[{"oa_version":"Published Version","file_date_updated":"2021-11-15T13:25:52Z","article_processing_charge":"Yes","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","date_updated":"2023-08-14T11:48:37Z","title":"Metamachines of pluripotent colloids","author":[{"first_name":"Antoine","last_name":"Aubret","full_name":"Aubret, Antoine"},{"first_name":"Quentin","full_name":"Martinet, Quentin","last_name":"Martinet","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","orcid":"0000-0002-2916-6632"},{"first_name":"Jérémie A","full_name":"Palacci, Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"}],"publication_identifier":{"eissn":["2041-1723"]},"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.","article_type":"original","year":"2021","article_number":"6398","intvolume":"        12","date_published":"2021-11-04T00:00:00Z","day":"04","doi":"10.1038/s41467-021-26699-6","file":[{"creator":"cchlebak","file_size":6282703,"date_created":"2021-11-15T13:25:52Z","file_name":"2021_NatComm_Aubret.pdf","success":1,"access_level":"open_access","date_updated":"2021-11-15T13:25:52Z","file_id":"10292","content_type":"application/pdf","checksum":"1c392b12b9b7b615d422d9fabe19cdb9","relation":"main_file"}],"oa":1,"ddc":["530"],"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Nature Communications","isi":1,"external_id":{"pmid":["34737315"],"isi":["000714754400010"]},"date_created":"2021-11-14T23:01:23Z","publication_status":"published","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"},"issue":"1","scopus_import":"1","month":"11","_id":"10280","quality_controlled":"1","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"}],"pmid":1,"type":"journal_article","citation":{"ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26699-6\">10.1038/s41467-021-26699-6</a>","apa":"Aubret, A., Martinet, Q., &#38; Palacci, J. A. (2021). Metamachines of pluripotent colloids. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26699-6\">https://doi.org/10.1038/s41467-021-26699-6</a>","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","chicago":"Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26699-6\">https://doi.org/10.1038/s41467-021-26699-6</a>.","mla":"Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” <i>Nature Communications</i>, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26699-6\">10.1038/s41467-021-26699-6</a>.","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021)."},"publisher":"Springer Nature","department":[{"_id":"JePa"}],"volume":12},{"department":[{"_id":"PreCl"}],"volume":22,"publisher":"EMBO Press","quality_controlled":"1","type":"journal_article","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"}],"citation":{"mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” <i>EMBO Reports</i>, vol. 22, e53824, EMBO Press, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>.","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.” <i>EMBO Reports</i>. EMBO Press, 2021. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>.","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. <i>EMBO Reports</i>. EMBO Press. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>","ieee":"L. Restivo <i>et al.</i>, “Towards best practices in research: Role of academic core facilities,” <i>EMBO Reports</i>, vol. 22. EMBO Press, 2021.","ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. <i>EMBO Reports</i>. 2021;22. doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>","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)."},"_id":"10283","scopus_import":"1","month":"11","date_created":"2021-11-14T23:01:24Z","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000714350000001"]},"publication":"EMBO Reports","isi":1,"ddc":["570"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        22","date_published":"2021-11-04T00:00:00Z","doi":"10.15252/embr.202153824","day":"04","oa":1,"file":[{"relation":"main_file","checksum":"74743baa6ef431ef60c3de3bc4da045a","content_type":"application/pdf","file_id":"11381","date_updated":"2022-05-16T07:07:41Z","access_level":"open_access","success":1,"file_name":"2021_EmboReports_Restivo.pdf","date_created":"2022-05-16T07:07:41Z","file_size":488583,"creator":"dernst"}],"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"year":"2021","article_type":"original","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.","article_number":"e53824","date_updated":"2023-08-14T11:47:35Z","author":[{"full_name":"Restivo, Leonardo","last_name":"Restivo","first_name":"Leonardo"},{"last_name":"Gerlach","full_name":"Gerlach, Björn","first_name":"Björn"},{"first_name":"Michael","last_name":"Tsoory","full_name":"Tsoory, Michael"},{"last_name":"Bikovski","full_name":"Bikovski, Lior","first_name":"Lior"},{"last_name":"Badurek","full_name":"Badurek, Sylvia","first_name":"Sylvia"},{"first_name":"Claudia","last_name":"Pitzer","full_name":"Pitzer, Claudia"},{"last_name":"Kos-Braun","full_name":"Kos-Braun, Isabelle C.","first_name":"Isabelle C."},{"first_name":"Anne Laure Mj","last_name":"Mausset-Bonnefont","full_name":"Mausset-Bonnefont, Anne Laure Mj"},{"last_name":"Ward","full_name":"Ward, Jonathan","first_name":"Jonathan"},{"first_name":"Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","full_name":"Schunn, Michael","last_name":"Schunn","orcid":"0000-0003-4326-5300"},{"last_name":"Noldus","full_name":"Noldus, Lucas P.J.J.","first_name":"Lucas P.J.J."},{"first_name":"Anton","full_name":"Bespalov, Anton","last_name":"Bespalov"},{"first_name":"Vootele","last_name":"Voikar","full_name":"Voikar, Vootele"}],"title":"Towards best practices in research: Role of academic core facilities","file_date_updated":"2022-05-16T07:07:41Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"author":[{"last_name":"Dubach","full_name":"Dubach, Guillaume","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","orcid":"0000-0001-6892-8137","first_name":"Guillaume"}],"title":"On eigenvector statistics in the spherical and truncated unitary ensembles","date_updated":"2025-04-14T07:43:47Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-11-15T10:10:17Z","oa_version":"Published Version","publication":"Electronic Journal of Probability","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ddc":["519"],"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"1c975afb31460277ce4d22b93538e5f9","file_id":"10288","date_updated":"2021-11-15T10:10:17Z","access_level":"open_access","date_created":"2021-11-15T10:10:17Z","file_name":"2021_ElecJournalProb_Dubach.pdf","success":1,"file_size":735940,"creator":"cchlebak"}],"oa":1,"doi":"10.1214/21-EJP686","day":"28","date_published":"2021-09-28T00:00:00Z","intvolume":"        26","article_number":"124","publication_identifier":{"eissn":["1083-6489"]},"year":"2021","article_type":"original","acknowledgement":"We acknowledge partial support from the grants NSF DMS-1812114 of P. Bourgade (PI) and NSF CAREER DMS-1653602 of L.-P. Arguin (PI). This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We would like to thank Paul Bourgade and László Erdős for many helpful comments.","ec_funded":1,"_id":"10285","month":"09","scopus_import":"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"},"publication_status":"published","date_created":"2021-11-14T23:01:25Z","volume":26,"department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","citation":{"ama":"Dubach G. On eigenvector statistics in the spherical and truncated unitary ensembles. <i>Electronic Journal of Probability</i>. 2021;26. doi:<a href=\"https://doi.org/10.1214/21-EJP686\">10.1214/21-EJP686</a>","apa":"Dubach, G. (2021). On eigenvector statistics in the spherical and truncated unitary ensembles. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-EJP686\">https://doi.org/10.1214/21-EJP686</a>","ieee":"G. Dubach, “On eigenvector statistics in the spherical and truncated unitary ensembles,” <i>Electronic Journal of Probability</i>, vol. 26. Institute of Mathematical Statistics, 2021.","ista":"Dubach G. 2021. On eigenvector statistics in the spherical and truncated unitary ensembles. Electronic Journal of Probability. 26, 124.","chicago":"Dubach, Guillaume. “On Eigenvector Statistics in the Spherical and Truncated Unitary Ensembles.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2021. <a href=\"https://doi.org/10.1214/21-EJP686\">https://doi.org/10.1214/21-EJP686</a>.","mla":"Dubach, Guillaume. “On Eigenvector Statistics in the Spherical and Truncated Unitary Ensembles.” <i>Electronic Journal of Probability</i>, vol. 26, 124, Institute of Mathematical Statistics, 2021, doi:<a href=\"https://doi.org/10.1214/21-EJP686\">10.1214/21-EJP686</a>.","short":"G. Dubach, Electronic Journal of Probability 26 (2021)."