[{"quality_controlled":"1","citation":{"ista":"Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. 2023. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. 18(2), e0279838.","short":"J.C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J.G. Mitchell, J.A. Filar, PLoS One 18 (2023) e0279838.","ieee":"J. C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J. G. Mitchell, and J. A. Filar, “Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations,” <i>PLoS One</i>, vol. 18, no. 2. Public Library of Science, p. e0279838, 2023.","ama":"Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. <i>PLoS One</i>. 2023;18(2):e0279838. doi:<a href=\"https://doi.org/10.1371/journal.pone.0279838\">10.1371/journal.pone.0279838</a>","mla":"Mckerral, Jody C., et al. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” <i>PLoS One</i>, vol. 18, no. 2, Public Library of Science, 2023, p. e0279838, doi:<a href=\"https://doi.org/10.1371/journal.pone.0279838\">10.1371/journal.pone.0279838</a>.","chicago":"Mckerral, Jody C., Maria Kleshnina, Vladimir Ejov, Louise Bartle, James G. Mitchell, and Jerzy A. Filar. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” <i>PLoS One</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0279838\">https://doi.org/10.1371/journal.pone.0279838</a>.","apa":"Mckerral, J. C., Kleshnina, M., Ejov, V., Bartle, L., Mitchell, J. G., &#38; Filar, J. A. (2023). Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0279838\">https://doi.org/10.1371/journal.pone.0279838</a>"},"date_created":"2023-03-05T23:01:05Z","oa":1,"title":"Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations","page":"e0279838","date_published":"2023-02-27T00:00:00Z","has_accepted_license":"1","intvolume":"        18","pmid":1,"day":"27","acknowledgement":"This research was supported by an Australian Government Research Training Program\r\n(RTP) Scholarship to JCM (https://www.dese.gov.au), and LB is supported by the Centre de\r\nrecherche sur le vieillissement Fellowship Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","publication":"PLoS One","volume":18,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","file_date_updated":"2023-03-07T10:26:45Z","doi":"10.1371/journal.pone.0279838","external_id":{"isi":["000996122900022"],"pmid":["36848357"]},"publication_status":"published","_id":"12706","issue":"2","file":[{"file_name":"2023_PLOSOne_Mckerral.pdf","relation":"main_file","file_id":"12712","creator":"cchlebak","date_updated":"2023-03-07T10:26:45Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-03-07T10:26:45Z","file_size":1257003,"checksum":"798ed5739a4117b03173e5d56e0534c9","success":1}],"ddc":["000"],"oa_version":"Published Version","type":"journal_article","publisher":"Public Library of Science","article_type":"original","department":[{"_id":"KrCh"}],"month":"02","year":"2023","publication_identifier":{"eissn":["1932-6203"]},"isi":1,"scopus_import":"1","abstract":[{"text":"Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-10-17T12:53:30Z","status":"public","author":[{"first_name":"Jody C.","full_name":"Mckerral, Jody C.","last_name":"Mckerral"},{"id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Kleshnina, Maria","last_name":"Kleshnina"},{"first_name":"Vladimir","last_name":"Ejov","full_name":"Ejov, Vladimir"},{"full_name":"Bartle, Louise","last_name":"Bartle","first_name":"Louise"},{"last_name":"Mitchell","full_name":"Mitchell, James G.","first_name":"James G."},{"first_name":"Jerzy A.","last_name":"Filar","full_name":"Filar, Jerzy A."}]},{"oa":1,"quality_controlled":"1","arxiv":1,"citation":{"ista":"Erdös L, Xu Y. 2023. Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. 29(2), 1063–1079.","short":"L. Erdös, Y. Xu, Bernoulli 29 (2023) 1063–1079.","ieee":"L. Erdös and Y. Xu, “Small deviation estimates for the largest eigenvalue of Wigner matrices,” <i>Bernoulli</i>, vol. 29, no. 2. Bernoulli Society for Mathematical Statistics and Probability, pp. 1063–1079, 2023.","ama":"Erdös L, Xu Y. Small deviation estimates for the largest eigenvalue of Wigner matrices. <i>Bernoulli</i>. 2023;29(2):1063-1079. doi:<a href=\"https://doi.org/10.3150/22-BEJ1490\">10.3150/22-BEJ1490</a>","mla":"Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest Eigenvalue of Wigner Matrices.” <i>Bernoulli</i>, vol. 29, no. 2, Bernoulli Society for Mathematical Statistics and Probability, 2023, pp. 1063–79, doi:<a href=\"https://doi.org/10.3150/22-BEJ1490\">10.3150/22-BEJ1490</a>.","chicago":"Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest Eigenvalue of Wigner Matrices.” <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability, 2023. <a href=\"https://doi.org/10.3150/22-BEJ1490\">https://doi.org/10.3150/22-BEJ1490</a>.","apa":"Erdös, L., &#38; Xu, Y. (2023). Small deviation estimates for the largest eigenvalue of Wigner matrices. <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability. <a href=\"https://doi.org/10.3150/22-BEJ1490\">https://doi.org/10.3150/22-BEJ1490</a>"},"date_created":"2023-03-05T23:01:05Z","page":"1063-1079","title":"Small deviation estimates for the largest eigenvalue of Wigner matrices","day":"01","publication":"Bernoulli","volume":29,"date_published":"2023-05-01T00:00:00Z","intvolume":"        29","doi":"10.3150/22-BEJ1490","ec_funded":1,"article_processing_charge":"No","publisher":"Bernoulli Society for Mathematical Statistics and Probability","publication_status":"published","external_id":{"isi":["000947270100008"],"arxiv":["2112.12093 "]},"_id":"12707","issue":"2","type":"journal_article","oa_version":"Preprint","project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"year":"2023","month":"05","publication_identifier":{"issn":["1350-7265"]},"isi":1,"article_type":"original","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-04T10:21:07Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2112.12093","open_access":"1"}],"abstract":[{"text":"We establish precise right-tail small deviation estimates for the largest eigenvalue of real symmetric and complex Hermitian matrices whose entries are independent random variables with uniformly bounded moments. The proof relies on a Green function comparison along a continuous interpolating matrix flow for a long time. Less precise estimates are also obtained in the left tail.","lang":"eng"}],"status":"public","author":[{"full_name":"Erdös, László","last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1559-1205","last_name":"Xu","full_name":"Xu, Yuanyuan","first_name":"Yuanyuan","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3"}]},{"publication":"Soft Matter","day":"06","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).","volume":19,"date_published":"2023-02-06T00:00:00Z","has_accepted_license":"1","intvolume":"        19","file_date_updated":"2023-03-07T09:19:41Z","doi":"10.1039/d2sm01562e","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","ec_funded":1,"oa":1,"quality_controlled":"1","arxiv":1,"citation":{"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.","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.","ieee":"N. A. M. Araújo <i>et al.