"2021-12-06T14:53:41Z"}],"oa_version":"Published Version","intvolume":" 4","title":"Generation of spin currents by a temperature gradient in a two-terminal device","status":"public","ddc":["530"],"_id":"10401","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","abstract":[{"lang":"eng","text":"Theoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect."}],"type":"journal_article","date_published":"2021-11-26T00:00:00Z","article_type":"original","citation":{"chicago":"Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7.","short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021).","mla":"Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no. 1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7.","apa":"Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7","ieee":"R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation of spin currents by a temperature gradient in a two-terminal device,” Communications Physics, vol. 4, no. 1. Springer Nature, 2021.","ista":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 4(1), 252.","ama":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 2021;4(1). doi:10.1038/s42005-021-00753-7"},"publication":"Communications Physics","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1"},{"date_created":"2021-12-05T23:01:40Z","date_updated":"2023-08-14T13:11:42Z","volume":40,"author":[{"last_name":"Sietzen","first_name":"Stefan","full_name":"Sietzen, Stefan"},{"full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Borowski, Judy","last_name":"Borowski","first_name":"Judy"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"full_name":"Waldner, Manuela","last_name":"Waldner","first_name":"Manuela"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"ToHe"}],"year":"2021","acknowledgement":"We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n","month":"11","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"language":[{"iso":"eng"}],"doi":"10.1111/cgf.14418","quality_controlled":"1","isi":1,"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2110.07667","open_access":"1"}],"external_id":{"arxiv":["2110.07667"],"isi":["000722952000024"]},"abstract":[{"text":"While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models.","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Preprint","status":"public","title":"Interactive analysis of CNN robustness","intvolume":" 40","_id":"10404","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"27","article_processing_charge":"No","scopus_import":"1","date_published":"2021-11-27T00:00:00Z","article_type":"original","page":"253-264","publication":"Computer Graphics Forum","citation":{"mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.14418.","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418","ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021). Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14418"}}]