},"abstract":[{"text":"We study the overlaps between right and left eigenvectors for random matrices of the spherical ensemble, as well as truncated unitary ensembles in the regime where half of the matrix at least is truncated. These two integrable models exhibit a form of duality, and the essential steps of our investigation can therefore be performed in parallel. In every case, conditionally on all eigenvalues, diagonal overlaps are shown to be distributed as a product of independent random variables with explicit distributions. This enables us to prove that the scaled diagonal overlaps, conditionally on one eigenvalue, converge in distribution to a heavy-tail limit, namely, the inverse of a γ2 distribution. We also provide formulae for the conditional expectation of diagonal and off-diagonal overlaps, either with respect to one eigenvalue, or with respect to the whole spectrum. These results, analogous to what is known for the complex Ginibre ensemble, can be obtained in these cases thanks to integration techniques inspired from a previous work by Forrester & Krishnapur.","lang":"eng"}],"type":"journal_article","quality_controlled":"1"},{"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","year":"2021","publication_identifier":{"issn":["1047-8477"]},"article_type":"original","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"article_number":"107808","intvolume":"       213","date_published":"2021-11-03T00:00:00Z","doi":"10.1016/j.jsb.2021.107808","day":"03","oa":1,"file":[{"content_type":"application/pdf","checksum":"6b209e4d44775d4e02b50f78982c15fa","relation":"main_file","date_updated":"2021-11-15T13:11:27Z","file_id":"10291","access_level":"open_access","date_created":"2021-11-15T13:11:27Z","file_name":"2021_JournalStructBiol_Dimchev.pdf","success":1,"creator":"cchlebak","file_size":16818304}],"ddc":["572"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF"}],"publication":"Journal of Structural Biology","isi":1,"keyword":["Structural Biology"],"oa_version":"Published Version","file_date_updated":"2021-11-15T13:11:27Z","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-04-15T08:25:41Z","related_material":{"record":[{"status":"public","id":"14502","relation":"software"}]},"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","first_name":"Georgi A"},{"last_name":"Amiri","full_name":"Amiri, Behnam","first_name":"Behnam"},{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","full_name":"Fäßler, Florian","first_name":"Florian"},{"last_name":"Falcke","full_name":"Falcke, Martin","first_name":"Martin"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"quality_controlled":"1","abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}],"type":"journal_article","citation":{"ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” <i>Journal of Structural Biology</i>, vol. 213, no. 4. Elsevier , 2021.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. 2021;213(4). doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>.","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>, vol. 213, no. 4, 107808, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021)."},"publisher":"Elsevier ","corr_author":"1","department":[{"_id":"FlSc"}],"volume":213,"external_id":{"isi":["000720259500002"]},"date_created":"2021-11-15T12:21:42Z","publication_status":"published","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"},"scopus_import":"1","issue":"4","month":"11","_id":"10290"},{"quality_controlled":"1","citation":{"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).","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. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>","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. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>","ieee":"M. J. Conde-Dusman <i>et al.</i>, “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","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.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>.","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.","mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” <i>ELife</i>, vol. 10, e71575, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>."},"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","department":[{"_id":"GaNo"}],"volume":10,"publisher":"eLife Sciences Publications","date_created":"2021-11-18T06:59:45Z","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"},"publication_status":"published","external_id":{"isi":["000720945900001"]},"_id":"10301","scopus_import":"1","month":"11","date_published":"2021-11-17T00:00:00Z","intvolume":"        10","file":[{"file_id":"10302","date_updated":"2021-11-18T07:02:02Z","relation":"main_file","content_type":"application/pdf","checksum":"59318e9e41507cec83c2f4070e6ad540","success":1,"date_created":"2021-11-18T07:02:02Z","file_name":"elife-71575-v1.pdf","file_size":2477302,"creator":"lgarciar","access_level":"open_access"}],"oa":1,"day":"17","doi":"10.7554/elife.71575","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).","year":"2021","publication_identifier":{"issn":["2050-084X"]},"article_type":"original","article_number":"e71575","isi":1,"publication":"eLife","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"date_updated":"2024-10-21T06:02:05Z","author":[{"first_name":"María J","last_name":"Conde-Dusman","full_name":"Conde-Dusman, María J"},{"last_name":"Dey","full_name":"Dey, Partha N","first_name":"Partha N"},{"first_name":"Óscar","last_name":"Elía-Zudaire","full_name":"Elía-Zudaire, Óscar"},{"id":"33D1B084-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Rabaneda, Luis E","last_name":"Garcia Rabaneda","first_name":"Luis E"},{"first_name":"Carmen","last_name":"García-Lira","full_name":"García-Lira, Carmen"},{"first_name":"Teddy","full_name":"Grand, Teddy","last_name":"Grand"},{"first_name":"Victor","last_name":"Briz","full_name":"Briz, Victor"},{"first_name":"Eric R","full_name":"Velasco, Eric R","last_name":"Velasco"},{"first_name":"Raül","full_name":"Andero Galí, Raül","last_name":"Andero Galí"},{"full_name":"Niñerola, Sergio","last_name":"Niñerola","first_name":"Sergio"},{"first_name":"Angel","last_name":"Barco","full_name":"Barco, Angel"},{"first_name":"Pierre","full_name":"Paoletti, Pierre","last_name":"Paoletti"},{"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","last_name":"Tavalin","first_name":"Steven J"},{"last_name":"Perez-Otaño","full_name":"Perez-Otaño, Isabel","first_name":"Isabel"}],"title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-11-18T07:02:02Z","status":"public","language":[{"iso":"eng"}]},{"isi":1,"publication":"Communications Biology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"file":[{"access_level":"open_access","success":1,"date_created":"2021-11-19T15:09:18Z","file_name":"2021_CommBio_Çoruh.pdf","creator":"cchlebak","file_size":6030261,"content_type":"application/pdf","checksum":"8ffd39f2bba7152a2441802ff313bf0b","relation":"main_file","date_updated":"2021-11-19T15:09:18Z","file_id":"10318"}],"oa":1,"doi":"10.1038/s42003-021-01808-9","day":"08","date_published":"2021-03-08T00:00:00Z","intvolume":"         4","article_number":"304","publication_identifier":{"issn":["2399-3642"]},"article_type":"original","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","author":[{"first_name":"Mehmet Orkun","orcid":"0000-0002-3219-2022","full_name":"Çoruh, Mehmet Orkun","last_name":"Çoruh","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef"},{"first_name":"Anna","last_name":"Frank","full_name":"Frank, Anna"},{"first_name":"Hideaki","last_name":"Tanaka","full_name":"Tanaka, Hideaki"},{"last_name":"Kawamoto","full_name":"Kawamoto, Akihiro","first_name":"Akihiro"},{"first_name":"Eithar","full_name":"El-Mohsnawy, Eithar","last_name":"El-Mohsnawy"},{"full_name":"Kato, Takayuki","last_name":"Kato","first_name":"Takayuki"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"full_name":"Gerle, Christoph","last_name":"Gerle","first_name":"Christoph"},{"first_name":"Marc M.","full_name":"Nowaczyk, Marc M.","last_name":"Nowaczyk"},{"first_name":"Genji","full_name":"Kurisu, Genji","last_name":"Kurisu"}],"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","date_updated":"2023-08-14T11:51:19Z","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-11-19T15:09:18Z","oa_version":"Published Version","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"volume":4,"department":[{"_id":"LeSa"}],"publisher":"Springer ","citation":{"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. <i>Communications Biology</i>. 2021;4(1). doi:<a href=\"https://doi.org/10.1038/s42003-021-01808-9\">10.1038/s42003-021-01808-9</a>","ieee":"M. O. Çoruh <i>et al.</i>, “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” <i>Communications Biology</i>, 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. <i>Communications Biology</i>. Springer . <a href=\"https://doi.org/10.1038/s42003-021-01808-9\">https://doi.org/10.1038/s42003-021-01808-9</a>","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” <i>Communications Biology</i>, vol. 4, no. 1, 304, Springer , 2021, doi:<a href=\"https://doi.org/10.1038/s42003-021-01808-9\">10.1038/s42003-021-01808-9</a>.","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.","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.” <i>Communications Biology</i>. Springer , 2021. <a href=\"https://doi.org/10.1038/s42003-021-01808-9\">https://doi.org/10.1038/s42003-021-01808-9</a>.","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)."