</i>, “Steering self-organisation through confinement,” <i>Soft Matter</i>, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. <i>Soft Matter</i>. 2023;19:1695-1704. doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>","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.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>.","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. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>."},"date_created":"2023-03-05T23:01:06Z","page":"1695-1704","title":"Steering self-organisation through confinement","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T13:28:39Z","scopus_import":"1","abstract":[{"lang":"eng","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."}],"status":"public","author":[{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"full_name":"Janssen, Liesbeth M.C.","last_name":"Janssen","first_name":"Liesbeth M.C."},{"first_name":"Thomas","last_name":"Barois","full_name":"Barois, Thomas"},{"first_name":"Guido","full_name":"Boffetta, Guido","last_name":"Boffetta"},{"first_name":"Itai","last_name":"Cohen","full_name":"Cohen, Itai"},{"last_name":"Corbetta","full_name":"Corbetta, Alessandro","first_name":"Alessandro"},{"first_name":"Olivier","last_name":"Dauchot","full_name":"Dauchot, Olivier"},{"last_name":"Dijkstra","full_name":"Dijkstra, Marjolein","first_name":"Marjolein"},{"first_name":"William M.","last_name":"Durham","full_name":"Durham, William M."},{"full_name":"Dussutour, Audrey","last_name":"Dussutour","first_name":"Audrey"},{"full_name":"Garnier, Simon","last_name":"Garnier","first_name":"Simon"},{"first_name":"Hanneke","last_name":"Gelderblom","full_name":"Gelderblom, Hanneke"},{"first_name":"Ramin","last_name":"Golestanian","full_name":"Golestanian, Ramin"},{"last_name":"Isa","full_name":"Isa, Lucio","first_name":"Lucio"},{"last_name":"Koenderink","full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H."},{"last_name":"Löwen","full_name":"Löwen, Hartmut","first_name":"Hartmut"},{"first_name":"Ralf","last_name":"Metzler","full_name":"Metzler, Ralf"},{"full_name":"Polin, Marco","last_name":"Polin","first_name":"Marco"},{"full_name":"Royall, C. Patrick","last_name":"Royall","first_name":"C. Patrick"},{"full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"last_name":"Sengupta","full_name":"Sengupta, Anupam","first_name":"Anupam"},{"full_name":"Sykes, Cécile","last_name":"Sykes","first_name":"Cécile"},{"full_name":"Trianni, Vito","last_name":"Trianni","first_name":"Vito"},{"full_name":"Tuval, Idan","last_name":"Tuval","first_name":"Idan"},{"first_name":"Nicolas","last_name":"Vogel","full_name":"Vogel, Nicolas"},{"first_name":"Julia M.","last_name":"Yeomans","full_name":"Yeomans, Julia M."},{"last_name":"Zuriguel","full_name":"Zuriguel, Iker","first_name":"Iker"},{"last_name":"Marin","full_name":"Marin, Alvaro","first_name":"Alvaro"},{"first_name":"Giorgio","last_name":"Volpe","full_name":"Volpe, Giorgio"}],"publisher":"Royal Society of Chemistry","external_id":{"arxiv":["2204.10059"],"isi":["000940388100001"]},"publication_status":"published","_id":"12708","file":[{"date_updated":"2023-03-07T09:19:41Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-03-07T09:19:41Z","success":1,"file_size":3581939,"checksum":"af95aa18b9b01e32fb8f13477c0e2687","file_name":"2023_SoftMatter_Araujo.pdf","relation":"main_file","creator":"cchlebak","file_id":"12711"}],"type":"journal_article","oa_version":"Published Version","ddc":["540"],"project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"year":"2023","month":"02","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"isi":1,"article_type":"original","department":[{"_id":"AnSa"}]},{"volume":70,"acknowledgement":"We thank the anonymous reviewers for many helpful comments and suggestions, which led to substantial improvements of the paper. The first two authors were supported by the Austrian Science Fund (FWF) grant number P 29984-N35 and W1230. The first author was partly supported by an Austrian Marshall Plan Scholarship, and by the Brummer & Partners MathDataLab. A conference version of this paper was presented at the 37th International Symposium on Computational Geometry (SoCG 2021). Open access funding provided by the Royal Institute of Technology.","day":"01","publication":"Discrete and Computational Geometry","intvolume":"        70","has_accepted_license":"1","date_published":"2023-09-01T00:00:00Z","doi":"10.1007/s00454-022-00476-8","file_date_updated":"2023-03-07T14:40:14Z","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"date_created":"2023-03-05T23:01:06Z","citation":{"ama":"Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration. <i>Discrete and Computational Geometry</i>. 2023;70:376-405. doi:<a href=\"https://doi.org/10.1007/s00454-022-00476-8\">10.1007/s00454-022-00476-8</a>","ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2023. Computing the multicover bifiltration. Discrete and Computational Geometry. 70, 376–405.","ieee":"R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover bifiltration,” <i>Discrete and Computational Geometry</i>, vol. 70. Springer Nature, pp. 376–405, 2023.","short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, Discrete and Computational Geometry 70 (2023) 376–405.","apa":"Corbet, R., Kerber, M., Lesnick, M., &#38; Osang, G. F. (2023). Computing the multicover bifiltration. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00476-8\">https://doi.org/10.1007/s00454-022-00476-8</a>","chicago":"Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing the Multicover Bifiltration.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-022-00476-8\">https://doi.org/10.1007/s00454-022-00476-8</a>.","mla":"Corbet, René, et al. “Computing the Multicover Bifiltration.” <i>Discrete and Computational Geometry</i>, vol. 70, Springer Nature, 2023, pp. 376–405, doi:<a href=\"https://doi.org/10.1007/s00454-022-00476-8\">10.1007/s00454-022-00476-8</a>."},"quality_controlled":"1","arxiv":1,"page":"376-405","title":"Computing the multicover bifiltration","date_updated":"2023-10-04T12:03:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness.","lang":"eng"}],"related_material":{"record":[{"id":"9605","status":"public","relation":"earlier_version"}]},"scopus_import":"1","author":[{"full_name":"Corbet, René","last_name":"Corbet","first_name":"René"},{"last_name":"Kerber","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lesnick","full_name":"Lesnick, Michael","first_name":"Michael"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","last_name":"Osang","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116"}],"status":"public","publisher":"Springer Nature","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12715","creator":"cchlebak","file_name":"2023_DisCompGeo_Corbet.pdf","date_created":"2023-03-07T14:40:14Z","checksum":"71ce7e59f7ee4620acc704fecca620c2","file_size":1359323,"success":1,"date_updated":"2023-03-07T14:40:14Z","access_level":"open_access","content_type":"application/pdf"}],"type":"journal_article","ddc":["000"],"_id":"12709","external_id":{"isi":["000936496800001"],"arxiv":["2103.07823"]},"publication_status":"published","isi":1,"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"year":"2023","month":"09","department":[{"_id":"HeEd"}],"article_type":"original"},{"abstract":[{"lang":"eng","text":"Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes."}],"scopus_import":"1","date_updated":"2023-09-26T10:56:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","author":[{"first_name":"Barbara","full_name":"Schamberger, Barbara","last_name":"Schamberger"},{"first_name":"Ricardo","last_name":"Ziege","full_name":"Ziege, Ricardo"},{"last_name":"Anselme","full_name":"Anselme, Karine","first_name":"Karine"},{"first_name":"Martine","last_name":"Ben Amar","full_name":"Ben Amar, Martine"},{"last_name":"Bykowski","full_name":"Bykowski, Michał","first_name":"Michał"},{"full_name":"Castro, André P.G.","last_name":"Castro","first_name":"André P.G."},{"first_name":"Amaia","full_name":"Cipitria, Amaia","last_name":"Cipitria"},{"last_name":"Coles","full_name":"Coles, Rhoslyn A.","first_name":"Rhoslyn A."},{"first_name":"Rumiana","last_name":"Dimova","full_name":"Dimova, Rumiana"},{"first_name":"Michaela","full_name":"Eder, Michaela","last_name":"Eder"},{"last_name":"Ehrig","full_name":"Ehrig, Sebastian","first_name":"Sebastian"},{"first_name":"Luis M.","last_name":"Escudero","full_name":"Escudero, Luis M."},{"last_name":"Evans","full_name":"Evans, Myfanwy E.","first_name":"Myfanwy E."},{"full_name":"Fernandes, Paulo R.","last_name":"Fernandes","first_name":"Paulo R."},{"first_name":"Peter","last_name":"Fratzl","full_name":"Fratzl, Peter"},{"last_name":"Geris","full_name":"Geris, Liesbet","first_name":"Liesbet"},{"full_name":"Gierlinger, Notburga","last_name":"Gierlinger","first_name":"Notburga"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Iglič, Aleš","last_name":"Iglič","first_name":"Aleš"},{"full_name":"Kirkensgaard, Jacob J.K.","last_name":"Kirkensgaard","first_name":"Jacob J.K."},{"first_name":"Philip","full_name":"Kollmannsberger, Philip","last_name":"Kollmannsberger"},{"full_name":"Kowalewska, Łucja","last_name":"Kowalewska","first_name":"Łucja"},{"first_name":"Nicholas A.","last_name":"Kurniawan","full_name":"Kurniawan, Nicholas A."},{"first_name":"Ioannis","last_name":"Papantoniou","full_name":"Papantoniou, Ioannis"},{"first_name":"Laurent","last_name":"Pieuchot","full_name":"Pieuchot, Laurent"},{"first_name":"Tiago H.V.","last_name":"Pires","full_name":"Pires, Tiago H.V."},{"full_name":"Renner, Lars D.","last_name":"Renner","first_name":"Lars D."},{"first_name":"Andrew O.","last_name":"Sageman-Furnas","full_name":"Sageman-Furnas, Andrew O."},{"last_name":"Schröder-Turk","full_name":"Schröder-Turk, Gerd E.","first_name":"Gerd E."},{"first_name":"Anupam","last_name":"Sengupta","full_name":"Sengupta, Anupam"},{"first_name":"Vikas R.","full_name":"Sharma, Vikas R.","last_name":"Sharma"},{"first_name":"Antonio","last_name":"Tagua","full_name":"Tagua, Antonio"},{"last_name":"Tomba","full_name":"Tomba, Caterina","first_name":"Caterina"},{"last_name":"Trepat","full_name":"Trepat, Xavier","first_name":"Xavier"},{"full_name":"Waters, Sarah L.","last_name":"Waters","first_name":"Sarah L."},{"first_name":"Edwina F.","full_name":"Yeo, Edwina F.","last_name":"Yeo"},{"last_name":"Roschger","full_name":"Roschger, Andreas","first_name":"Andreas"},{"last_name":"Bidan","full_name":"Bidan, Cécile M.","first_name":"Cécile M."},{"first_name":"John W.C.","full_name":"Dunlop, John W.C.","last_name":"Dunlop"}],"oa_version":"Published Version","file":[{"file_name":"2023_AdvancedMaterials_Schamberger.pdf","relation":"main_file","file_id":"14373","creator":"dernst","date_updated":"2023-09-26T10:51:56Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-09-26T10:51:56Z","checksum":"5c04d68130e97a0ecd1ca27fbc15a246","file_size":2898063,"success":1}],"type":"journal_article","ddc":["570"],"publication_status":"published","external_id":{"isi":["000941068900001"],"pmid":["36461812"]},"issue":"13","_id":"12710","publisher":"Wiley","department":[{"_id":"EdHa"}],"article_type":"review","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"isi":1,"year":"2023","month":"03","has_accepted_license":"1","intvolume":"        35","date_published":"2023-03-29T00:00:00Z","publication":"Advanced Materials","day":"29","acknowledgement":"B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F. acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD. A.S. acknowledges that this work was partially supported by the ATTRACT Investigator Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research Fund. The author thanks Gerardo Ceada for his help in the graphical representations. N.A.K. acknowledges support from the European Research Council (grant 851960) and the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands Organization for Scientific Research (024.003.013). M.B.A. acknowledges support from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project “Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft (DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation (PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science.","volume":35,"pmid":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","doi":"10.1002/adma.202206110","file_date_updated":"2023-09-26T10:51:56Z","date_created":"2023-03-05T23:01:06Z","citation":{"mla":"Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” <i>Advanced Materials</i>, vol. 35, no. 13, 2206110, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/adma.202206110\">10.1002/adma.202206110</a>.","chicago":"Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar, Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” <i>Advanced Materials</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/adma.202206110\">https://doi.org/10.1002/adma.202206110</a>.","apa":"Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro, A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification, emergence, and implications across the scales. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.202206110\">https://doi.org/10.1002/adma.202206110</a>","ista":"Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 35(13), 2206110.","ieee":"B. Schamberger <i>et al.</i>, “Curvature in biological systems: Its quantification, emergence, and implications across the scales,” <i>Advanced Materials</i>, vol. 35, no. 13. Wiley, 2023.","short":"B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro, A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans, P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K. Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou, L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk, A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo, A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023).","ama":"Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems: Its quantification, emergence, and implications across the scales. <i>Advanced Materials</i>. 2023;35(13). doi:<a href=\"https://doi.org/10.1002/adma.202206110\">10.1002/adma.202206110</a>"},"quality_controlled":"1","oa":1,"article_number":"2206110","title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales"},{"oa":1,"citation":{"ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","apa":"Burnett, L. (2023). <i>To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>.","mla":"Burnett, Laura. <i>To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>."},"date_created":"2023-03-08T15:19:45Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"page":"178","title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","day":"10","has_accepted_license":"1","degree_awarded":"PhD","date_published":"2023-03-10T00:00:00Z","doi":"10.15479/at:ista:12716","file_date_updated":"2023-03-08T15:08:46Z","article_processing_charge":"No","ec_funded":1,"supervisor":[{"last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"}],"publisher":"Institute of Science and Technology Austria","file":[{"checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_size":23029260,"date_created":"2023-03-08T15:08:46Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2023-03-08T15:08:46Z","creator":"lburnett","file_id":"12717","relation":"source_file","file_name":"Burnett_Thesis_2023.docx"},{"relation":"main_file","creator":"lburnett","file_id":"12718","file_name":"Burnett_Thesis_2023_pdfA.pdf","date_created":"2023-03-08T15:08:46Z","checksum":"cebc77705288bf4382db9b3541483cd0","success":1,"file_size":11959869,"date_updated":"2023-03-08T15:08:46Z","content_type":"application/pdf","access_level":"open_access"}],"type":"dissertation","oa_version":"Published Version","ddc":["599","573"],"_id":"12716","alternative_title":["ISTA Thesis"],"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"year":"2023","month":"03","project":[{"grant_number":"756502","call_identifier":"H2020","name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"date_updated":"2023-04-05T10:59:04Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism."}],"author":[{"id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Burnett, Laura","last_name":"Burnett","orcid":"0000-0002-8937-410X"}],"status":"public"},{"date_updated":"2023-08-01T13:38:12Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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"}],"scopus_import":"1","status":"public","author":[{"last_name":"Bernabeu","full_name":"Bernabeu, Elena","first_name":"Elena"},{"full_name":"Mccartney, Daniel L.","last_name":"Mccartney","first_name":"Daniel L."},{"full_name":"Gadd, Danni A.","last_name":"Gadd","first_name":"Danni A."},{"full_name":"Hillary, Robert F.","last_name":"Hillary","first_name":"Robert F."},{"full_name":"Lu, Ake T.","last_name":"Lu","first_name":"Ake T."},{"full_name":"Murphy, Lee","last_name":"Murphy","first_name":"Lee"},{"first_name":"Nicola","last_name":"Wrobel","full_name":"Wrobel, Nicola"},{"first_name":"Archie","last_name":"Campbell","full_name":"Campbell, Archie"},{"last_name":"Harris","full_name":"Harris, Sarah E.","first_name":"Sarah E."},{"first_name":"David","last_name":"Liewald","full_name":"Liewald, David"},{"last_name":"Hayward","full_name":"Hayward, Caroline","first_name":"Caroline"},{"first_name":"Cathie","last_name":"Sudlow","full_name":"Sudlow, Cathie"},{"full_name":"Cox, Simon R.","last_name":"Cox","first_name":"Simon R."},{"first_name":"Kathryn L.","last_name":"Evans","full_name":"Evans, Kathryn L."},{"last_name":"Horvath","full_name":"Horvath, Steve","first_name":"Steve"},{"first_name":"Andrew M.","full_name":"Mcintosh, Andrew M.","last_name":"Mcintosh"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"first_name":"Catalina A.","full_name":"Vallejos, Catalina A.","last_name":"Vallejos"},{"last_name":"Marioni","full_name":"Marioni, Riccardo E.","first_name":"Riccardo E."}],"publisher":"Springer Nature","oa_version":"Published Version","type":"journal_article","ddc":["570"],"file":[{"file_size":4275987,"checksum":"833b837910c4db42fb5f0f34125f77a7","success":1,"date_created":"2023-03-14T10:29:47Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-03-14T10:29:47Z","creator":"cchlebak","file_id":"12722","relation":"main_file","file_name":"2023_GenomeMed_Bernabeu.pdf"}],"publication_status":"published","external_id":{"isi":["000940286600001"]},"_id":"12719","publication_identifier":{"eissn":["1756-994X"]},"isi":1,"year":"2023","month":"02","department":[{"_id":"MaRo"}],"article_type":"original","day":"28","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.","publication":"Genome Medicine","volume":15,"intvolume":"        15","has_accepted_license":"1","date_published":"2023-02-28T00:00:00Z","doi":"10.1186/s13073-023-01161-y","file_date_updated":"2023-03-14T10:29:47Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","oa":1,"article_number":"12","citation":{"ama":"Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. <i>Genome Medicine</i>. 2023;15. doi:<a href=\"https://doi.org/10.1186/s13073-023-01161-y\">10.1186/s13073-023-01161-y</a>","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).","ieee":"E. Bernabeu <i>et al.</i>, “Refining epigenetic prediction of chronological and biological age,” <i>Genome Medicine</i>, vol. 15. Springer Nature, 2023.","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.","mla":"Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” <i>Genome Medicine</i>, vol. 15, 12, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13073-023-01161-y\">10.1186/s13073-023-01161-y</a>.","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. <i>Genome Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13073-023-01161-y\">https://doi.org/10.1186/s13073-023-01161-y</a>","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.” <i>Genome Medicine</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13073-023-01161-y\">https://doi.org/10.1186/s13073-023-01161-y</a>."