[{"publication_identifier":{"eissn":["1097-4199"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2023.01.006","quality_controlled":"1","isi":1,"external_id":{"isi":["000994473300001"]},"volume":111,"date_updated":"2023-08-01T13:10:27Z","date_created":"2023-02-12T23:00:58Z","author":[{"first_name":"Ana","last_name":"Villalba Requena","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Elsevier","department":[{"_id":"SiHi"}],"publication_status":"published","year":"2023","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-02-01T00:00:00Z","page":"291-293","article_type":"letter_note","citation":{"chicago":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron. Elsevier, 2023. https://doi.org/10.1016/j.neuron.2023.01.006.","mla":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:10.1016/j.neuron.2023.01.006.","short":"A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293.","ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293.","ieee":"A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” Neuron, vol. 111, no. 3. Elsevier, pp. 291–293, 2023.","apa":"Villalba Requena, A., & Hippenmeyer, S. (2023). Going back in time with TEMPO. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.01.006","ama":"Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. Neuron. 2023;111(3):291-293. doi:10.1016/j.neuron.2023.01.006"},"publication":"Neuron","issue":"3","abstract":[{"text":"In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 111","status":"public","title":"Going back in time with TEMPO","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12542"},{"abstract":[{"text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12569","date_created":"2023-02-20T07:09:27Z","date_updated":"2023-02-20T07:09:27Z","checksum":"69a35dcd3e0249f902ab881b06ee2e58","success":1,"file_name":"2023_IJMS_Mrestani.pdf","access_level":"open_access","file_size":2823025,"content_type":"application/pdf","creator":"dernst"}],"_id":"12567","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","status":"public","ddc":["570"],"intvolume":" 24","day":"21","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-01-21T00:00:00Z","publication":"International Journal of Molecular Sciences","citation":{"chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128.","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128.","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023.","ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128"},"article_type":"original","file_date_updated":"2023-02-20T07:09:27Z","article_number":"2128","author":[{"last_name":"Mrestani","first_name":"Achmed","full_name":"Mrestani, Achmed"},{"id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","first_name":"Katharina","last_name":"Lichter","full_name":"Lichter, Katharina"},{"full_name":"Sirén, Anna Leena","first_name":"Anna Leena","last_name":"Sirén"},{"first_name":"Manfred","last_name":"Heckmann","full_name":"Heckmann, Manfred"},{"full_name":"Paul, Mila M.","first_name":"Mila M.","last_name":"Paul"},{"last_name":"Pauli","first_name":"Martin","full_name":"Pauli, Martin"}],"date_created":"2023-02-19T23:00:56Z","date_updated":"2023-08-01T13:16:36Z","volume":24,"acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","year":"2023","publication_status":"published","publisher":"MDPI","department":[{"_id":"PeJo"}],"month":"01","publication_identifier":{"eissn":["1422-0067"]},"doi":"10.3390/ijms24032128","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000930324700001"]},"oa":1,"quality_controlled":"1","isi":1},{"_id":"12566","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Wait-free approximate agreement on graphs","ddc":["000"],"intvolume":" 948","oa_version":"Published Version","file":[{"file_id":"12570","relation":"main_file","date_updated":"2023-02-20T07:30:20Z","date_created":"2023-02-20T07:30:20Z","success":1,"checksum":"b27c5290f2f1500c403494364ee39c9f","file_name":"2023_TheoreticalCompScience_Alistarh.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":602333}],"type":"journal_article","abstract":[{"text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs.","lang":"eng"}],"issue":"2","publication":"Theoretical Computer Science","citation":{"apa":"Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023.","ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733."