[{"citation":{"ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>","mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>, vol. 10, 72132, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>.","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132.","chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>.","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","apa":"Marconi, M., Gallemi, M., Benková, E., &#38; Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>"},"has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","article_number":"72132","author":[{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi","orcid":"0000-0003-4675-6893","first_name":"Marçal"},{"full_name":"Benková, Eva","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"full_name":"Wabnik, Krzysztof","last_name":"Wabnik","first_name":"Krzysztof"}],"file_date_updated":"2022-05-13T09:00:29Z","_id":"10270","publisher":"eLife Sciences Publications","intvolume":"        10","type":"journal_article","isi":1,"year":"2021","publication":"eLife","article_type":"original","external_id":{"isi":["000734671200001"],"pmid":["34723798"]},"title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","volume":10,"publication_identifier":{"issn":["2050-084X"]},"acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","date_created":"2021-11-11T10:05:18Z","article_processing_charge":"Yes","department":[{"_id":"EvBe"}],"date_updated":"2023-08-14T11:49:23Z","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"day":"01","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2022-05-13T09:00:29Z","content_type":"application/pdf","relation":"main_file","checksum":"fad13c509b53bb7a2bef9c946a7ca60a","date_created":"2022-05-13T09:00:29Z","file_id":"11372","success":1,"file_size":14137503,"file_name":"2021_eLife_Marconi.pdf"}],"abstract":[{"text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.","lang":"eng"}],"publication_status":"published","ddc":["570"],"status":"public","date_published":"2021-11-01T00:00:00Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"11","doi":"10.7554/elife.72132","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"file":[{"content_type":"application/pdf","relation":"main_file","creator":"cchlebak","access_level":"open_access","date_updated":"2021-11-15T13:25:52Z","success":1,"file_name":"2021_NatComm_Aubret.pdf","file_size":6282703,"checksum":"1c392b12b9b7b615d422d9fabe19cdb9","date_created":"2021-11-15T13:25:52Z","file_id":"10292"}],"day":"04","oa":1,"language":[{"iso":"eng"}],"issue":"1","date_updated":"2023-08-14T11:48:37Z","oa_version":"Published Version","doi":"10.1038/s41467-021-26699-6","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"11","status":"public","date_published":"2021-11-04T00:00:00Z","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"}],"publication_status":"published","ddc":["530"],"type":"journal_article","isi":1,"publisher":"Springer Nature","intvolume":"        12","author":[{"full_name":"Aubret, Antoine","last_name":"Aubret","first_name":"Antoine"},{"full_name":"Martinet, Quentin","orcid":"0000-0002-2916-6632","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","last_name":"Martinet","first_name":"Quentin"},{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","orcid":"0000-0002-7253-9465","first_name":"Jérémie A"}],"file_date_updated":"2021-11-15T13:25:52Z","_id":"10280","citation":{"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>.","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","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>","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","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>."},"has_accepted_license":"1","article_number":"6398","scopus_import":"1","quality_controlled":"1","department":[{"_id":"JePa"}],"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.","date_created":"2021-11-14T23:01:23Z","article_processing_charge":"Yes","year":"2021","publication":"Nature Communications","external_id":{"isi":["000714754400010"],"pmid":["34737315"]},"article_type":"original","title":"Metamachines of pluripotent colloids","volume":12},{"oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2023-08-14T11:47:35Z","file":[{"checksum":"74743baa6ef431ef60c3de3bc4da045a","date_created":"2022-05-16T07:07:41Z","file_id":"11381","success":1,"file_size":488583,"file_name":"2021_EmboReports_Restivo.pdf","creator":"dernst","access_level":"open_access","date_updated":"2022-05-16T07:07:41Z","content_type":"application/pdf","relation":"main_file"}],"day":"04","status":"public","date_published":"2021-11-04T00:00:00Z","publication_status":"published","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"}],"ddc":["570"],"doi":"10.15252/embr.202153824","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"month":"11","author":[{"first_name":"Leonardo","last_name":"Restivo","full_name":"Restivo, Leonardo"},{"full_name":"Gerlach, Björn","first_name":"Björn","last_name":"Gerlach"},{"last_name":"Tsoory","first_name":"Michael","full_name":"Tsoory, Michael"},{"last_name":"Bikovski","first_name":"Lior","full_name":"Bikovski, Lior"},{"full_name":"Badurek, Sylvia","last_name":"Badurek","first_name":"Sylvia"},{"last_name":"Pitzer","first_name":"Claudia","full_name":"Pitzer, Claudia"},{"first_name":"Isabelle C.","last_name":"Kos-Braun","full_name":"Kos-Braun, Isabelle C."},{"first_name":"Anne Laure Mj","last_name":"Mausset-Bonnefont","full_name":"Mausset-Bonnefont, Anne Laure Mj"},{"first_name":"Jonathan","last_name":"Ward","full_name":"Ward, Jonathan"},{"last_name":"Schunn","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300","first_name":"Michael","full_name":"Schunn, Michael"},{"first_name":"Lucas P.J.J.","last_name":"Noldus","full_name":"Noldus, Lucas P.J.J."},{"last_name":"Bespalov","first_name":"Anton","full_name":"Bespalov, Anton"},{"full_name":"Voikar, Vootele","first_name":"Vootele","last_name":"Voikar"}],"file_date_updated":"2022-05-16T07:07:41Z","_id":"10283","citation":{"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>","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>.","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.","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.","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>.","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>","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)."