},"date_created":"2023-03-12T23:01:02Z","quality_controlled":"1","title":"Refining epigenetic prediction of chronological and biological age"},{"article_processing_charge":"No","doi":"10.1007/978-1-0716-3004-4_3","editor":[{"last_name":"Scarlett","full_name":"Scarlett, Garry","first_name":"Garry"}],"intvolume":"      2633","date_published":"2023-03-01T00:00:00Z","volume":2633,"publication":"DNA Manipulation and Analysis","day":"01","place":"New York, NY, United States","pmid":1,"title":"Molecular Cloning Using In Vivo DNA Assembly","page":"33-44","date_created":"2023-03-12T23:01:02Z","citation":{"chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In <i>DNA Manipulation and Analysis</i>, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">https://doi.org/10.1007/978-1-0716-3004-4_3</a>.","apa":"Arroyo-Urea, S., Watson, J., &#38; García-Nafría, J. (2023). Molecular Cloning Using In Vivo DNA Assembly. In G. Scarlett (Ed.), <i>DNA Manipulation and Analysis</i> (Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">https://doi.org/10.1007/978-1-0716-3004-4_3</a>","mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” <i>DNA Manipulation and Analysis</i>, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">10.1007/978-1-0716-3004-4_3</a>.","ieee":"S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using In Vivo DNA Assembly,” in <i>DNA Manipulation and Analysis</i>, vol. 2633, G. Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44.","short":"S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023, pp. 33–44.","ista":"Arroyo-Urea S, Watson J, García-Nafría J. 2023.Molecular Cloning Using In Vivo DNA Assembly. In: DNA Manipulation and Analysis. Methods in Molecular Biology, vol. 2633, 33–44.","ama":"Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. In: Scarlett G, ed. <i>DNA Manipulation and Analysis</i>. Vol 2633. MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">10.1007/978-1-0716-3004-4_3</a>"},"quality_controlled":"1","author":[{"first_name":"Sandra","full_name":"Arroyo-Urea, Sandra","last_name":"Arroyo-Urea"},{"orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"last_name":"García-Nafría","full_name":"García-Nafría, Javier","first_name":"Javier"}],"status":"public","abstract":[{"text":"Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues.","lang":"eng"}],"scopus_import":"1","series_title":"MIMB","date_updated":"2023-03-16T08:34:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"publication_identifier":{"eisbn":["978-1-0716-3004-4"],"eissn":["1940-6029"],"isbn":["978-1-0716-3003-7"],"issn":["1064-3745"]},"month":"03","year":"2023","type":"book_chapter","oa_version":"None","_id":"12720","external_id":{"pmid":["36853454"]},"publication_status":"published","alternative_title":["Methods in Molecular Biology"],"publisher":"Springer Nature"},{"article_number":"106901","oa":1,"arxiv":1,"quality_controlled":"1","citation":{"ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. <i>Physical Review Letters</i>. 2023;130(10). doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106901\">10.1103/physrevlett.130.106901</a>","ieee":"A. Volosniev <i>et al.</i>, “Spin-electric coupling in lead halide perovskites,” <i>Physical Review Letters</i>, vol. 130, no. 10. American Physical Society, 2023.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.130.106901\">https://doi.org/10.1103/physrevlett.130.106901</a>","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.130.106901\">https://doi.org/10.1103/physrevlett.130.106901</a>.","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” <i>Physical Review Letters</i>, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106901\">10.1103/physrevlett.130.106901</a>."},"date_created":"2023-03-14T13:11:59Z","title":"Spin-electric coupling in lead halide perovskites","volume":130,"day":"10","publication":"Physical Review Letters","date_published":"2023-03-10T00:00:00Z","intvolume":"       130","doi":"10.1103/physrevlett.130.106901","article_processing_charge":"No","publisher":"American Physical Society","_id":"12723","issue":"10","publication_status":"published","external_id":{"isi":["000982435900002"],"arxiv":["2203.09443"]},"oa_version":"Preprint","type":"journal_article","year":"2023","month":"03","isi":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"article_type":"original","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T13:39:04Z","scopus_import":"1","abstract":[{"text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order.","lang":"eng"}],"keyword":["General Physics and Astronomy"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.09443"}],"author":[{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev"},{"full_name":"Shiva Kumar, Abhishek","last_name":"Shiva Kumar","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","first_name":"Abhishek"},{"first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan","last_name":"Lorenc"},{"full_name":"Ashourishokri, Younes","last_name":"Ashourishokri","id":"e32c111f-f6e0-11ea-865d-eb955baea334","first_name":"Younes"},{"last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A.","first_name":"Ayan A."},{"last_name":"Bakr","full_name":"Bakr, Osman M.","first_name":"Osman M."},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","orcid":"0000-0002-7183-5203"}],"status":"public"},{"publication_status":"published","external_id":{"arxiv":["2204.04022"],"isi":["000972602200006"]},"_id":"12724","issue":"12","type":"journal_article","oa_version":"Preprint","publisher":"American Physical Society","article_type":"original","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"month":"03","year":"2023","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"isi":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2204.04022"}],"abstract":[{"lang":"eng","text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation."}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T13:39:47Z","status":"public","author":[{"last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shiva Kumar, Abhishek","last_name":"Shiva Kumar","first_name":"Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","last_name":"Lorenc","full_name":"Lorenc, Dusan"},{"last_name":"Ashourishokri","full_name":"Ashourishokri, Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","first_name":"Younes"},{"first_name":"Ayan","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan"},{"full_name":"Bakr, Osman M.","last_name":"Bakr","first_name":"Osman M."},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek"}],"arxiv":1,"quality_controlled":"1","citation":{"apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.107.125201\">https://doi.org/10.1103/physrevb.107.125201</a>","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.107.125201\">https://doi.org/10.1103/physrevb.107.125201</a>.","mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” <i>Physical Review B</i>, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.107.125201\">10.1103/physrevb.107.125201</a>.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. <i>Physical Review B</i>. 2023;107(12). doi:<a href=\"https://doi.org/10.1103/physrevb.107.125201\">10.1103/physrevb.107.125201</a>","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201.","ieee":"A. Volosniev <i>et al.</i>, “Effective model for studying optical properties of lead halide perovskites,” <i>Physical Review B</i>, vol. 107, no. 12. American Physical Society, 2023."