},"article_type":"original","date_published":"2023-02-28T00:00:00Z","scopus_import":"1","day":"28","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","year":"2023","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Elsevier","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Ellen, Faith","first_name":"Faith","last_name":"Ellen"},{"full_name":"Rybicki, Joel","first_name":"Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646"}],"date_updated":"2023-08-01T13:17:20Z","date_created":"2023-02-19T23:00:55Z","volume":948,"article_number":"113733","file_date_updated":"2023-02-20T07:30:20Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000934262700001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"},{"grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020"}],"doi":"10.1016/j.tcs.2023.113733","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["0304-3975"]}},{"date_published":"2023-01-19T00:00:00Z","citation":{"chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-032822-025933.","short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:10.1146/annurev-fluid-032822-025933.","ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” Annual Review of Fluid Mechanics, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","apa":"Dubief, Y., Terrapon, V. E., & Hof, B. (2023). Elasto-inertial turbulence. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-032822-025933","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 2023;55(1):675-705. doi:10.1146/annurev-fluid-032822-025933"},"publication":"Annual Review of Fluid Mechanics","page":"675-705","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"19","scopus_import":"1","file":[{"date_created":"2023-02-27T09:23:02Z","date_updated":"2023-02-27T09:23:02Z","success":1,"checksum":"2666aa3af2a25252d35eb8681d3edff7","file_id":"12690","relation":"main_file","creator":"dernst","file_size":4036706,"content_type":"application/pdf","file_name":"2023_AnnReviewFluidMech_Dubief.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"12681","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 55","ddc":["530"],"status":"public","title":"Elasto-inertial turbulence","issue":"1","abstract":[{"lang":"eng","text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT."}],"type":"journal_article","doi":"10.1146/annurev-fluid-032822-025933","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000915418100026"]},"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1545-4479"],"issn":["0066-4189"]},"month":"01","author":[{"full_name":"Dubief, Yves","last_name":"Dubief","first_name":"Yves"},{"last_name":"Terrapon","first_name":"Vincent E.","full_name":"Terrapon, Vincent E."},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"volume":55,"date_created":"2023-02-26T23:01:01Z","date_updated":"2023-08-01T13:19:47Z","year":"2023","acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","publisher":"Annual Reviews","department":[{"_id":"BjHo"}],"publication_status":"published","file_date_updated":"2023-02-27T09:23:02Z"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_AnnReviewFluidMech_Avila.pdf","creator":"dernst","file_size":4769537,"content_type":"application/pdf","file_id":"12691","relation":"main_file","success":1,"checksum":"f99ef30f76cabc9e5e1946b380c16db4","date_updated":"2023-02-27T09:35:52Z","date_created":"2023-02-27T09:35:52Z"}],"intvolume":" 55","ddc":["530"],"status":"public","title":"Transition to turbulence in pipe flow","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12682","abstract":[{"text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed.","lang":"eng"}],"type":"journal_article","date_published":"2023-01-19T00:00:00Z","page":"575-602","article_type":"original","citation":{"ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 2023;55:575-602. doi:10.1146/annurev-fluid-120720-025957","ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","apa":"Avila, M., Barkley, D., & Hof, B. (2023). Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-120720-025957","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” Annual Review of Fluid Mechanics, vol. 55. Annual Reviews, pp. 575–602, 2023.","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:10.1146/annurev-fluid-120720-025957.","short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602.","chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-120720-025957."},"publication":"Annual Review of Fluid Mechanics","article_processing_charge":"No","has_accepted_license":"1","day":"19","scopus_import":"1","volume":55,"date_created":"2023-02-26T23:01:01Z","date_updated":"2023-08-01T13:20:30Z","author":[{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"first_name":"Dwight","last_name":"Barkley","full_name":"Barkley, Dwight"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"publisher":"Annual