},"has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","article_number":"e53824","type":"journal_article","isi":1,"publisher":"EMBO Press","intvolume":"        22","year":"2021","publication":"EMBO Reports","title":"Towards best practices in research: Role of academic core facilities","article_type":"original","external_id":{"isi":["000714350000001"]},"volume":22,"department":[{"_id":"PreCl"}],"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"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.","date_created":"2021-11-14T23:01:24Z","article_processing_charge":"Yes (in subscription journal)"},{"intvolume":"        26","publisher":"Institute of Mathematical Statistics","type":"journal_article","scopus_import":"1","article_number":"124","quality_controlled":"1","has_accepted_license":"1","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>","ista":"Dubach G. 2021. On eigenvector statistics in the spherical and truncated unitary ensembles. Electronic Journal of Probability. 26, 124.","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>.","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.","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>.","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>","short":"G. Dubach, Electronic Journal of Probability 26 (2021)."},"_id":"10285","file_date_updated":"2021-11-15T10:10:17Z","author":[{"orcid":"0000-0001-6892-8137","last_name":"Dubach","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Guillaume","full_name":"Dubach, Guillaume"}],"article_processing_charge":"No","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.","date_created":"2021-11-14T23:01:25Z","publication_identifier":{"eissn":["1083-6489"]},"department":[{"_id":"LaEr"}],"volume":26,"title":"On eigenvector statistics in the spherical and truncated unitary ensembles","article_type":"original","publication":"Electronic Journal of Probability","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"year":"2021","day":"28","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","date_updated":"2021-11-15T10:10:17Z","file_size":735940,"file_name":"2021_ElecJournalProb_Dubach.pdf","success":1,"checksum":"1c975afb31460277ce4d22b93538e5f9","file_id":"10288","date_created":"2021-11-15T10:10:17Z"}],"date_updated":"2025-04-14T07:43:47Z","oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"month":"09","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1214/21-EJP686","ddc":["519"],"publication_status":"published","abstract":[{"lang":"eng","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."}],"date_published":"2021-09-28T00:00:00Z","status":"public"},{"corr_author":"1","file":[{"success":1,"file_name":"2021_JournalStructBiol_Dimchev.pdf","file_size":16818304,"checksum":"6b209e4d44775d4e02b50f78982c15fa","date_created":"2021-11-15T13:11:27Z","file_id":"10291","content_type":"application/pdf","relation":"main_file","creator":"cchlebak","access_level":"open_access","date_updated":"2021-11-15T13:11:27Z"}],"day":"03","language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-04-15T08:25:41Z","oa_version":"Published Version","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.jsb.2021.107808","month":"11","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-11-03T00:00:00Z","status":"public","ddc":["572"],"publication_status":"published","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"}],"isi":1,"type":"journal_article","intvolume":"       213","publisher":"Elsevier ","file_date_updated":"2021-11-15T13:11:27Z","_id":"10290","author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","orcid":"0000-0001-8370-6161","first_name":"Georgi A","full_name":"Dimchev, Georgi A"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","full_name":"Fäßler, Florian"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"article_number":"107808","quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","keyword":["Structural Biology"],"citation":{"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>","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","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>.","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.","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.","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>"},"department":[{"_id":"FlSc"}],"article_processing_charge":"Yes (via OA deal)","date_created":"2021-11-15T12:21:42Z","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.","publication_identifier":{"issn":["1047-8477"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"volume":213,"external_id":{"isi":["000720259500002"]},"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","article_type":"original","publication":"Journal of Structural Biology","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF"}],"year":"2021","related_material":{"record":[{"relation":"software","id":"14502","status":"public"}]}},{"department":[{"_id":"GaNo"}],"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).","date_created":"2021-11-18T06:59:45Z","article_processing_charge":"No","publication_identifier":{"issn":["2050-084X"]},"article_type":"original","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","external_id":{"isi":["000720945900001"]},"volume":10,"year":"2021","publication":"eLife","type":"journal_article","isi":1,"intvolume":"        10","publisher":"eLife Sciences Publications","author":[{"full_name":"Conde-Dusman, María J","last_name":"Conde-Dusman","first_name":"María J"},{"full_name":"Dey, Partha N","first_name":"Partha N","last_name":"Dey"},{"full_name":"Elía-Zudaire, Óscar","last_name":"Elía-Zudaire","first_name":"Óscar"},{"id":"33D1B084-F248-11E8-B48F-1D18A9856A87","last_name":"Garcia Rabaneda","first_name":"Luis E","full_name":"Garcia Rabaneda, Luis