},"date_created":"2023-03-14T13:13:05Z","oa":1,"article_number":"125201","title":"Effective model for studying optical properties of lead halide perovskites","date_published":"2023-03-15T00:00:00Z","intvolume":"       107","publication":"Physical Review B","day":"15","volume":107,"article_processing_charge":"No","doi":"10.1103/physrevb.107.125201"},{"day":"23","degree_awarded":"PhD","has_accepted_license":"1","date_published":"2023-03-23T00:00:00Z","doi":"10.15479/at:ista:12726","file_date_updated":"2023-11-24T11:57:46Z","article_processing_charge":"No","citation":{"ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>.","mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>."},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"date_created":"2023-03-15T13:22:13Z","page":"260","title":"Synchronization in collectively moving active matter","date_updated":"2023-11-30T10:55:13Z","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"10703","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10791"},{"id":"7932","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"461"},{"id":"14530","relation":"new_edition","status":"public"}]},"abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex."}],"status":"public","author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Riedl, Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"oa_version":"None","type":"dissertation","ddc":["530"],"file":[{"file_name":"Thesis_Riedl_2023.pdf","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","creator":"cchlebak","file_id":"12745","relation":"main_file","content_type":"application/pdf","access_level":"closed","date_updated":"2023-11-24T11:57:46Z","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","file_size":63734746,"date_created":"2023-03-23T12:49:23Z"},{"date_updated":"2023-09-24T22:30:03Z","access_level":"closed","content_type":"application/octet-stream","embargo_to":"open_access","date_created":"2023-03-23T12:54:34Z","file_size":339473651,"checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","file_name":"Thesis_Riedl_2023_source.rar","relation":"source_file","file_id":"12746","creator":"cchlebak"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","_id":"12726","publication_identifier":{"issn":["2663-337X"]},"month":"03","year":"2023","department":[{"_id":"GradSch"},{"_id":"BjHo"}]},{"file_date_updated":"2023-03-23T16:43:14Z","doi":"10.15479/at:ista:12732","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"article_processing_charge":"No","ec_funded":1,"day":"21","date_published":"2023-03-21T00:00:00Z","degree_awarded":"PhD","has_accepted_license":"1","page":"158","title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","oa":1,"date_created":"2023-03-17T13:30:48Z","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>.","apa":"Brighi, P. (2023). <i>Ergodicity breaking in disordered and kinetically constrained quantum many-body systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>","mla":"Brighi, Pietro. <i>Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>.","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","status":"public","author":[{"full_name":"Brighi, Pietro","last_name":"Brighi","orcid":"0000-0002-7969-2729","first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"date_updated":"2023-09-20T10:44:12Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11470"},{"status":"public","relation":"part_of_dissertation","id":"8308"},{"relation":"part_of_dissertation","status":"public","id":"11469"},{"id":"12750","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings."}],"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"month":"03","year":"2023","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","_id":"12732","file":[{"date_created":"2023-03-23T16:42:56Z","checksum":"5d2de651ef9449c1b8dc27148ca74777","file_size":42167561,"date_updated":"2023-03-23T16:42:56Z","access_level":"closed","content_type":"application/zip","relation":"source_file","file_id":"12753","creator":"pbrighi","file_name":"Thesis_sub_PBrighi.zip"},{"file_name":"Thesis_PBrighi.pdf","creator":"pbrighi","file_id":"12754","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-03-23T16:43:14Z","file_size":13977000,"checksum":"7caa153d4a5b0873a79358787d2dfe1e","success":1,"date_created":"2023-03-23T16:43:14Z"}],"oa_version":"None","ddc":["530"],"type":"dissertation"},{"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-03-20T07:29:28Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04986"}],"abstract":[{"lang":"eng","text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations."}],"status":"public","author":[{"last_name":"Koval","full_name":"Koval, Nikita","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Elizarov, Roman","last_name":"Elizarov","first_name":"Roman"}],"publisher":"Association for Computing Machinery","external_id":{"arxiv":["2211.04986"]},"publication_status":"published","_id":"12735","oa_version":"Preprint","type":"conference","year":"2023","month":"02","publication_identifier":{"isbn":["9798400700156"]},"department":[{"_id":"DaAl"}],"day":"25","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577481","article_processing_charge":"No","oa":1,"quality_controlled":"1","arxiv":1,"conference":{"start_date":"2023-02-25","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","location":"Montreal, QC, Canada","end_date":"2023-03-01"},"date_created":"2023-03-19T23:00:58Z","citation":{"chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 107–18. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3572848.3577481\">https://doi.org/10.1145/3572848.3577481</a>.","apa":"Koval, N., Alistarh, D.-A., &#38; Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3572848.3577481\">https://doi.org/10.1145/3572848.3577481</a>","mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2023, pp. 107–18, doi:<a href=\"https://doi.org/10.1145/3572848.3577481\">10.1145/3572848.3577481</a>.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Montreal, QC, Canada, 2023, pp. 107–118.","ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2023:107-118. doi:<a href=\"https://doi.org/10.1145/3572848.3577481\">10.1145/3572848.3577481</a>"},"page":"107-118","title":"Fast and scalable channels in Kotlin Coroutines"},{"article_processing_charge":"No","author":[{"full_name":"Aksenov, Vitaly","last_name":"Aksenov","first_name":"Vitaly"},{"full_name":"Brown, Trevor A","last_name":"Brown","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","full_name":"Fedorov, Alexander","last_name":"Fedorov"},{"last_name":"Kokorin","full_name":"Kokorin, Ilya","first_name":"Ilya"}],"status":"public","doi":"10.1145/3572848.3577512","date_published":"2023-02-25T00:00:00Z","abstract":[{"lang":"eng","text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-03-20T07:57:27Z","day":"25","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","title":"Unexpected scaling in path copying trees","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"month":"02","year":"2023","page":"438-440","publication_identifier":{"isbn":["9798400700156"]},"conference":{"end_date":"2023-03-01","location":"Montreal, QB, Canada","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","start_date":"2023-02-25"},"_id":"12736","publication_status":"published","quality_controlled":"1","citation":{"ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. <i>Unexpected Scaling in Path Copying Trees</i>. Association for Computing Machinery; 2023:438-440. doi:<a href=\"https://doi.org/10.1145/3572848.3577512\">10.1145/3572848.3577512</a>","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, <i>Unexpected scaling in path copying trees</i>. Association for Computing Machinery, 2023, pp. 438–440.