Reviews","department":[{"_id":"BjHo"}],"publication_status":"published","acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).","year":"2023","file_date_updated":"2023-02-27T09:35:52Z","language":[{"iso":"eng"}],"doi":"10.1146/annurev-fluid-120720-025957","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000915418100023"]},"publication_identifier":{"issn":["0066-4189"]},"month":"01"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"06","page":"1695-1704","article_type":"original","citation":{"chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e.","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e.","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e","ieee":"N. A. M. Araújo et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e"},"publication":"Soft Matter","date_published":"2023-02-06T00:00:00Z","type":"journal_article","abstract":[{"text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.","lang":"eng"}],"intvolume":" 19","status":"public","title":"Steering self-organisation through confinement","ddc":["540"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12708","oa_version":"Published Version","file":[{"date_updated":"2023-03-07T09:19:41Z","date_created":"2023-03-07T09:19:41Z","checksum":"af95aa18b9b01e32fb8f13477c0e2687","success":1,"relation":"main_file","file_id":"12711","content_type":"application/pdf","file_size":3581939,"creator":"cchlebak","file_name":"2023_SoftMatter_Araujo.pdf","access_level":"open_access"}],"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"month":"02","project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2204.10059"],"isi":["000940388100001"]},"language":[{"iso":"eng"}],"doi":"10.1039/d2sm01562e","ec_funded":1,"file_date_updated":"2023-03-07T09:19:41Z","department":[{"_id":"AnSa"}],"publisher":"Royal Society of Chemistry","publication_status":"published","acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","year":"2023","volume":19,"date_updated":"2023-08-01T13:28:39Z","date_created":"2023-03-05T23:01:06Z","author":[{"first_name":"Nuno A.M.","last_name":"Araújo","full_name":"Araújo, Nuno A.M."},{"first_name":"Liesbeth M.C.","last_name":"Janssen","full_name":"Janssen, Liesbeth M.C."},{"last_name":"Barois","first_name":"Thomas","full_name":"Barois, Thomas"},{"last_name":"Boffetta","first_name":"Guido","full_name":"Boffetta, Guido"},{"full_name":"Cohen, Itai","first_name":"Itai","last_name":"Cohen"},{"full_name":"Corbetta, Alessandro","last_name":"Corbetta","first_name":"Alessandro"},{"full_name":"Dauchot, Olivier","last_name":"Dauchot","first_name":"Olivier"},{"first_name":"Marjolein","last_name":"Dijkstra","full_name":"Dijkstra, Marjolein"},{"full_name":"Durham, William M.","first_name":"William M.","last_name":"Durham"},{"last_name":"Dussutour","first_name":"Audrey","full_name":"Dussutour, Audrey"},{"full_name":"Garnier, Simon","first_name":"Simon","last_name":"Garnier"},{"full_name":"Gelderblom, Hanneke","last_name":"Gelderblom","first_name":"Hanneke"},{"last_name":"Golestanian","first_name":"Ramin","full_name":"Golestanian, Ramin"},{"full_name":"Isa, Lucio","first_name":"Lucio","last_name":"Isa"},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."},{"first_name":"Hartmut","last_name":"Löwen","full_name":"Löwen, Hartmut"},{"full_name":"Metzler, Ralf","last_name":"Metzler","first_name":"Ralf"},{"full_name":"Polin, Marco","last_name":"Polin","first_name":"Marco"},{"full_name":"Royall, C. Patrick","last_name":"Royall","first_name":"C. Patrick"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"full_name":"Sengupta, Anupam","last_name":"Sengupta","first_name":"Anupam"},{"last_name":"Sykes","first_name":"Cécile","full_name":"Sykes, Cécile"},{"full_name":"Trianni, Vito","first_name":"Vito","last_name":"Trianni"},{"full_name":"Tuval, Idan","last_name":"Tuval","first_name":"Idan"},{"first_name":"Nicolas","last_name":"Vogel","full_name":"Vogel, Nicolas"},{"full_name":"Yeomans, Julia M.","first_name":"Julia M.","last_name":"Yeomans"},{"last_name":"Zuriguel","first_name":"Iker","full_name":"Zuriguel, Iker"},{"full_name":"Marin, Alvaro","last_name":"Marin","first_name":"Alvaro"},{"last_name":"Volpe","first_name":"Giorgio","full_name":"Volpe, Giorgio"}]},{"article_number":"1104","file_date_updated":"2023-03-07T10:58:00Z","pmid":1,"year":"2023","acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","department":[{"_id":"BiCh"}],"publisher":"Springer Nature","publication_status":"published","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"last_name":"Hamel","first_name":"Sebastien","full_name":"Hamel, Sebastien"},{"full_name":"Bethkenhagen, Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","first_name":"Mandy","last_name":"Bethkenhagen"}],"volume":14,"date_updated":"2023-08-01T13:36:11Z","date_created":"2023-03-05T23:01:04Z","publication_identifier":{"eissn":["2041-1723"]},"month":"02","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000939678300002"],"pmid":["36843123"]},"oa":1,"project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-023-36841-1","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12702","intvolume":" 