E"},{"full_name":"García-Lira, Carmen","last_name":"García-Lira","first_name":"Carmen"},{"full_name":"Grand, Teddy","first_name":"Teddy","last_name":"Grand"},{"full_name":"Briz, Victor","first_name":"Victor","last_name":"Briz"},{"last_name":"Velasco","first_name":"Eric R","full_name":"Velasco, Eric R"},{"full_name":"Andero Galí, Raül","last_name":"Andero Galí","first_name":"Raül"},{"full_name":"Niñerola, Sergio","last_name":"Niñerola","first_name":"Sergio"},{"last_name":"Barco","first_name":"Angel","full_name":"Barco, Angel"},{"first_name":"Pierre","last_name":"Paoletti","full_name":"Paoletti, Pierre"},{"full_name":"Wesseling, John F","last_name":"Wesseling","first_name":"John F"},{"full_name":"Gardoni, Fabrizio","last_name":"Gardoni","first_name":"Fabrizio"},{"first_name":"Steven J","last_name":"Tavalin","full_name":"Tavalin, Steven J"},{"full_name":"Perez-Otaño, Isabel","first_name":"Isabel","last_name":"Perez-Otaño"}],"_id":"10301","file_date_updated":"2021-11-18T07:02:02Z","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","article_number":"e71575","citation":{"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>","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.","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.","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>.","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>.","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>","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)."},"keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"doi":"10.7554/elife.71575","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"11","date_published":"2021-11-17T00:00:00Z","status":"public","abstract":[{"lang":"eng","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."}],"publication_status":"published","ddc":["570"],"file":[{"date_updated":"2021-11-18T07:02:02Z","access_level":"open_access","creator":"lgarciar","relation":"main_file","content_type":"application/pdf","file_id":"10302","date_created":"2021-11-18T07:02:02Z","checksum":"59318e9e41507cec83c2f4070e6ad540","file_name":"elife-71575-v1.pdf","file_size":2477302,"success":1}],"day":"17","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","date_updated":"2024-10-21T06:02:05Z"},{"keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"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>","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.","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>.","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.","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).","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>"},"scopus_import":"1","article_number":"304","quality_controlled":"1","has_accepted_license":"1","file_date_updated":"2021-11-19T15:09:18Z","_id":"10310","author":[{"full_name":"Çoruh, Mehmet Orkun","first_name":"Mehmet Orkun","orcid":"0000-0002-3219-2022","last_name":"Çoruh","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef"},{"full_name":"Frank, Anna","last_name":"Frank","first_name":"Anna"},{"full_name":"Tanaka, Hideaki","last_name":"Tanaka","first_name":"Hideaki"},{"first_name":"Akihiro","last_name":"Kawamoto","full_name":"Kawamoto, Akihiro"},{"full_name":"El-Mohsnawy, Eithar","first_name":"Eithar","last_name":"El-Mohsnawy"},{"last_name":"Kato","first_name":"Takayuki","full_name":"Kato, Takayuki"},{"full_name":"Namba, Keiichi","last_name":"Namba","first_name":"Keiichi"},{"full_name":"Gerle, Christoph","last_name":"Gerle","first_name":"Christoph"},{"last_name":"Nowaczyk","first_name":"Marc M.","full_name":"Nowaczyk, Marc M."},{"full_name":"Kurisu, Genji","first_name":"Genji","last_name":"Kurisu"}],"publisher":"Springer ","intvolume":"         4","isi":1,"type":"journal_article","publication":"Communications Biology","year":"2021","volume":4,"article_type":"original","external_id":{"pmid":["33686186"],"isi":["000627440700001"]},"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","publication_identifier":{"issn":["2399-3642"]},"article_processing_charge":"No","date_created":"2021-11-19T11:37:29Z","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.","department":[{"_id":"LeSa"}],"oa_version":"Published Version","date_updated":"2023-08-14T11:51:19Z","issue":"1","oa":1,"language":[{"iso":"eng"}],"day":"08","file":[{"checksum":"8ffd39f2bba7152a2441802ff313bf0b","file_id":"10318","date_created":"2021-11-19T15:09:18Z","file_size":6030261,"file_name":"2021_CommBio_Çoruh.pdf","success":1,"access_level":"open_access","creator":"cchlebak","date_updated":"2021-11-19T15:09:18Z","relation":"main_file","content_type":"application/pdf"}],"ddc":["570"],"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."}],"publication_status":"published","status":"public","date_published":"2021-03-08T00:00:00Z","month":"03","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"doi":"10.1038/s42003-021-01808-9"},{"month":"11","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"doi":"10.1371/journal.pbio.3001431","ddc":["570"],"publication_status":"published","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."}],"status":"public","date_published":"2021-11-01T00:00:00Z","day":"01","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2021-11-22T09:34:03Z","creator":"cchlebak","access_level":"open_access","success":1,"file_size":4069215,"file_name":"2021_PLoSBio_Chauve.pdf","date_created":"2021-11-22T09:34:03Z","file_id":"10330","checksum":"0c61b667f814fd9435b3ac42036fc36d"}],"date_updated":"2023-08-14T11:53:27Z","oa_version":"Published Version","issue":"11","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"article_processing_charge":"No","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.","date_created":"2021-11-21T23:01:28Z","department":[{"_id":"MaDe"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13069"}]},"publication":"PLoS Biology","year":"2021","volume":19,"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","article_type":"original","external_id":{"isi":["000715818400001"],"pmid":["34723964"]},"publisher":"Public Library of Science","intvolume":"        