},"pmid":1,"type":"journal_article","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","_id":"10310","month":"03","scopus_import":"1","issue":"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"},"publication_status":"published","date_created":"2021-11-19T11:37:29Z","external_id":{"pmid":["33686186"],"isi":["000627440700001"]}},{"citation":{"ieee":"L. Chauve <i>et al.</i>, “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans,” <i>PLoS Biology</i>, 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. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001431\">https://doi.org/10.1371/journal.pbio.3001431</a>","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. <i>PLoS Biology</i>. 2021;19(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001431\">10.1371/journal.pbio.3001431</a>","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.” <i>PLoS Biology</i>, vol. 19, no. 11, e3001431, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001431\">10.1371/journal.pbio.3001431</a>.","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.” <i>PLoS Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pbio.3001431\">https://doi.org/10.1371/journal.pbio.3001431</a>.","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)."},"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."}],"type":"journal_article","pmid":1,"quality_controlled":"1","publisher":"Public Library of Science","volume":19,"department":[{"_id":"MaDe"}],"external_id":{"isi":["000715818400001"],"pmid":["34723964"]},"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"},"publication_status":"published","date_created":"2021-11-21T23:01:28Z","month":"11","scopus_import":"1","issue":"11","_id":"10322","article_number":"e3001431","year":"2021","article_type":"original","publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"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.","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"0c61b667f814fd9435b3ac42036fc36d","file_id":"10330","date_updated":"2021-11-22T09:34:03Z","access_level":"open_access","file_size":4069215,"creator":"cchlebak","file_name":"2021_PLoSBio_Chauve.pdf","date_created":"2021-11-22T09:34:03Z","success":1}],"oa":1,"day":"01","doi":"10.1371/journal.pbio.3001431","date_published":"2021-11-01T00:00:00Z","intvolume":"        19","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"isi":1,"publication":"PLoS Biology","oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-11-22T09:34:03Z","author":[{"last_name":"Chauve","full_name":"Chauve, Laetitia","first_name":"Laetitia"},{"first_name":"Francesca","last_name":"Hodge","full_name":"Hodge, Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"full_name":"Masoudzadeh, Fatemah","last_name":"Masoudzadeh","first_name":"Fatemah"},{"first_name":"Harry Jack","full_name":"Mann, Harry Jack","last_name":"Mann"},{"first_name":"Andrea","last_name":"Lopez-Clavijo","full_name":"Lopez-Clavijo, Andrea"},{"full_name":"Okkenhaug, Hanneke","last_name":"Okkenhaug","first_name":"Hanneke"},{"first_name":"Greg","full_name":"West, Greg","last_name":"West"},{"first_name":"Bebiana C.","last_name":"Sousa","full_name":"Sousa, Bebiana C."},{"last_name":"Segonds-Pichon","full_name":"Segonds-Pichon, Anne","first_name":"Anne"},{"full_name":"Li, Cheryl","last_name":"Li","first_name":"Cheryl"},{"first_name":"Steven","last_name":"Wingett","full_name":"Wingett, Steven"},{"first_name":"Hermine","last_name":"Kienberger","full_name":"Kienberger, Hermine"},{"first_name":"Karin","full_name":"Kleigrewe, Karin","last_name":"Kleigrewe"},{"orcid":"0000-0001-8347-0443","last_name":"De Bono","full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"},{"full_name":"Wakelam, Michael","last_name":"Wakelam","first_name":"Michael"},{"first_name":"Olivia","full_name":"Casanueva, Olivia","last_name":"Casanueva"}],"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","related_material":{"record":[{"status":"public","id":"13069","relation":"research_data"}]},"date_updated":"2023-08-14T11:53:27Z"},{"publication_identifier":{"eissn":["2296-889X"]},"article_type":"original","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).","article_number":"762005","date_published":"2021-10-25T00:00:00Z","intvolume":"         8","file":[{"access_level":"open_access","date_created":"2021-11-23T15:06:58Z","success":1,"file_name":"2021_FrontiersMolBioSc_Sučec.pdf","creator":"cchlebak","file_size":4700798,"checksum":"a5c9dbf80dc2c5aaa737f456c941d964","content_type":"application/pdf","relation":"main_file","date_updated":"2021-11-23T15:06:58Z","file_id":"10333"}],"oa":1,"doi":"10.3389/fmolb.2021.762005","day":"25","ddc":["547"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"publication":"Frontiers in Molecular Biosciences","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2021-11-23T15:06:58Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-10-09T21:01:12Z","title":"How do chaperones bind (partly) unfolded client proteins?","author":[{"first_name":"Iva","last_name":"Sučec","full_name":"Sučec, Iva"},{"first_name":"Beate","full_name":"Bersch, Beate","last_name":"Bersch"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"quality_controlled":"1","citation":{"ieee":"I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” <i>Frontiers in Molecular Biosciences</i>, vol. 8. Frontiers, 2021.","apa":"Sučec, I., Bersch, B., &#38; Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? <i>Frontiers in Molecular Biosciences</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmolb.2021.762005\">https://doi.org/10.3389/fmolb.2021.762005</a>","ama":"Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? <i>Frontiers in Molecular Biosciences</i>. 2021;8. doi:<a href=\"https://doi.org/10.3389/fmolb.2021.762005\">10.3389/fmolb.2021.762005</a>","mla":"Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” <i>Frontiers in Molecular Biosciences</i>, vol. 8, 762005, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fmolb.2021.762005\">10.3389/fmolb.2021.762005</a>.","ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005.","chicago":"Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” <i>Frontiers in Molecular Biosciences</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fmolb.2021.762005\">https://doi.org/10.3389/fmolb.2021.762005</a>.","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021)."},"pmid":1,"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."}],"publisher":"Frontiers","corr_author":"1","department":[{"_id":"PaSc"}],"volume":8,"external_id":{"pmid":["34760928"],"isi":["000717241700001"]},"date_created":"2021-11-21T23:01:29Z","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"},"publication_status":"published","scopus_import":"1","month":"10","_id":"10323"},{"language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","author":[{"first_name":"Zeta","full_name":"Avarikioti, Zeta","last_name":"Avarikioti"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"first_name":"Roger","last_name":"Wattenhofer","full_name":"Wattenhofer, Roger"},{"first_name":"Dionysis","full_name":"Zindros, Dionysis","last_name":"Zindros"}],"title":"Brick: Asynchronous incentive-compatible payment channels","date_updated":"2023-08-14T12:59:58Z","page":"209-230","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"arxiv":1,"publication":"25th International Conference on Financial Cryptography and Data Security","year":"2021","acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","publication_identifier":{"eisbn":["978-3-662-64331-0"],"eissn":["1611-3349"],"isbn":["9-783-6626-4330-3"],"issn":["0302-9743"]},"oa":1,"doi":"10.1007/978-3-662-64331-0_11","day":"23","date_published":"2021-10-23T00:00:00Z","month":"10","scopus_import":"1","_id":"10324","conference":{"start_date":"2021-03-01","location":"Virtual","name":"FC: Financial Cryptography","end_date":"2021-03-05"},"alternative_title":["LNCS"],"external_id":{"isi":["000712016200011"],"arxiv":["1905.11360"]},"publication_status":"published","date_created":"2021-11-21T23:01:29Z","publisher":"Springer Nature","main_file_link":[{"url":"https://arxiv.org/abs/1905.11360","open_access":"1"}],"volume":"12675 ","department":[{"_id":"ElKo"}],"citation":{"chicago":"Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In <i>25th International Conference on Financial Cryptography and Data Security</i>, 12675:209–30. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-662-64331-0_11\">https://doi.org/10.1007/978-3-662-64331-0_11</a>.","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.","mla":"Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment Channels.” <i>25th International Conference on Financial Cryptography and Data Security</i>, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:<a href=\"https://doi.org/10.1007/978-3-662-64331-0_11\">10.1007/978-3-662-64331-0_11</a>.","ama":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous incentive-compatible payment channels. In: <i>25th International Conference on Financial Cryptography and Data Security</i>. Vol 12675. Springer Nature; 2021:209-230. doi:<a href=\"https://doi.org/10.1007/978-3-662-64331-0_11\">10.1007/978-3-662-64331-0_11</a>","ieee":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous incentive-compatible payment channels,” in <i>25th International Conference on Financial Cryptography and Data Security</i>, Virtual, 2021, vol. 12675, pp. 209–230.","apa":"Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., &#38; Zindros, D. (2021). Brick: Asynchronous incentive-compatible payment channels. In <i>25th International Conference on Financial Cryptography and Data Security</i> (Vol. 12675, pp. 209–230). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-64331-0_11\">https://doi.org/10.1007/978-3-662-64331-0_11</a>","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."},"type":"conference","abstract":[{"lang":"eng","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."}],"quality_controlled":"1"},{"publication":"25th International Conference on Financial Cryptography and Data Security","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"23","doi":"10.1007/978-3-662-64331-0_1","oa":1,"date_published":"2021-10-23T00:00:00Z","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.","publication_identifier":{"issn":["0302-9743"],"isbn":["9-783-6626-4330-3"],"eisbn":["978-3-662-64331-0"],"eissn":["1611-3349"]},"year":"2021","title":"SoK: Communication across distributed ledgers","author":[{"last_name":"Zamyatin","full_name":"Zamyatin, Alexei","first_name":"Alexei"},{"last_name":"Al-Bassam","full_name":"Al-Bassam, Mustafa","first_name":"Mustafa"},{"first_name":"Dionysis","full_name":"Zindros, Dionysis","last_name":"Zindros"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"full_name":"Moreno-Sanchez, Pedro","last_name":"Moreno-Sanchez","first_name":"Pedro"},{"last_name":"Kiayias","full_name":"Kiayias, Aggelos","first_name":"Aggelos"},{"full_name":"Knottenbelt, William J.","last_name":"Knottenbelt","first_name":"William J."}],"date_updated":"2023-08-14T12:59:26Z","page":"3-36","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Preprint","volume":"12675 ","department":[{"_id":"ElKo"}],"publisher":"Springer Nature","main_file_link":[{"url":"https://eprint.iacr.org/2019/1128","open_access":"1"}],"type":"conference","abstract":[{"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.","lang":"eng"}],"citation":{"apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., &#38; Knottenbelt, W. J. (2021). SoK: Communication across distributed ledgers. In <i>25th International Conference on Financial Cryptography and Data Security</i> (Vol. 12675, pp. 3–36). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-64331-0_1\">https://doi.org/10.1007/978-3-662-64331-0_1</a>","ieee":"A. Zamyatin <i>et al.</i>, “SoK: Communication across distributed ledgers,” in <i>25th International Conference on Financial Cryptography and Data Security</i>, Virtual, 2021, vol. 12675, pp. 3–36.","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. In: <i>25th International Conference on Financial Cryptography and Data Security</i>. Vol 12675. Springer Nature; 2021:3-36. doi:<a href=\"https://doi.org/10.1007/978-3-662-64331-0_1\">10.1007/978-3-662-64331-0_1</a>","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 <i>25th International Conference on Financial Cryptography and Data Security</i>, 12675:3–36. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-662-64331-0_1\">https://doi.org/10.1007/978-3-662-64331-0_1</a>.","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.","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” <i>25th International Conference on Financial Cryptography and Data Security</i>, vol. 12675, Springer Nature, 2021, pp. 3–36, doi:<a href=\"https://doi.org/10.1007/978-3-662-64331-0_1\">10.1007/978-3-662-64331-0_1</a>.","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."},"quality_controlled":"1","_id":"10325","month":"10","scopus_import":"1","publication_status":"published","date_created":"2021-11-21T23:01:29Z","conference":{"end_date":"2021-03-05","location":"Virtual","name":"FC: Financial Cryptography","start_date":"2021-03-01"},"external_id":{"isi":["000712016200001"]},"alternative_title":["LNCS"]},{"external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"date_created":"2021-11-21T23:01:30Z","publication_status":"published","scopus_import":"1","month":"11","_id":"10326","quality_controlled":"1","pmid":1,"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"}],"citation":{"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.","chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” <i>Nature Plants</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41477-021-01011-y\">https://doi.org/10.1038/s41477-021-01011-y</a>.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” <i>Nature Plants</i>, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:<a href=\"https://doi.org/10.1038/s41477-021-01011-y\">10.1038/s41477-021-01011-y</a>.","ieee":"E. Xu <i>et al.</i>, “Catabolism of strigolactones by a carboxylesterase,” <i>Nature Plants</i>, vol. 7. Springer Nature, pp. 1495–1504, 2021.","apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., &#38; Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-021-01011-y\">https://doi.org/10.1038/s41477-021-01011-y</a>","ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. <i>Nature Plants</i>. 2021;7:1495–1504. doi:<a href=\"https://doi.org/10.1038/s41477-021-01011-y\">10.1038/s41477-021-01011-y</a>","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504."},"publisher":"Springer Nature","department":[{"_id":"JiFr"}],"OA_type":"green","volume":7,"oa_version":"Submitted Version","file_date_updated":"2025-01-21T12:41:43Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-01-21T12:42:52Z","page":"1495–1504 ","title":"Catabolism of strigolactones by a carboxylesterase","author":[{"first_name":"Enjun","last_name":"Xu","full_name":"Xu, Enjun"},{"full_name":"Chai, Liang","last_name":"Chai","first_name":"Liang"},{"first_name":"Shiqi","full_name":"Zhang, Shiqi","last_name":"Zhang"},{"first_name":"Ruixue","last_name":"Yu","full_name":"Yu, Ruixue"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","first_name":"Xixi"},{"last_name":"Xu","full_name":"Xu, Chongyi","first_name":"Chongyi"},{"full_name":"Hu, Yuxin","last_name":"Hu","first_name":"Yuxin"}],"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).","article_type":"original","year":"2021","publication_identifier":{"eissn":["2055-0278"]},"intvolume":"         7","date_published":"2021-11-11T00:00:00Z","doi":"10.1038/s41477-021-01011-y","day":"11","file":[{"content_type":"application/pdf","checksum":"d20231806bea67f0fd19e96a94a048f4","relation":"main_file","date_updated":"2025-01-21T12:41:43Z","file_id":"18864","access_level":"open_access","file_name":"Accepted version_Xu et al.,2021 Catabolism of strigolactones by a carboxylesterase.pdf","success":1,"date_created":"2025-01-21T12:41:43Z","creator":"dernst","file_size":41109943}],"oa":1,"OA_place":"repository","ddc":["580"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Nature Plants","isi":1},{"title":"PbS–Pb–CuxS composites for thermoelectric application","author":[{"full_name":"Li, Mengyao","last_name":"Li","first_name":"Mengyao"},{"first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu","last_name":"Liu"},{"first_name":"Yu","full_name":"Zhang, Yu","last_name":"Zhang"},{"first_name":"Xu","full_name":"Han, Xu","last_name":"Han"},{"last_name":"Xiao","full_name":"Xiao, Ke","first_name":"Ke"},{"full_name":"Nabahat, Mehran","last_name":"Nabahat","first_name":"Mehran"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"page":"51373–51382","date_updated":"2025-04-14T07:43:47Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa_version":"Submitted Version","keyword":["CuxS","PbS","energy conversion","nanocomposite","nanoparticle","solution synthesis","thermoelectric"],"publication":"ACS Applied Materials and Interfaces","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"doi":"10.1021/acsami.1c15609","day":"19","oa":1,"intvolume":"        13","date_published":"2021-10-19T00:00:00Z","ec_funded":1,"acknowledgement":"This work was supported by the European Regional Development Funds. M.L., Y.Z., X.H., and K.X. thank the China Scholarship Council for scholarship support. M. I. has been financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. J.L. is a Serra Húnter fellow and is grateful to ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project NANOGEN (PID2020-116093RB-C43). ICN2 was supported by the Severo Ochoa program from Spanish MINECO (grant no. SEV-2017-0706) and was funded by the CERCA Programme/Generalitat de Catalunya. X.H. thanks China Scholarship Council for scholarship support (201804910551). Part of the present work was performed in the framework of Universitat Autònoma de Barcelona Materials Science Ph.D. program.","article_type":"original","year":"2021","publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"_id":"10327","month":"10","scopus_import":"1","issue":"43","publication_status":"published","date_created":"2021-11-21T23:01:30Z","external_id":{"isi":["000715852100070"],"pmid":["34665616"]},"volume":13,"department":[{"_id":"MaIb"}],"corr_author":"1","publisher":"American Chemical Society ","main_file_link":[{"open_access":"1","url":"https://upcommons.upc.edu/bitstream/2117/363528/1/Pb%20mengyao.pdf"}],"pmid":1,"type":"journal_article","abstract":[{"lang":"eng","text":"Composite materials offer