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., &#38; Kokorin, I. (2023). <i>Unexpected scaling in path copying trees</i>. <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3572848.3577512\">https://doi.org/10.1145/3572848.3577512</a>","chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. <i>Unexpected Scaling in Path Copying Trees</i>. <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3572848.3577512\">https://doi.org/10.1145/3572848.3577512</a>.","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2023, pp. 438–40, doi:<a href=\"https://doi.org/10.1145/3572848.3577512\">10.1145/3572848.3577512</a>."},"date_created":"2023-03-19T23:00:58Z","oa_version":"Published Version","type":"conference_poster","oa":1,"publisher":"Association for Computing Machinery"},{"title":"Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals","page":"4625-4636","quality_controlled":"1","date_created":"2023-03-19T23:00:59Z","citation":{"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.","ieee":"Á. García-Romero <i>et al.</i>, “Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals,” <i>Inorganic Chemistry</i>, vol. 62, no. 11. American Chemical Society, pp. 4625–4636, 2023.","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.","ama":"García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. <i>Inorganic Chemistry</i>. 2023;62(11):4625-4636. doi:<a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">10.1021/acs.inorgchem.3c00057</a>","mla":"García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” <i>Inorganic Chemistry</i>, vol. 62, no. 11, American Chemical Society, 2023, pp. 4625–36, doi:<a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">10.1021/acs.inorgchem.3c00057</a>.","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.” <i>Inorganic Chemistry</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">https://doi.org/10.1021/acs.inorgchem.3c00057</a>.","apa":"García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A. L., García-Rodríguez, R., &#38; Wright, D. S. (2023). Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. <i>Inorganic Chemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">https://doi.org/10.1021/acs.inorgchem.3c00057</a>"},"article_processing_charge":"No","doi":"10.1021/acs.inorgchem.3c00057","date_published":"2023-03-08T00:00:00Z","intvolume":"        62","pmid":1,"volume":62,"day":"08","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.","publication":"Inorganic Chemistry","article_type":"original","department":[{"_id":"StFr"}],"year":"2023","month":"03","isi":1,"publication_identifier":{"issn":["0020-1669"],"eissn":["1520-510X"]},"issue":"11","_id":"12737","external_id":{"isi":["000956110300001"],"pmid":["36883367"]},"publication_status":"published","type":"journal_article","oa_version":"None","publisher":"American Chemical Society","author":[{"first_name":"Álvaro","full_name":"García-Romero, Álvaro","last_name":"García-Romero"},{"last_name":"Waters","full_name":"Waters, Jessica E.","first_name":"Jessica E."},{"orcid":"0000-0002-0404-4356","full_name":"Jethwa, Rajesh B","last_name":"Jethwa","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","first_name":"Rajesh B"},{"full_name":"Bond, Andrew D.","last_name":"Bond","first_name":"Andrew D."},{"last_name":"Colebatch","full_name":"Colebatch, Annie L.","first_name":"Annie L."},{"last_name":"García-Rodríguez","full_name":"García-Rodríguez, Raúl","first_name":"Raúl"},{"full_name":"Wright, Dominic S.","last_name":"Wright","first_name":"Dominic S."}],"status":"public","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-01T13:42:59Z"},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8272"}]},"main_file_link":[{"url":"https://doi.org/10.1007/s10703-023-00411-4","open_access":"1"}],"abstract":[{"lang":"eng","text":"We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies."}],"scopus_import":"1","date_updated":"2025-07-14T09:10:14Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Katoen, Joost P","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P"},{"last_name":"Mohr","full_name":"Mohr, Stefanie","first_name":"Stefanie"},{"last_name":"Weininger","full_name":"Weininger, Maximilian","first_name":"Maximilian"},{"first_name":"Tobias","last_name":"Winkler","full_name":"Winkler, Tobias"}],"type":"journal_article","ddc":["000"],"oa_version":"Published Version","publication_status":"epub_ahead","external_id":{"isi":["000946174300001"]},"_id":"12738","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"article_type":"original","publication_identifier":{"eissn":["1572-8102"]},"isi":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"month":"03","year":"2023","date_published":"2023-03-08T00:00:00Z","publication":"Formal Methods in System Design","day":"08","acknowledgement":"Tobias Winkler and Joost-Pieter Katoen are supported by the DFG RTG 2236 UnRAVeL and the innovation programme under the Marie Skłodowska-Curie grant agreement No. 101008233 (Mission). Krishnendu Chatterjee is supported by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) Project ICT15-003. Maximilian Weininger is supported by the DFG projects 383882557 Statistical Unbounded Verification (SUV) and 427755713 Group-By Objectives in Probabilistic Verification (GOPro). Stefanie Mohr is supported by the DFG RTG 2428 CONVEY. Open Access funding enabled and organized by Projekt DEAL.","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No","doi":"10.1007/s10703-023-00411-4","date_created":"2023-03-19T23:00:59Z","citation":{"ista":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. 