19","isi":1,"type":"journal_article","citation":{"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).","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>","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>.","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>.","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.","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.","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>"},"quality_controlled":"1","scopus_import":"1","article_number":"e3001431","has_accepted_license":"1","file_date_updated":"2021-11-22T09:34:03Z","_id":"10322","author":[{"last_name":"Chauve","first_name":"Laetitia","full_name":"Chauve, Laetitia"},{"full_name":"Hodge, Francesca","first_name":"Francesca","last_name":"Hodge"},{"last_name":"Murdoch","first_name":"Sharlene","full_name":"Murdoch, Sharlene"},{"full_name":"Masoudzadeh, Fatemah","first_name":"Fatemah","last_name":"Masoudzadeh"},{"last_name":"Mann","first_name":"Harry Jack","full_name":"Mann, Harry Jack"},{"first_name":"Andrea","last_name":"Lopez-Clavijo","full_name":"Lopez-Clavijo, Andrea"},{"full_name":"Okkenhaug, Hanneke","first_name":"Hanneke","last_name":"Okkenhaug"},{"full_name":"West, Greg","last_name":"West","first_name":"Greg"},{"full_name":"Sousa, Bebiana C.","first_name":"Bebiana C.","last_name":"Sousa"},{"full_name":"Segonds-Pichon, Anne","first_name":"Anne","last_name":"Segonds-Pichon"},{"first_name":"Cheryl","last_name":"Li","full_name":"Li, Cheryl"},{"full_name":"Wingett, Steven","first_name":"Steven","last_name":"Wingett"},{"last_name":"Kienberger","first_name":"Hermine","full_name":"Kienberger, Hermine"},{"full_name":"Kleigrewe, Karin","last_name":"Kleigrewe","first_name":"Karin"},{"full_name":"De Bono, Mario","first_name":"Mario","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443"},{"first_name":"Michael","last_name":"Wakelam","full_name":"Wakelam, Michael"},{"first_name":"Olivia","last_name":"Casanueva","full_name":"Casanueva, Olivia"}]},{"article_number":"762005","scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","citation":{"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>","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.","ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005.","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>.","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>.","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>","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021)."},"_id":"10323","file_date_updated":"2021-11-23T15:06:58Z","author":[{"first_name":"Iva","last_name":"Sučec","full_name":"Sučec, Iva"},{"full_name":"Bersch, Beate","first_name":"Beate","last_name":"Bersch"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul"}],"intvolume":"         8","publisher":"Frontiers","isi":1,"type":"journal_article","volume":8,"title":"How do chaperones bind (partly) unfolded client proteins?","article_type":"original","external_id":{"pmid":["34760928"],"isi":["000717241700001"]},"publication":"Frontiers in Molecular Biosciences","year":"2021","article_processing_charge":"Yes (via OA deal)","date_created":"2021-11-21T23:01:29Z","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).","publication_identifier":{"eissn":["2296-889X"]},"department":[{"_id":"PaSc"}],"oa_version":"Published Version","date_updated":"2024-10-09T21:01:12Z","language":[{"iso":"eng"}],"oa":1,"day":"25","corr_author":"1","file":[{"success":1,"file_name":"2021_FrontiersMolBioSc_Sučec.pdf","file_size":4700798,"checksum":"a5c9dbf80dc2c5aaa737f456c941d964","date_created":"2021-11-23T15:06:58Z","file_id":"10333","content_type":"application/pdf","relation":"main_file","creator":"cchlebak","access_level":"open_access","date_updated":"2021-11-23T15:06:58Z"}],"ddc":["547"],"publication_status":"published","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."}],"date_published":"2021-10-25T00:00:00Z","status":"public","month":"10","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"doi":"10.3389/fmolb.2021.762005"},{"publication_status":"published","abstract":[{"text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity.","lang":"eng"}],"date_published":"2021-10-23T00:00:00Z","status":"public","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1905.11360","open_access":"1"}],"doi":"10.1007/978-3-662-64331-0_11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-14T12:59:58Z","alternative_title":["LNCS"],"oa_version":"Preprint","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"day":"23","page":"209-230","title":"Brick: Asynchronous incentive-compatible payment channels","external_id":{"arxiv":["1905.11360"],"isi":["000712016200011"]},"volume":"12675 ","year":"2021","publication":"25th International Conference on Financial Cryptography and Data Security","date_created":"2021-11-21T23:01:29Z","acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","article_processing_charge":"No","publication_identifier":{"eisbn":["978-3-662-64331-0"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-6626-4330-3"]},"conference":{"location":"Virtual","end_date":"2021-03-05","start_date":"2021-03-01","name":"FC: Financial Cryptography"},"department":[{"_id":"ElKo"}],"quality_controlled":"1","scopus_import":"1","citation":{"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>","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>.","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.","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.","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>.","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."