numerous advantages in a wide range of applications, including thermoelectrics. Here, semiconductor–metal composites are produced by just blending nanoparticles of a sulfide semiconductor obtained in aqueous solution and at room temperature with a metallic Cu powder. The obtained blend is annealed in a reducing atmosphere and afterward consolidated into dense polycrystalline pellets through spark plasma sintering (SPS). We observe that, during the annealing process, the presence of metallic copper activates a partial reduction of the PbS, resulting in the formation of PbS–Pb–CuxS composites. The presence of metallic lead during the SPS process habilitates the liquid-phase sintering of the composite. Besides, by comparing the transport properties of PbS, the PbS–Pb–CuxS composites, and PbS–CuxS composites obtained by blending PbS and CuxS nanoparticles, we demonstrate that the presence of metallic lead decisively contributes to a strong increase of the charge carrier concentration through spillover of charge carriers enabled by the low work function of lead. The increase in charge carrier concentration translates into much higher electrical conductivities and moderately lower Seebeck coefficients. These properties translate into power factors up to 2.1 mW m–1 K–2 at ambient temperature, well above those of PbS and PbS + CuxS. Additionally, the presence of multiple phases in the final composite results in a notable decrease in the lattice thermal conductivity. Overall, the introduction of metallic copper in the initial blend results in a significant improvement of the thermoelectric performance of PbS, reaching a dimensionless thermoelectric figure of merit ZT = 1.1 at 750 K, which represents about a 400% increase over bare PbS. Besides, an average ZTave = 0.72 in the temperature range 320–773 K is demonstrated."}],"citation":{"short":"M. Li, Y. Liu, Y. Zhang, X. Han, K. Xiao, M. Nabahat, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 13 (2021) 51373–51382.","mla":"Li, Mengyao, et al. “PbS–Pb–CuxS Composites for Thermoelectric Application.” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 43, American Chemical Society , 2021, pp. 51373–51382, doi:<a href=\"https://doi.org/10.1021/acsami.1c15609\">10.1021/acsami.1c15609</a>.","ista":"Li M, Liu Y, Zhang Y, Han X, Xiao K, Nabahat M, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2021. PbS–Pb–CuxS composites for thermoelectric application. ACS Applied Materials and Interfaces. 13(43), 51373–51382.","chicago":"Li, Mengyao, Yu Liu, Yu Zhang, Xu Han, Ke Xiao, Mehran Nabahat, Jordi Arbiol, Jordi Llorca, Maria Ibáñez, and Andreu Cabot. “PbS–Pb–CuxS Composites for Thermoelectric Application.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society , 2021. <a href=\"https://doi.org/10.1021/acsami.1c15609\">https://doi.org/10.1021/acsami.1c15609</a>.","apa":"Li, M., Liu, Y., Zhang, Y., Han, X., Xiao, K., Nabahat, M., … Cabot, A. (2021). PbS–Pb–CuxS composites for thermoelectric application. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society . <a href=\"https://doi.org/10.1021/acsami.1c15609\">https://doi.org/10.1021/acsami.1c15609</a>","ama":"Li M, Liu Y, Zhang Y, et al. PbS–Pb–CuxS composites for thermoelectric application. <i>ACS Applied Materials and Interfaces</i>. 2021;13(43):51373–51382. doi:<a href=\"https://doi.org/10.1021/acsami.1c15609\">10.1021/acsami.1c15609</a>","ieee":"M. Li <i>et al.</i>, “PbS–Pb–CuxS composites for thermoelectric application,” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 43. American Chemical Society , pp. 51373–51382, 2021."},"quality_controlled":"1"},{"oa_version":"None","keyword":["cell biology"],"author":[{"first_name":"Longhui","full_name":"Zeng, Longhui","last_name":"Zeng"},{"full_name":"Palaia, Ivan","last_name":"Palaia","first_name":"Ivan"},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"full_name":"Su, Xiaolei","last_name":"Su","first_name":"Xiaolei"}],"title":"PLCγ1 promotes phase separation of T cell signaling components","date_updated":"2021-11-25T15:33:08Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","day":"30","doi":"10.1083/jcb.202009154","intvolume":"       220","date_published":"2021-04-30T00:00:00Z","article_number":"e202009154","year":"2021","article_type":"original","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"acknowledgement":"Charles H. Hood Foundation (NO AWARD) ; Rally Foundation (NO AWARD)","publication":"Journal of Cell Biology","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publication_status":"published","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"date_created":"2021-11-25T15:21:30Z","external_id":{"pmid":["33929486"]},"_id":"10337","month":"04","issue":"6","scopus_import":"1","abstract":[{"lang":"eng","text":"The T cell receptor (TCR) pathway receives, processes, and amplifies the signal from pathogenic antigens to the activation of T cells. Although major components in this pathway have been identified, the knowledge on how individual components cooperate to effectively transduce signals remains limited. Phase separation emerges as a biophysical principle in organizing signaling molecules into liquid-like condensates. Here, we report that phospholipase Cγ1 (PLCγ1) promotes phase separation of LAT, a key adaptor protein in the TCR pathway. PLCγ1 directly cross-links LAT through its two SH2 domains. PLCγ1 also protects LAT from dephosphorylation by the phosphatase CD45 and promotes LAT-dependent ERK activation and SLP76 phosphorylation. Intriguingly, a nonmonotonic effect of PLCγ1 on LAT clustering was discovered. Computer simulations, based on patchy particles, revealed how the cluster size is regulated by protein compositions. Together, these results define a critical function of PLCγ1 in promoting phase separation of the LAT complex and TCR signal transduction."}],"extern":"1","type":"journal_article","pmid":1,"citation":{"ama":"Zeng L, Palaia I, Šarić A, Su X. PLCγ1 promotes phase separation of T cell signaling components. <i>Journal of Cell Biology</i>. 2021;220(6). doi:<a href=\"https://doi.org/10.1083/jcb.202009154\">10.1083/jcb.202009154</a>","ieee":"L. Zeng, I. Palaia, A. Šarić, and X. Su, “PLCγ1 promotes phase separation of T cell signaling components,” <i>Journal of Cell Biology</i>, vol. 220, no. 6. Rockefeller University Press, 2021.","apa":"Zeng, L., Palaia, I., Šarić, A., &#38; Su, X. (2021). PLCγ1 promotes phase separation of T cell signaling components. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202009154\">https://doi.org/10.1083/jcb.202009154</a>","chicago":"Zeng, Longhui, Ivan Palaia, Anđela Šarić, and Xiaolei Su. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202009154\">https://doi.org/10.1083/jcb.202009154</a>.","ista":"Zeng L, Palaia I, Šarić A, Su X. 2021. PLCγ1 promotes phase separation of T cell signaling components. Journal of Cell Biology. 220(6), e202009154.","mla":"Zeng, Longhui, et al. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” <i>Journal of Cell Biology</i>, vol. 220, no. 6, e202009154, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202009154\">10.1083/jcb.202009154</a>.","short":"L. Zeng, I. Palaia, A. Šarić, X. Su, Journal of Cell Biology 220 (2021)."},"quality_controlled":"1","volume":220,"publisher":"Rockefeller University Press"},{"month":"02","scopus_import":"1","issue":"9","_id":"10338","external_id":{"pmid":["33617830"]},"publication_status":"published","date_created":"2021-11-25T15:36:36Z","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.10.01.322156"}],"volume":120,"citation":{"short":"L.K. Davis, A. Šarić, B.W. Hoogenboom, A. Zilman, Biophysical Journal 120 (2021) 1565–1577.","ista":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. 2021. Physical modeling of multivalent interactions in the nuclear pore complex. Biophysical Journal. 120(9), 1565–1577.","chicago":"Davis, Luke K., Anđela Šarić, Bart W. Hoogenboom, and Anton Zilman. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” <i>Biophysical Journal</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">https://doi.org/10.1016/j.bpj.2021.01.039</a>.","mla":"Davis, Luke K., et al. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” <i>Biophysical Journal</i>, vol. 120, no. 9, Elsevier, 2021, pp. 1565–77, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">10.1016/j.bpj.2021.01.039</a>.","ieee":"L. K. Davis, A. Šarić, B. W. Hoogenboom, and A. Zilman, “Physical modeling of multivalent interactions in the nuclear pore complex,” <i>Biophysical Journal</i>, vol. 120, no. 9. Elsevier, pp. 1565–1577, 2021.","apa":"Davis, L. K., Šarić, A., Hoogenboom, B. W., &#38; Zilman, A. (2021). Physical modeling of multivalent interactions in the nuclear pore complex. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">https://doi.org/10.1016/j.bpj.2021.01.039</a>","ama":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. Physical modeling of multivalent interactions in the nuclear pore complex. <i>Biophysical Journal</i>. 2021;120(9):1565-1577. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">10.1016/j.bpj.2021.01.039</a>"},"extern":"1","pmid":1,"abstract":[{"text":"In the nuclear pore complex, intrinsically disordered proteins (FG Nups), along with their interactions with more globular proteins called nuclear transport receptors (NTRs), are vital to the selectivity of transport into and out of the cell nucleus. Although such interactions can be modeled at different levels of coarse graining, in vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, in which the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and noncohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity in a minimal fashion and compare them with experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does play a role in determining equilibrium binding properties but is of much greater significance when it comes to unbinding and binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","author":[{"last_name":"Davis","full_name":"Davis, Luke K.","first_name":"Luke K."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"first_name":"Bart W.","last_name":"Hoogenboom","full_name":"Hoogenboom, Bart W."},{"first_name":"Anton","full_name":"Zilman, Anton","last_name":"Zilman"}],"title":"Physical modeling of multivalent interactions in the nuclear pore complex","date_updated":"2022-04-01T10:34:38Z","page":"1565-1577","keyword":["biophysics"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Biophysical Journal","publication_identifier":{"issn":["0006-3495"]},"article_type":"original","year":"2021","oa":1,"doi":"10.1016/j.bpj.2021.01.039","day":"19","date_published":"2021-02-19T00:00:00Z","intvolume":"       120"},{"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","license":"https://creativecommons.org/licenses/by-nc/3.0/","OA_place":"publisher","publication":"Soft Matter","acknowledgement":"We acknowledge support from the Royal Society (C. V. C. and A. Sˇ.), the Medical Research Council (C. V. C. and A. Sˇ.), and the European Research Council (Starting grant ‘‘NEPA’’ 802960 to A. Sˇ.). We thank Johannes Krausser and Ivan Palaia for fruitful discussions.","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"year":"2021","article_type":"original","oa":1,"day":"16","doi":"10.1039/d0sm02012e","date_published":"2021-02-16T00:00:00Z","intvolume":"        17","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Modelling the dynamics of vesicle reshaping and scission under osmotic shocks","author":[{"last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian","first_name":"Christian"},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"date_updated":"2024-10-14T14:20:59Z","page":"3798-3806","related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.11.16.384602v2","relation":"earlier_version"}]},"keyword":["condensed matter physics","general chemistry"],"oa_version":"Published Version","publisher":"Royal Society of Chemistry","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2021/sm/d0sm02012e","open_access":"1"}],"volume":17,"OA_type":"hybrid","citation":{"short":"C. Vanhille-Campos, A. Šarić, Soft Matter 17 (2021) 3798–3806.","ama":"Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. 2021;17(14):3798-3806. doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>","ieee":"C. Vanhille-Campos and A. Šarić, “Modelling the dynamics of vesicle reshaping and scission under osmotic shocks,” <i>Soft Matter</i>, vol. 17, no. 14. Royal Society of Chemistry, pp. 3798–3806, 2021.","apa":"Vanhille-Campos, C., &#38; Šarić, A. (2021). Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>","ista":"Vanhille-Campos C, Šarić A. 2021. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. 17(14), 3798–3806.","chicago":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” <i>Soft Matter</i>. Royal Society of Chemistry, 2021. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>.","mla":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” <i>Soft Matter</i>, vol. 17, no. 14, Royal Society of Chemistry, 2021, pp. 3798–806, doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>."},"abstract":[{"text":"We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation.","lang":"eng"}],"extern":"1","type":"journal_article","pmid":1,"quality_controlled":"1","month":"02","issue":"14","scopus_import":"1","_id":"10339","external_id":{"pmid":["33629089"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png"},"publication_status":"published","date_created":"2021-11-25T16:06:42Z"},{"publication_status":"published","date_created":"2021-11-25T16:18:23Z","external_id":{"pmid":["33460596"]},"_id":"10340","month":"01","scopus_import":"1","issue":"4","citation":{"ista":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. 2021. Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical Journal. 120(4), 598–606.","chicago":"Paraschiv, Alexandru, Thibaut J. Lagny, Christian Vanhille Campos, Evelyne Coudrier, Patricia Bassereau, and Anđela Šarić. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” <i>Biophysical Journal</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>.","mla":"Paraschiv, Alexandru, et al. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” <i>Biophysical Journal</i>, vol. 120, no. 4, Cell Press, 2021, pp. 598–606, doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>.","ieee":"A. Paraschiv, T. J. Lagny, C. V. Campos, E. Coudrier, P. Bassereau, and A. Šarić, “Influence of membrane-cortex linkers on the extrusion of membrane tubes,” <i>Biophysical Journal</i>, vol. 120, no. 4. Cell Press, pp. 598–606, 2021.","apa":"Paraschiv, A., Lagny, T. J., Campos, C. V., Coudrier, E., Bassereau, P., &#38; Šarić, A. (2021). Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>","ama":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. 2021;120(4):598-606. doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>","short":"A. Paraschiv, T.J. Lagny, C.V. Campos, E. Coudrier, P. Bassereau, A. Šarić, Biophysical Journal 120 (2021) 598–606."},"pmid":1,"abstract":[{"text":"The cell membrane is an inhomogeneous system composed of phospholipids, sterols, carbohydrates, and proteins that can be directly attached to underlying cytoskeleton. The protein linkers between the membrane and the cytoskeleton are believed to have a profound effect on the mechanical properties of the cell membrane and its ability to reshape. Here, we investigate the role of membrane-cortex linkers on the extrusion of membrane tubes using computer simulations and experiments. In simulations, we find that the force for tube extrusion has a nonlinear dependence on the density of membrane-cortex attachments: at a range of low and intermediate linker densities, the force is not significantly influenced by the presence of the membrane-cortex attachments and resembles that of the bare membrane. For large concentrations of linkers, however, the force substantially increases compared with the bare membrane. In both cases, the linkers provided membrane tubes with increased stability against coalescence. We then pulled tubes from HEK cells using optical tweezers for varying expression levels of the membrane-cortex attachment protein Ezrin. In line with simulations, we observed that overexpression of Ezrin led to an increased extrusion force, while Ezrin depletion had a negligible effect on the force. Our results shed light on the importance of local protein rearrangements for membrane reshaping at nanoscopic scales.","lang":"eng"}],"type":"journal_article","extern":"1","quality_controlled":"1","volume":120,"publisher":"Cell Press","main_file_link":[{"url":"https://doi.org/10.1101/2020.07.28.224741","open_access":"1"}],"oa_version":"Preprint","keyword":["biophysics"],"author":[{"first_name":"Alexandru","last_name":"Paraschiv","full_name":"Paraschiv, Alexandru"},{"full_name":"Lagny, Thibaut J.","last_name":"Lagny","first_name":"Thibaut J."},{"full_name":"Campos, Christian Vanhille","last_name":"Campos","first_name":"Christian Vanhille"},{"full_name":"Coudrier, Evelyne","last_name":"Coudrier","first_name":"Evelyne"},{"full_name":"Bassereau, Patricia","last_name":"Bassereau","first_name":"Patricia"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"}],"title":"Influence of membrane-cortex linkers on the extrusion of membrane tubes","date_updated":"2024-10-14T11:13:03Z","page":"598-606","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa":1,"doi":"10.1016/j.bpj.2020.12.028","day":"16","date_published":"2021-01-16T00:00:00Z","intvolume":"       120","year":"2021","publication_identifier":{"issn":["0006-3495"]},"acknowledgement":"We thank Ewa Paluch, Alba Diz-Muñoz, Guillaume Salbreux, Guillaume Charras, and Shiladitya Banerjee for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P., C.V.C., and A.Š.), the Royal Society (C.V.C. and A.Š.), and the European Research Council (Starting grant EP/R011818/1 to A.