14","ddc":["540"],"status":"public","title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","file":[{"access_level":"open_access","file_name":"2023_NatComm_Cheng.pdf","creator":"cchlebak","file_size":1946443,"content_type":"application/pdf","file_id":"12713","relation":"main_file","success":1,"checksum":"5ff61ad21511950c15abb73b18613883","date_updated":"2023-03-07T10:58:00Z","date_created":"2023-03-07T10:58:00Z"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"27","citation":{"ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1","ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-36841-1","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature, 2023, doi:10.1038/s41467-023-36841-1.","chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1."},"publication":"Nature Communications","article_type":"original","date_published":"2023-02-27T00:00:00Z"},{"type":"journal_article","abstract":[{"text":"Background\r\nEpigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.","lang":"eng"}],"intvolume":" 15","status":"public","title":"Refining epigenetic prediction of chronological and biological age","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12719","oa_version":"Published Version","file":[{"file_size":4275987,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2023_GenomeMed_Bernabeu.pdf","checksum":"833b837910c4db42fb5f0f34125f77a7","success":1,"date_created":"2023-03-14T10:29:47Z","date_updated":"2023-03-14T10:29:47Z","relation":"main_file","file_id":"12722"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"28","article_type":"original","citation":{"chicago":"Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary, Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01161-y.","short":"E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy, N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox, K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Genome Medicine 15 (2023).","mla":"Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y.","ieee":"E. Bernabeu et al., “Refining epigenetic prediction of chronological and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023.","apa":"Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy, L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y","ista":"Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 15, 12.","ama":"Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y"},"publication":"Genome Medicine","date_published":"2023-02-28T00:00:00Z","article_number":"12","file_date_updated":"2023-03-14T10:29:47Z","publisher":"Springer Nature","department":[{"_id":"MaRo"}],"publication_status":"published","acknowledgement":"We are grateful to all the families who took part, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the whole GS team that includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses.","year":"2023","volume":15,"date_updated":"2023-08-01T13:38:12Z","date_created":"2023-03-12T23:01:02Z","author":[{"full_name":"Bernabeu, Elena","last_name":"Bernabeu","first_name":"Elena"},{"full_name":"Mccartney, Daniel L.","first_name":"Daniel L.","last_name":"Mccartney"},{"last_name":"Gadd","first_name":"Danni A.","full_name":"Gadd, Danni A."},{"last_name":"Hillary","first_name":"Robert F.","full_name":"Hillary, Robert F."},{"full_name":"Lu, Ake T.","first_name":"Ake T.","last_name":"Lu"},{"full_name":"Murphy, Lee","first_name":"Lee","last_name":"Murphy"},{"first_name":"Nicola","last_name":"Wrobel","full_name":"Wrobel, Nicola"},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"last_name":"Harris","first_name":"Sarah E.","full_name":"Harris, Sarah E."},{"full_name":"Liewald, David","first_name":"David","last_name":"Liewald"},{"first_name":"Caroline","last_name":"Hayward","full_name":"Hayward, Caroline"},{"last_name":"Sudlow","first_name":"Cathie","full_name":"Sudlow, Cathie"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"full_name":"Evans, Kathryn L.","last_name":"Evans","first_name":"Kathryn L."},{"full_name":"Horvath, Steve","last_name":"Horvath","first_name":"Steve"},{"last_name":"Mcintosh","first_name":"Andrew M.","full_name":"Mcintosh, Andrew M."},{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Catalina A.","last_name":"Vallejos","full_name":"Vallejos, Catalina A."},{"first_name":"Riccardo E.","last_name":"Marioni","full_name":"Marioni, Riccardo E."