},"author":[{"last_name":"Avarikioti","first_name":"Zeta","full_name":"Avarikioti, Zeta"},{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Wattenhofer, Roger","last_name":"Wattenhofer","first_name":"Roger"},{"last_name":"Zindros","first_name":"Dionysis","full_name":"Zindros, Dionysis"}],"_id":"10324","publisher":"Springer Nature","type":"conference","isi":1},{"date_updated":"2023-08-14T12:59:26Z","alternative_title":["LNCS"],"oa_version":"Preprint","oa":1,"language":[{"iso":"eng"}],"day":"23","publication_status":"published","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"}],"date_published":"2021-10-23T00:00:00Z","status":"public","month":"10","main_file_link":[{"url":"https://eprint.iacr.org/2019/1128","open_access":"1"}],"doi":"10.1007/978-3-662-64331-0_1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","scopus_import":"1","citation":{"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>","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>.","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.","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.","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>.","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.","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>"},"author":[{"full_name":"Zamyatin, Alexei","first_name":"Alexei","last_name":"Zamyatin"},{"last_name":"Al-Bassam","first_name":"Mustafa","full_name":"Al-Bassam, Mustafa"},{"full_name":"Zindros, Dionysis","first_name":"Dionysis","last_name":"Zindros"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"full_name":"Moreno-Sanchez, Pedro","first_name":"Pedro","last_name":"Moreno-Sanchez"},{"full_name":"Kiayias, Aggelos","last_name":"Kiayias","first_name":"Aggelos"},{"full_name":"Knottenbelt, William J.","first_name":"William J.","last_name":"Knottenbelt"}],"_id":"10325","publisher":"Springer Nature","type":"conference","isi":1,"page":"3-36","external_id":{"isi":["000712016200001"]},"title":"SoK: Communication across distributed ledgers","volume":"12675 ","year":"2021","publication":"25th International Conference on Financial Cryptography and Data Security","acknowledgement":"We would like express our gratitude to Georgia Avarikioti, Daniel Perez and Dominik Harz for helpful comments and feedback on earlier versions of this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler, Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages of this research. We also wish to thank the anonymous reviewers for their valuable comments that helped improve the presentation of our results. This research was funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian Doppler Laboratory for Security and Quality Improvement in the Production System Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs through the project SLN: Scalability for the Lightning Network; and by the Austrian Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted the early stages of this work during his time at SBA Research, and was supported by a Binance Research Fellowship.","date_created":"2021-11-21T23:01:29Z","article_processing_charge":"No","publication_identifier":{"isbn":["9-783-6626-4330-3"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-662-64331-0"]},"conference":{"end_date":"2021-03-05","start_date":"2021-03-01","location":"Virtual","name":"FC: Financial Cryptography"},"department":[{"_id":"ElKo"}]},{"author":[{"first_name":"Enjun","last_name":"Xu","full_name":"Xu, Enjun"},{"last_name":"Chai","first_name":"Liang","full_name":"Chai, Liang"},{"first_name":"Shiqi","last_name":"Zhang","full_name":"Zhang, Shiqi"},{"first_name":"Ruixue","last_name":"Yu","full_name":"Yu, Ruixue"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","first_name":"Xixi"},{"first_name":"Chongyi","last_name":"Xu","full_name":"Xu, Chongyi"},{"last_name":"Hu","first_name":"Yuxin","full_name":"Hu, Yuxin"}],"_id":"10326","file_date_updated":"2025-01-21T12:41:43Z","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","citation":{"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.","ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. <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.","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>","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>."},"type":"journal_article","isi":1,"intvolume":"         7","publisher":"Springer Nature","title":"Catabolism of strigolactones by a carboxylesterase","external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"article_type":"original","volume":7,"year":"2021","publication":"Nature Plants","OA_place":"repository","page":"1495–1504 ","department":[{"_id":"JiFr"}],"date_created":"2021-11-21T23:01:30Z","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_processing_charge":"No","publication_identifier":{"eissn":["2055-0278"]},"language":[{"iso":"eng"}],"oa":1,"oa_version":"Submitted Version","date_updated":"2025-01-21T12:42:52Z","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2025-01-21T12:41:43Z","file_size":41109943,"file_name":"Accepted version_Xu et al.,2021 Catabolism of strigolactones by a carboxylesterase.pdf","success":1,"checksum":"d20231806bea67f0fd19e96a94a048f4","file_id":"18864","date_created":"2025-01-21T12:41:43Z"}],"day":"11","date_published":"2021-11-11T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","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."}],"ddc":["580"],"pmid":1,"doi":"10.1038/s41477-021-01011-y","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","month":"11"},{"department":[{"_id":"MaIb"}],"article_processing_charge":"No","date_created":"2021-11-21T23:01:30Z","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.","publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"volume":13,"title":"PbS–Pb–CuxS composites for thermoelectric application","external_id":{"isi":["000715852100070"],"pmid":["34665616"]},"article_type":"original","publication":"ACS Applied Materials and Interfaces","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"year":"2021","page":"51373–51382","isi":1,"type":"journal_article","intvolume":"        13","publisher":"American Chemical Society ","_id":"10327","author":[{"full_name":"Li, Mengyao","first_name":"Mengyao","last_name":"Li"},{"first_name":"Yu","orcid":"0000-0001-7313-6740","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"last_name":"Han","first_name":"Xu","full_name":"Han, Xu"},{"first_name":"Ke","last_name":"Xiao","full_name":"Xiao, Ke"},{"full_name":"Nabahat, Mehran","first_name":"Mehran","last_name":"Nabahat"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"last_name":"Llorca","first_name":"Jordi","full_name":"Llorca, Jordi"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"scopus_import":"1","quality_controlled":"1","keyword":["CuxS","PbS","energy conversion","nanocomposite","nanoparticle","solution synthesis","thermoelectric"],"citation":{"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>","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.","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>.","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.","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.","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>.","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1021/acsami.1c15609","month":"10","main_file_link":[{"url":"https://upcommons.upc.edu/bitstream/2117/363528/1/Pb%20mengyao.pdf","open_access":"1"}],"date_published":"2021-10-19T00:00:00Z","status":"public","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."