Š.; E.C. and P.B. are partners of the advanced grant, project 339847) and from Institut Curie (E.C. and P.B.) and Centre National de la Recherche Scientifique (CNRS) (E.C. and P.B.). The P.B. and E.C. groups belong to Labex CelTisPhyBio (ANR-11-LABX0038) and to Paris Sciences et Lettres (ANR-10-IDEX-0001-02). T.L. received a PhD grant from Paris Sciences et Lettres Research University and support from the Institut Curie.","article_type":"original","publication":"Biophysical Journal","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","date_updated":"2023-08-14T13:01:38Z","author":[{"first_name":"Jungmin","full_name":"Lee, Jungmin","last_name":"Lee"},{"first_name":"Andyna","last_name":"Vernet","full_name":"Vernet, Andyna"},{"first_name":"Nathalie","full_name":"Gruber, Nathalie","last_name":"Gruber","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425"},{"last_name":"Kready","full_name":"Kready, Kasia M.","first_name":"Kasia M."},{"last_name":"Burrill","full_name":"Burrill, Devin R.","first_name":"Devin R."},{"last_name":"Way","full_name":"Way, Jeffrey C.","first_name":"Jeffrey C."},{"full_name":"Silver, Pamela A.","last_name":"Silver","first_name":"Pamela A."}],"title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_published":"2021-11-01T00:00:00Z","intvolume":"        34","oa":1,"day":"01","doi":"10.1093/protein/gzab025","article_type":"original","year":"2021","publication_identifier":{"eissn":["1741-0134"],"issn":["1741-0126"]},"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.","article_number":"gzab025","isi":1,"publication":"Protein Engineering, Design and Selection","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-11-28T23:01:28Z","publication_status":"published","external_id":{"isi":["000746596900001"],"pmid":["34725710"]},"_id":"10363","scopus_import":"1","month":"11","quality_controlled":"1","citation":{"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).","ieee":"J. Lee <i>et al.</i>, “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” <i>Protein Engineering, Design and Selection</i>, vol. 34. Oxford University Press, 2021.","apa":"Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., &#38; Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. <i>Protein Engineering, Design and Selection</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/protein/gzab025\">https://doi.org/10.1093/protein/gzab025</a>","ama":"Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. <i>Protein Engineering, Design and Selection</i>. 2021;34. doi:<a href=\"https://doi.org/10.1093/protein/gzab025\">10.1093/protein/gzab025</a>","mla":"Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” <i>Protein Engineering, Design and Selection</i>, vol. 34, gzab025, Oxford University Press, 2021, doi:<a href=\"https://doi.org/10.1093/protein/gzab025\">10.1093/protein/gzab025</a>.","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.","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.” <i>Protein Engineering, Design and Selection</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/protein/gzab025\">https://doi.org/10.1093/protein/gzab025</a>."},"abstract":[{"lang":"eng","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."}],"type":"journal_article","pmid":1,"department":[{"_id":"CaGu"}],"volume":34,"main_file_link":[{"url":"https://doi.org/10.1093/protein/gzab025","open_access":"1"}],"publisher":"Oxford University Press"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis"},{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"}],"ddc":["530"],"publication":"Nature Physics","isi":1,"ec_funded":1,"article_type":"original","acknowledgement":"S.G. acknowledges funding from FEDER Prostem Research Project no. 1510614 (Wallonia DG06), F.R.S.-FNRS Epiforce Research Project no. T.0092.21 and Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional, FEDER-ERDF). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme grant agreement 851288 (to E.H.), and by the Austrian Science Fund (FWF) (P 31639; to E.H.). L.R.M. acknowledges funding from the Agence National de la Recherche (ANR), as part of the ‘Investments d’Avenir’ Programme (I-SITE ULNE/ANR-16-IDEX-0004 ULNE). This work benefited from ANR-10-EQPX-04-01 and FEDER 12001407 grants to F.L. W.D.V. is supported by the Research Foundation Flanders (FWO 1516619N, FWO GOO5819N, FWO I003420N, FWO IRI I000321N) and is member of the Research Excellence Consortium µNEURO at the University of Antwerp. M.L. is financially supported by FRIA (F.R.S.-FNRS). M.S. is a Senior Research Associate of the Fund for Scientific Research (F.R.S.-FNRS) and acknowledges EOS grant no. 30650939 (PRECISION). Sketches in Figs. 1a and 5e and Extended Data Fig. 9 were drawn by C. Levicek.","year":"2021","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"doi":"10.1038/s41567-021-01374-1","day":"18","oa":1,"file":[{"date_updated":"2023-10-11T09:31:43Z","file_id":"14420","checksum":"5d6d76750a71d7cb632bb15417c38ef7","content_type":"application/pdf","relation":"main_file","creator":"channezo","file_size":40285498,"date_created":"2023-10-11T09:31:43Z","file_name":"50145_4_merged_1630498627.pdf","success":1,"access_level":"open_access"}],"intvolume":"        17","date_published":"2021-11-18T00:00:00Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2023-10-11T09:31:43Z","article_processing_charge":"No","has_accepted_license":"1","author":[{"first_name":"Marine","full_name":"Luciano, Marine","last_name":"Luciano"},{"last_name":"Xue","full_name":"Xue, Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei"},{"first_name":"Winnok H.","last_name":"De Vos","full_name":"De Vos, Winnok H."},{"last_name":"Redondo-Morata","full_name":"Redondo-Morata, Lorena","first_name":"Lorena"},{"first_name":"Mathieu","full_name":"Surin, Mathieu","last_name":"Surin"},{"first_name":"Frank","last_name":"Lafont","full_name":"Lafont, Frank"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Sylvain","full_name":"Gabriele, Sylvain","last_name":"Gabriele"}],"title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-cells-feel-curvature/","description":"News on IST Webpage"}]},"date_updated":"2025-04-14T07:52:26Z","page":"1382–1390","oa_version":"Submitted Version","publisher":"Springer Nature","corr_author":"1","volume":17,"department":[{"_id":"EdHa"}],"abstract":[{"text":"The early development of many organisms involves the folding of cell monolayers, but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic causes and effects of local curvature remain unclear. Here we study epithelial cell monolayers on corrugated hydrogels engineered into wavy patterns, examining how concave and convex curvatures affect cellular and nuclear shape. We find that substrate curvature affects monolayer thickness, which is larger in valleys than crests. We show that this feature generically arises in a vertex model, leading to the hypothesis that cells may sense curvature by modifying the thickness of the tissue. We find that local curvature also affects nuclear morphology and positioning, which we explain by extending the vertex model to take into account membrane–nucleus interactions, encoding thickness modulation in changes to nuclear deformation and position. We propose that curvature governs the spatial distribution of yes-associated proteins via nuclear shape and density changes. We show that curvature also induces significant variations in lamins, chromatin condensation and cell proliferation rate in folded epithelial tissues. Together, this work identifies active cell mechanics and nuclear mechanoadaptation as the key players of the mechanistic regulation of epithelia to substrate curvature.","lang":"eng"}],"type":"journal_article","citation":{"short":"M. Luciano, S. Xue, W.H. De Vos, L. Redondo-Morata, M. Surin, F. Lafont, E.B. Hannezo, S. Gabriele, Nature Physics 17 (2021) 1382–1390.","apa":"Luciano, M., Xue, S., De Vos, W. H., Redondo-Morata, L., Surin, M., Lafont, F., … Gabriele, S. (2021). Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-021-01374-1\">https://doi.org/10.1038/s41567-021-01374-1</a>","ama":"Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. <i>Nature Physics</i>. 2021;17(12):1382–1390. doi:<a href=\"https://doi.org/10.1038/s41567-021-01374-1\">10.1038/s41567-021-01374-1</a>","ieee":"M. Luciano <i>et al.</i>, “Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation,” <i>Nature Physics</i>, vol. 17, no. 12. Springer Nature, pp. 1382–1390, 2021.","chicago":"Luciano, Marine, Shi-lei Xue, Winnok H. De Vos, Lorena Redondo-Morata, Mathieu Surin, Frank Lafont, Edouard B Hannezo, and Sylvain Gabriele. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-021-01374-1\">https://doi.org/10.1038/s41567-021-01374-1</a>.","ista":"Luciano M, Xue S, De Vos WH, Redondo-Morata L, Surin M, Lafont F, Hannezo EB, Gabriele S. 2021. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 17(12), 1382–1390.","mla":"Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” <i>Nature Physics</i>, vol. 17, no. 12, Springer Nature, 2021, pp. 1382–1390, doi:<a href=\"https://doi.org/10.1038/s41567-021-01374-1\">10.1038/s41567-021-01374-1</a>."},"quality_controlled":"1","month":"11","issue":"12","scopus_import":"1","_id":"10365","external_id":{"isi":["000720204300004"]},"publication_status":"published","date_created":"2021-11-28T23:01:29Z"},{"publication_status":"published","date_created":"2021-11-28T23:01:30Z","external_id":{"isi":["000974771600028"],"pmid":["34800748"]},"_id":"10366","month":"11","issue":"12","scopus_import":"1","citation":{"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.","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” <i>Cells and Development</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">https://doi.org/10.1016/j.cdev.2021.203758</a>.","mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” <i>Cells and Development</i>, vol. 168, no. 12, 203758, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">10.1016/j.cdev.2021.203758</a>.","ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” <i>Cells and Development</i>. 