}],"publication_identifier":{"eissn":["1756-994X"]},"month":"02","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000940286600001"]},"language":[{"iso":"eng"}],"doi":"10.1186/s13073-023-01161-y"},{"page":"1595-1602","article_type":"original","citation":{"chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LRA.2023.3240930.","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023.","apa":"Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LRA.2023.3240930","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602. doi:10.1109/LRA.2023.3240930"},"publication":"IEEE Robotics and Automation Letters","date_published":"2023-03-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","intvolume":" 8","ddc":["000"],"status":"public","title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12704","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_IEEERobAutLetters_Lechner.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":944052,"file_id":"12714","relation":"main_file","success":1,"checksum":"5a75dcd326ea66685de2b1aaec259e85","date_updated":"2023-03-07T12:22:23Z","date_created":"2023-03-07T12:22:23Z"}],"type":"journal_article","issue":"3","abstract":[{"text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice.","lang":"eng"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000936534100012"],"arxiv":["2204.07373"]},"language":[{"iso":"eng"}],"doi":"10.1109/LRA.2023.3240930","publication_identifier":{"eissn":["2377-3766"]},"month":"03","department":[{"_id":"ToHe"}],"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","year":"2023","volume":8,"date_updated":"2023-08-01T13:36:50Z","date_created":"2023-03-05T23:01:04Z","related_material":{"record":[{"id":"11366","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Amini","full_name":"Amini, Alexander"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"}],"file_date_updated":"2023-03-07T12:22:23Z"},{"month":"03","publication_identifier":{"eissn":["1520-510X"],"issn":["0020-1669"]},"language":[{"iso":"eng"}],"doi":"10.1021/acs.inorgchem.3c00057","isi":1,"quality_controlled":"1","external_id":{"isi":["000956110300001"],"pmid":["36883367"]},"date_created":"2023-03-19T23:00:59Z","date_updated":"2023-08-01T13:42:59Z","volume":62,"author":[{"first_name":"Álvaro","last_name":"García-Romero","full_name":"García-Romero, Álvaro"},{"full_name":"Waters, Jessica E.","first_name":"Jessica E.","last_name":"Waters"},{"full_name":"Jethwa, Rajesh B","first_name":"Rajesh B","last_name":"Jethwa","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","orcid":"0000-0002-0404-4356"},{"full_name":"Bond, Andrew D.","last_name":"Bond","first_name":"Andrew D."},{"full_name":"Colebatch, Annie L.","first_name":"Annie L.","last_name":"Colebatch"},{"full_name":"García-Rodríguez, Raúl","last_name":"García-Rodríguez","first_name":"Raúl"},{"last_name":"Wright","first_name":"Dominic S.","full_name":"Wright, Dominic S."}],"publication_status":"published","department":[{"_id":"StFr"}],"publisher":"American Chemical Society","acknowledgement":"The authors thank the Walters-Kundert Studentship of Selwyn College (scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146), the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities (MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER, UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc. (I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are grateful for the calculation time used.","year":"2023","pmid":1,"day":"08","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-08T00:00:00Z","article_type":"original","page":"4625-4636","publication":"Inorganic Chemistry","citation":{"ama":"García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 2023;62(11):4625-4636. doi:10.1021/acs.inorgchem.3c00057","ieee":"Á. García-Romero et al., “Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals,” Inorganic Chemistry, vol. 62, no. 11. American Chemical Society, pp. 4625–4636, 2023.","apa":"García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A. L., García-Rodríguez, R., & Wright, D. S. (2023). Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.inorgchem.3c00057","ista":"García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 62(11), 4625–4636.","short":"Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R. García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636.","mla":"García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry, vol. 62, no. 11, American Chemical Society, 2023, pp. 4625–36, doi:10.1021/acs.inorgchem.3c00057.","chicago":"García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond, Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry. American Chemical Society, 2023. https://doi.org/10.1021/acs.inorgchem.3c00057."},"abstract":[{"lang":"eng","text":"The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed."}],"issue":"11","type":"journal_article","oa_version":"None","status":"public","title":"Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals","intvolume":" 62","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12737"}]