}],"publication_status":"published","corr_author":"1","day":"19","language":[{"iso":"eng"}],"oa":1,"ec_funded":1,"date_updated":"2025-04-14T07:43:47Z","oa_version":"Submitted Version","issue":"43"},{"article_type":"original","title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","external_id":{"pmid":["34725710"],"isi":["000746596900001"]},"volume":34,"year":"2021","publication":"Protein Engineering, Design and Selection","date_created":"2021-11-28T23:01:28Z","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_processing_charge":"No","publication_identifier":{"issn":["1741-0126"],"eissn":["1741-0134"]},"department":[{"_id":"CaGu"}],"quality_controlled":"1","article_number":"gzab025","scopus_import":"1","citation":{"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.","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.","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>.","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).","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>"},"author":[{"last_name":"Lee","first_name":"Jungmin","full_name":"Lee, Jungmin"},{"last_name":"Vernet","first_name":"Andyna","full_name":"Vernet, Andyna"},{"full_name":"Gruber, Nathalie","first_name":"Nathalie","last_name":"Gruber","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425"},{"full_name":"Kready, Kasia M.","first_name":"Kasia M.","last_name":"Kready"},{"first_name":"Devin R.","last_name":"Burrill","full_name":"Burrill, Devin R."},{"full_name":"Way, Jeffrey C.","first_name":"Jeffrey C.","last_name":"Way"},{"first_name":"Pamela A.","last_name":"Silver","full_name":"Silver, Pamela A."}],"_id":"10363","intvolume":"        34","publisher":"Oxford University Press","type":"journal_article","isi":1,"publication_status":"published","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."}],"date_published":"2021-11-01T00:00:00Z","status":"public","month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/protein/gzab025"}],"pmid":1,"doi":"10.1093/protein/gzab025","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-14T13:01:38Z","oa_version":"Published Version","oa":1,"language":[{"iso":"eng"}],"day":"01"},{"corr_author":"1","file":[{"date_updated":"2023-10-11T09:31:43Z","creator":"channezo","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2023-10-11T09:31:43Z","file_id":"14420","checksum":"5d6d76750a71d7cb632bb15417c38ef7","success":1,"file_name":"50145_4_merged_1630498627.pdf","file_size":40285498}],"day":"18","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-04-14T07:52:26Z","oa_version":"Submitted Version","issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41567-021-01374-1","month":"11","date_published":"2021-11-18T00:00:00Z","status":"public","ddc":["530"],"abstract":[{"lang":"eng","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."}],"publication_status":"published","isi":1,"type":"journal_article","intvolume":"        17","publisher":"Springer Nature","_id":"10365","file_date_updated":"2023-10-11T09:31:43Z","author":[{"full_name":"Luciano, Marine","last_name":"Luciano","first_name":"Marine"},{"full_name":"Xue, Shi-lei","first_name":"Shi-lei","last_name":"Xue","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Vos, Winnok H.","first_name":"Winnok H.","last_name":"De Vos"},{"full_name":"Redondo-Morata, Lorena","first_name":"Lorena","last_name":"Redondo-Morata"},{"full_name":"Surin, Mathieu","last_name":"Surin","first_name":"Mathieu"},{"last_name":"Lafont","first_name":"Frank","full_name":"Lafont, Frank"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"first_name":"Sylvain","last_name":"Gabriele","full_name":"Gabriele, Sylvain"}],"quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","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>","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>.","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.","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>.","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>"},"department":[{"_id":"EdHa"}],"article_processing_charge":"No","date_created":"2021-11-28T23:01:29Z","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.","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"volume":17,"title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","article_type":"original","external_id":{"isi":["000720204300004"]},"project":[{"grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","grant_number":"P31639"}],"publication":"Nature Physics","year":"2021","page":"1382–1390","related_material":{"link":[{"description":"News on IST Webpage","url":"https://ist.ac.at/en/news/how-cells-feel-curvature/","relation":"press_release"}]}},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cdev.2021.203758"}],"month":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"doi":"10.1016/j.cdev.2021.203758","publication_status":"published","status":"public","date_published":"2021-11-17T00:00:00Z","day":"17","corr_author":"1","date_updated":"2024-10-09T21:01:13Z","oa_version":"Published Version","issue":"12","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2667-2901"]},"article_processing_charge":"No","date_created":"2021-11-28T23:01:30Z","department":[{"_id":"CaHe"}],"publication":"Cells and Development","year":"2021","volume":168,"article_type":"letter_note","external_id":{"isi":["000974771600028"],"pmid":["34800748"]},"title":"Special rebranding issue: “Quantitative cell and developmental biology”","publisher":"Elsevier","intvolume":"       168","isi":1,"type":"journal_article","citation":{"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>.","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).","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.","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>.","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."