2021;168(12). doi:<a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">10.1016/j.cdev.2021.203758</a>","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” <i>Cells and Development</i>, vol. 168, no. 12. Elsevier, 2021.","apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., &#38; Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” <i>Cells and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">https://doi.org/10.1016/j.cdev.2021.203758</a>","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021)."},"type":"journal_article","pmid":1,"quality_controlled":"1","volume":168,"department":[{"_id":"CaHe"}],"corr_author":"1","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cdev.2021.203758"}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"last_name":"Lennon","full_name":"Lennon, Ana Maria","first_name":"Ana Maria"},{"full_name":"Mayor, Roberto","last_name":"Mayor","first_name":"Roberto"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"}],"title":"Special rebranding issue: “Quantitative cell and developmental biology”","date_updated":"2024-10-09T21:01:13Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa":1,"doi":"10.1016/j.cdev.2021.203758","day":"17","date_published":"2021-11-17T00:00:00Z","intvolume":"       168","article_number":"203758","article_type":"letter_note","publication_identifier":{"issn":["2667-2901"]},"year":"2021","isi":1,"publication":"Cells and Development","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa_version":"Published Version","file_date_updated":"2021-11-29T08:41:00Z","article_processing_charge":"No","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"page":"29-30","date_updated":"2022-01-26T14:26:36Z","title":"Recognizing multimodal entailment","author":[{"first_name":"Cesar","last_name":"Ilharco","full_name":"Ilharco, Cesar"},{"first_name":"Afsaneh","full_name":"Shirazi, Afsaneh","last_name":"Shirazi"},{"first_name":"Arjun","last_name":"Gopalan","full_name":"Gopalan, Arjun"},{"first_name":"Arsha","last_name":"Nagrani","full_name":"Nagrani, Arsha"},{"first_name":"Blaž","last_name":"Bratanič","full_name":"Bratanič, Blaž"},{"full_name":"Bregler, Chris","last_name":"Bregler","first_name":"Chris"},{"last_name":"Liu","full_name":"Liu, Christina","first_name":"Christina"},{"last_name":"Ferreira","full_name":"Ferreira, Felipe","first_name":"Felipe"},{"first_name":"Gabriek","last_name":"Barcik","full_name":"Barcik, Gabriek"},{"first_name":"Gabriel","last_name":"Ilharco","full_name":"Ilharco, Gabriel"},{"first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","full_name":"Osang, Georg F"},{"first_name":"Jannis","last_name":"Bulian","full_name":"Bulian, Jannis"},{"full_name":"Frank, Jared","last_name":"Frank","first_name":"Jared"},{"first_name":"Lucas","last_name":"Smaira","full_name":"Smaira, Lucas"},{"first_name":"Qin","last_name":"Cao","full_name":"Cao, Qin"},{"first_name":"Ricardo","full_name":"Marino, Ricardo","last_name":"Marino"},{"last_name":"Patel","full_name":"Patel, Roma","first_name":"Roma"},{"full_name":"Leung, Thomas","last_name":"Leung","first_name":"Thomas"},{"first_name":"Vaiva","last_name":"Imbrasaite","full_name":"Imbrasaite, Vaiva"}],"year":"2021","acknowledgement":"We would like to thank Abby Schantz, Abe Ittycheriah, Aliaksei Severyn, Allan Heydon, Aly\r\nGrealish, Andrey Vlasov, Arkaitz Zubiaga, Ashwin Kakarla, Chen Sun, Clayton Williams, Cong\r\nYu, Cordelia Schmid, Da-Cheng Juan, Dan Finnie, Dani Valevski, Daniel Rocha, David Price, David Sklar, Devi Krishna, Elena Kochkina, Enrique Alfonseca, Franc¸oise Beaufays, Isabelle Augenstein, Jialu Liu, John Cantwell, John Palowitch, Jordan Boyd-Graber, Lei Shi, Luis Valente, Maria Voitovich, Mehmet Aktuna, Mogan Brown, Mor Naaman, Natalia P, Nidhi Hebbar, Pete Aykroyd, Rahul Sukthankar, Richa Dixit, Steve Pucci, Tania Bedrax-Weiss, Tobias Kaufmann, Tom Boulos, Tu Tsao, Vladimir Chtchetkine, Yair Kurzion, Yifan Xu and Zach Hynes.","publication_identifier":{"isbn":["9-781-9540-8557-2"]},"date_published":"2021-08-01T00:00:00Z","doi":"10.18653/v1/2021.acl-tutorials.6","day":"01","oa":1,"file":[{"access_level":"open_access","date_created":"2021-11-29T08:41:00Z","success":1,"file_name":"2021_ACL_Ilharco.pdf","creator":"cchlebak","file_size":1227703,"content_type":"application/pdf","checksum":"b14052a025a6ecf675bdfe51db98c0d7","relation":"main_file","date_updated":"2021-11-29T08:41:00Z","file_id":"10368"}],"ddc":["000"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts","conference":{"start_date":"2021-08-01","location":"Bangkok, Thailand","name":"ACL: Association for Computational Linguistics ; IJCNLP: International Joint Conference on Natural Language Processing","end_date":"2021-08-06"},"date_created":"2021-11-28T23:01:30Z","publication_status":"published","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"},"scopus_import":"1","month":"08","_id":"10367","quality_controlled":"1","abstract":[{"lang":"eng","text":"How information is created, shared and consumed has changed rapidly in recent decades, in part thanks to new social platforms and technologies on the web. With ever-larger amounts of unstructured and limited labels, organizing and reconciling information from different sources and modalities is a central challenge in machine learning. This cutting-edge tutorial aims to introduce the multimodal entailment task, which can be useful for detecting semantic alignments when a single modality alone does not suffice for a whole content understanding. Starting with a brief overview of natural language processing, computer vision, structured data and neural graph learning, we lay the foundations for the multimodal sections to follow. We then discuss recent multimodal learning literature covering visual, audio and language streams, and explore case studies focusing on tasks which require fine-grained understanding of visual and linguistic semantics question answering, veracity and hatred classification. Finally, we introduce a new dataset for recognizing multimodal entailment, exploring it in a hands-on collaborative section. Overall, this tutorial gives an overview of multimodal learning, introduces a multimodal entailment dataset, and encourages future research in the topic."}],"type":"conference","citation":{"short":"C. Ilharco, A. Shirazi, A. Gopalan, A. Nagrani, B. Bratanič, C. Bregler, C. Liu, F. Ferreira, G. Barcik, G. Ilharco, G.F. Osang, J. Bulian, J. Frank, L. Smaira, Q. Cao, R. Marino, R. Patel, T. Leung, V. Imbrasaite, in:, 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts, Association for Computational Linguistics, 2021, pp. 29–30.","mla":"Ilharco, Cesar, et al. “Recognizing Multimodal Entailment.” <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i>, Association for Computational Linguistics, 2021, pp. 29–30, doi:<a href=\"https://doi.org/10.18653/v1/2021.acl-tutorials.6\">10.18653/v1/2021.acl-tutorials.6</a>.","ista":"Ilharco C, Shirazi A, Gopalan A, Nagrani A, Bratanič B, Bregler C, Liu C, Ferreira F, Barcik G, Ilharco G, Osang GF, Bulian J, Frank J, Smaira L, Cao Q, Marino R, Patel R, Leung T, Imbrasaite V. 2021. Recognizing multimodal entailment. 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts. ACL: Association for Computational Linguistics ; IJCNLP: International Joint Conference on Natural Language Processing, 29–30.","chicago":"Ilharco, Cesar, Afsaneh Shirazi, Arjun Gopalan, Arsha Nagrani, Blaž Bratanič, Chris Bregler, Christina Liu, et al. “Recognizing Multimodal Entailment.” In <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i>, 29–30. Association for Computational Linguistics, 2021. <a href=\"https://doi.org/10.18653/v1/2021.acl-tutorials.6\">https://doi.org/10.18653/v1/2021.acl-tutorials.6</a>.","ama":"Ilharco C, Shirazi A, Gopalan A, et al. Recognizing multimodal entailment. In: <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i>. Association for Computational Linguistics; 2021:29-30. doi:<a href=\"https://doi.org/10.18653/v1/2021.acl-tutorials.6\">10.18653/v1/2021.acl-tutorials.6</a>","ieee":"C. Ilharco <i>et al.</i>, “Recognizing multimodal entailment,” in <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i>, Bangkok, Thailand, 2021, pp. 29–30.","apa":"Ilharco, C., Shirazi, A., Gopalan, A., Nagrani, A., Bratanič, B., Bregler, C., … Imbrasaite, V. (2021). Recognizing multimodal entailment. In <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i> (pp. 29–30). Bangkok, Thailand: Association for Computational Linguistics. <a href=\"https://doi.org/10.18653/v1/2021.acl-tutorials.6\">https://doi.org/10.18653/v1/2021.acl-tutorials.6</a>"},"main_file_link":[{"url":"https://aclanthology.org/2021.acl-tutorials.6/","open_access":"1"}],"publisher":"Association for Computational Linguistics","department":[{"_id":"HeEd"}]}]