},"scopus_import":"1","article_number":"203758","quality_controlled":"1","_id":"10366","author":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"full_name":"Lennon, Ana Maria","first_name":"Ana Maria","last_name":"Lennon"},{"full_name":"Mayor, Roberto","last_name":"Mayor","first_name":"Roberto"},{"last_name":"Salbreux","first_name":"Guillaume","full_name":"Salbreux, Guillaume"}]},{"file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2021-11-29T08:41:00Z","creator":"cchlebak","access_level":"open_access","success":1,"file_size":1227703,"file_name":"2021_ACL_Ilharco.pdf","date_created":"2021-11-29T08:41:00Z","file_id":"10368","checksum":"b14052a025a6ecf675bdfe51db98c0d7"}],"day":"01","oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2022-01-26T14:26:36Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.18653/v1/2021.acl-tutorials.6","month":"08","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://aclanthology.org/2021.acl-tutorials.6/","open_access":"1"}],"date_published":"2021-08-01T00:00:00Z","status":"public","ddc":["000"],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","type":"conference","publisher":"Association for Computational Linguistics","file_date_updated":"2021-11-29T08:41:00Z","_id":"10367","author":[{"full_name":"Ilharco, Cesar","first_name":"Cesar","last_name":"Ilharco"},{"last_name":"Shirazi","first_name":"Afsaneh","full_name":"Shirazi, Afsaneh"},{"full_name":"Gopalan, Arjun","last_name":"Gopalan","first_name":"Arjun"},{"last_name":"Nagrani","first_name":"Arsha","full_name":"Nagrani, Arsha"},{"full_name":"Bratanič, Blaž","last_name":"Bratanič","first_name":"Blaž"},{"first_name":"Chris","last_name":"Bregler","full_name":"Bregler, Chris"},{"last_name":"Liu","first_name":"Christina","full_name":"Liu, Christina"},{"full_name":"Ferreira, Felipe","last_name":"Ferreira","first_name":"Felipe"},{"full_name":"Barcik, Gabriek","first_name":"Gabriek","last_name":"Barcik"},{"full_name":"Ilharco, Gabriel","last_name":"Ilharco","first_name":"Gabriel"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F","full_name":"Osang, Georg F"},{"first_name":"Jannis","last_name":"Bulian","full_name":"Bulian, Jannis"},{"full_name":"Frank, Jared","first_name":"Jared","last_name":"Frank"},{"full_name":"Smaira, Lucas","last_name":"Smaira","first_name":"Lucas"},{"full_name":"Cao, Qin","first_name":"Qin","last_name":"Cao"},{"full_name":"Marino, Ricardo","first_name":"Ricardo","last_name":"Marino"},{"first_name":"Roma","last_name":"Patel","full_name":"Patel, Roma"},{"full_name":"Leung, Thomas","last_name":"Leung","first_name":"Thomas"},{"full_name":"Imbrasaite, Vaiva","first_name":"Vaiva","last_name":"Imbrasaite"}],"scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","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.","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>","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>.","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.","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.","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>.","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>"},"conference":{"name":"ACL: Association for Computational Linguistics ; IJCNLP: International Joint Conference on Natural Language Processing","start_date":"2021-08-01","end_date":"2021-08-06","location":"Bangkok, Thailand"},"department":[{"_id":"HeEd"}],"article_processing_charge":"No","date_created":"2021-11-28T23:01:30Z","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"]},"title":"Recognizing multimodal entailment","publication":"59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts","year":"2021","page":"29-30"},{"type":"journal_article","isi":1,"intvolume":"        12","publisher":"Springer Nature","author":[{"first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"first_name":"Dmitrii","last_name":"Kamenev","full_name":"Kamenev, Dmitrii"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"full_name":"Fachet, Dominik C","first_name":"Dominik C","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","last_name":"Fachet"},{"full_name":"Lallemend, Francois","first_name":"Francois","last_name":"Lallemend"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"},{"full_name":"Hadjab, Saida","last_name":"Hadjab","first_name":"Saida"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"}],"file_date_updated":"2021-12-10T08:54:09Z","_id":"10402","has_accepted_license":"1","scopus_import":"1","article_number":"6830","quality_controlled":"1","citation":{"ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-27135-5\">10.1038/s41467-021-27135-5</a>","ieee":"M. C. Ucar <i>et al.</i>, “Theory of branching morphogenesis by local interactions and global guidance,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” <i>Nature Communications</i>, vol. 12, 6830, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-27135-5\">10.1038/s41467-021-27135-5</a>.","ista":"Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830.","chicago":"Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-27135-5\">https://doi.org/10.1038/s41467-021-27135-5</a>.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","apa":"Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-27135-5\">https://doi.org/10.1038/s41467-021-27135-5</a>"},"department":[{"_id":"EdHa"}],"date_created":"2021-12-05T23:01:40Z","acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","article_processing_charge":"No","publication_identifier":{"eissn":["2041-1723"]},"external_id":{"isi":["000722322900020"],"pmid":["34819507"]},"article_type":"original","title":"Theory of branching morphogenesis by local interactions and global guidance","volume":12,"year":"2021","publication":"Nature Communications","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"related_material":{"record":[{"relation":"research_data","id":"13058","status":"public"}]},"file":[{"file_name":"2021_NatComm_Ucar.pdf","file_size":2303405,"success":1,"checksum":"63c56ec75314a71e63e7dd2920b3c5b5","file_id":"10529","date_created":"2021-12-10T08:54:09Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","date_updated":"2021-12-10T08:54:09Z"}],"day":"24","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-04-14T07:43:47Z","oa_version":"Published Version","doi":"10.1038/s41467-021-27135-5","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"11","date_published":"2021-11-24T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales."}],"ddc":["573"]},{"oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-03-07T08:12:39Z","oa_version":"Published Version","file":[{"success":1,"file_name":"2021_eLife_Biane.pdf","file_size":13131322,"date_created":"2021-12-10T08:31:41Z","file_id":"10528","checksum":"c7c33c3319428d56e332e22349c50ed3","content_type":"application/pdf","relation":"main_file","date_updated":"2021-12-10T08:31:41Z","creator":"cchlebak","access_level":"open_access"}],"day":"03","status":"public","date_published":"2021-11-03T00:00:00Z","ddc":["570"],"publication_status":"published","abstract":[{"lang":"eng","text":"Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.7554/eLife.65954","pmid":1,"month":"11","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-12-10T08:31:41Z","_id":"10403","author":[{"first_name":"Celia","last_name":"Biane","full_name":"Biane, Celia"},{"first_name":"Florian","last_name":"Rückerl","full_name":"Rückerl, Florian"},{"first_name":"Therese","last_name":"Abrahamsson","full_name":"Abrahamsson, Therese"},{"full_name":"Saint-Cloment, Cécile","last_name":"Saint-Cloment","first_name":"Cécile"},{"full_name":"Mariani, Jean","last_name":"Mariani","first_name":"Jean"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"full_name":"Digregorio, David A.","last_name":"Digregorio","first_name":"David A."},{"last_name":"Sherrard","first_name":"Rachel M.","full_name":"Sherrard, Rachel M."},{"last_name":"Cathala","first_name":"Laurence","full_name":"Cathala, Laurence"}],"citation":{"apa":"Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.65954\">https://doi.org/10.7554/eLife.65954</a>","short":"C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).","chicago":"Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.65954\">https://doi.org/10.7554/eLife.65954</a>.","ieee":"C. Biane <i>et al.</i>, “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954.","mla":"Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” <i>ELife</i>, vol. 10, e65954, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.65954\">10.7554/eLife.65954</a>.","ama":"Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.65954\">10.7554/eLife.65954</a>"},"quality_controlled":"1","scopus_import":"1","article_number":"e65954","has_accepted_license":"1","isi":1,"type":"journal_article","publisher":"eLife Sciences Publications","intvolume":"        10","publication":"eLife","year":"2021","volume":10,"title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","external_id":{"isi":["000715789500001"],"pmid":["34730085"]},"article_type":"original","department":[{"_id":"RySh"}],"publication_identifier":{"eissn":["2050-084X"]},"article_processing_charge":"No","acknowledgement":"This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript.","date_created":"2021-12-05T23:01:40Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1111/cgf.14418","month":"11","main_file_link":[{"url":"https://arxiv.org/abs/2110.07667","open_access":"1"}],"date_published":"2021-11-27T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models."}],"publication_status":"published","day":"27","oa":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","date_updated":"2025-04-15T06:25:55Z","issue":"7","arxiv":1,"department":[{"_id":"ToHe"}],"article_processing_charge":"No","acknowledgement":"We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n","date_created":"2021-12-05T23:01:40Z","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"volume":40,"article_type":"original","title":"Interactive analysis of CNN robustness","external_id":{"arxiv":["2110.07667"],"isi":["000722952000024"]},"project":[{"grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"publication":"Computer Graphics Forum","year":"2021","page":"253-264","isi":1,"type":"journal_article","intvolume":"        40","publisher":"Wiley","_id":"10404","author":[{"last_name":"Sietzen","first_name":"Stefan","full_name":"Sietzen, Stefan"},{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"},{"full_name":"Borowski, Judy","first_name":"Judy","last_name":"Borowski"},{"first_name":"Ramin","last_name":"Hasani","full_name":"Hasani, Ramin"},{"full_name":"Waldner, Manuela","first_name":"Manuela","last_name":"Waldner"}],"quality_controlled":"1","scopus_import":"1","citation":{"ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” <i>Computer Graphics Forum</i>, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” <i>Computer Graphics Forum</i>, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:<a href=\"https://doi.org/10.1111/cgf.14418\">10.1111/cgf.14418</a>.","ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. <i>Computer Graphics Forum</i>. 2021;40(7):253-264. doi:<a href=\"https://doi.org/10.1111/cgf.14418\">10.1111/cgf.14418</a>","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., &#38; Waldner, M. (2021). Interactive analysis of CNN robustness. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14418\">https://doi.org/10.1111/cgf.14418</a>","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” <i>Computer Graphics Forum</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/cgf.14418\">https://doi.org/10.1111/cgf.14418</a>."}}]