2023. Stochastic games with lexicographic objectives. Formal Methods in System Design.","ieee":"K. Chatterjee, J. P. Katoen, S. Mohr, M. Weininger, and T. Winkler, “Stochastic games with lexicographic objectives,” <i>Formal Methods in System Design</i>. Springer Nature, 2023.","short":"K. Chatterjee, J.P. Katoen, S. Mohr, M. Weininger, T. Winkler, Formal Methods in System Design (2023).","ama":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. Stochastic games with lexicographic objectives. <i>Formal Methods in System Design</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s10703-023-00411-4\">10.1007/s10703-023-00411-4</a>","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Stefanie Mohr, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Objectives.” <i>Formal Methods in System Design</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s10703-023-00411-4\">https://doi.org/10.1007/s10703-023-00411-4</a>.","apa":"Chatterjee, K., Katoen, J. P., Mohr, S., Weininger, M., &#38; Winkler, T. (2023). Stochastic games with lexicographic objectives. <i>Formal Methods in System Design</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10703-023-00411-4\">https://doi.org/10.1007/s10703-023-00411-4</a>","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Objectives.” <i>Formal Methods in System Design</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s10703-023-00411-4\">10.1007/s10703-023-00411-4</a>."},"quality_controlled":"1","oa":1,"title":"Stochastic games with lexicographic objectives"},{"author":[{"first_name":"Fredrik","full_name":"Hurtig, Fredrik","last_name":"Hurtig"},{"first_name":"Thomas C.Q.","last_name":"Burgers","full_name":"Burgers, Thomas C.Q."},{"last_name":"Cezanne","full_name":"Cezanne, Alice","first_name":"Alice"},{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"last_name":"Mol","full_name":"Mol, Frank N.","first_name":"Frank N."},{"last_name":"Traparić","full_name":"Traparić, Jovan","first_name":"Jovan"},{"last_name":"Pulschen","full_name":"Pulschen, Andre Arashiro","first_name":"Andre Arashiro"},{"first_name":"Tim","full_name":"Nierhaus, Tim","last_name":"Nierhaus"},{"first_name":"Gabriel","full_name":"Tarrason-Risa, Gabriel","last_name":"Tarrason-Risa"},{"first_name":"Lena","last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena"},{"first_name":"Jan","full_name":"Löwe, Jan","last_name":"Löwe"},{"orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Rifka","full_name":"Vlijm, Rifka","last_name":"Vlijm"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"}],"status":"public","scopus_import":"1","abstract":[{"text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T13:45:54Z","article_type":"original","department":[{"_id":"AnSa"}],"month":"03","year":"2023","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960"}],"isi":1,"publication_identifier":{"eissn":["2375-2548"]},"_id":"12756","issue":"11","external_id":{"isi":["000968083500010"]},"publication_status":"published","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2023-03-27T06:24:49Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-03-27T06:24:49Z","success":1,"checksum":"6d7dbe9ed86a116c8a002d62971202c5","file_size":1826471,"file_name":"2023_ScienceAdvances_Hurtig.pdf","relation":"main_file","creator":"dernst","file_id":"12768"}],"ddc":["570"],"publisher":"American Association for the Advancement of Science","article_processing_charge":"No","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-03-27T06:24:49Z","doi":"10.1126/sciadv.ade5224","date_published":"2023-03-17T00:00:00Z","intvolume":"         9","has_accepted_license":"1","volume":9,"publication":"Science Advances","acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","day":"17","title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","quality_controlled":"1","citation":{"ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. 2023;9(11). doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023).","ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","ieee":"F. Hurtig <i>et al.</i>, “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” <i>Science Advances</i>, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>.","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>."},"date_created":"2023-03-26T22:01:06Z","article_number":"eade5224","oa":1},{"author":[{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"status":"public","date_updated":"2023-08-01T13:45:12Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1042/BCJ20210285","open_access":"1"}],"scopus_import":"1","isi":1,"publication_identifier":{"issn":["0264-6021"],"eissn":["1470-8728"]},"month":"03","year":"2023","department":[{"_id":"LeSa"}],"article_type":"review","publisher":"Portland Press","ddc":["570"],"type":"journal_article","oa_version":"Published Version","_id":"12757","issue":"5","external_id":{"pmid":["36920092"],"isi":["000957065700001"]},"publication_status":"published","doi":"10.1042/BCJ20210285","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":480,"day":"15","publication":"The Biochemical Journal","pmid":1,"has_accepted_license":"1","intvolume":"       480","date_published":"2023-03-15T00:00:00Z","page":"319-333","title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","oa":1,"date_created":"2023-03-26T22:01:06Z","citation":{"ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. <i>The Biochemical Journal</i>. 2023;480(5):319-333. doi:<a href=\"https://doi.org/10.1042/BCJ20210285\">10.1042/BCJ20210285</a>","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” <i>The Biochemical Journal</i>, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.","mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” <i>The Biochemical Journal</i>, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:<a href=\"https://doi.org/10.1042/BCJ20210285\">10.1042/BCJ20210285</a>.","apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. <i>The Biochemical Journal</i>. Portland Press. <a href=\"https://doi.org/10.1042/BCJ20210285\">https://doi.org/10.1042/BCJ20210285</a>","chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” <i>The Biochemical Journal</i>. Portland Press, 2023. <a href=\"https://doi.org/10.1042/BCJ20210285\">https://doi.org/10.1042/BCJ20210285</a>."},"quality_controlled":"1"},{"author":[{"first_name":"Marina A.","full_name":"Pak, Marina A.","last_name":"Pak"},{"first_name":"Karina A.","last_name":"Markhieva","full_name":"Markhieva, Karina A."},{"last_name":"Novikova","full_name":"Novikova, Mariia S.","first_name":"Mariia S."},{"first_name":"Dmitry S.","full_name":"Petrov, Dmitry S.","last_name":"Petrov"},{"first_name":"Ilya S.","full_name":"Vorobyev, Ilya S.","last_name":"Vorobyev"},{"full_name":"Maksimova, Ekaterina","last_name":"Maksimova","first_name":"Ekaterina","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry N.","last_name":"Ivankov","full_name":"Ivankov, Dmitry N."}],"status":"public","date_updated":"2023-08-01T13:47:14Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and <pLDDT> metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding."}],"scopus_import":"1","isi":1,"publication_identifier":{"eissn":["1932-6203"]},"year":"2023","month":"03","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"article_type":"original","publisher":"Public Library of Science","type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-03-27T07:09:08Z","file_size":856625,"success":1,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6","date_created":"2023-03-27T07:09:08Z","file_name":"2023_PLoSOne_Pak.pdf","creator":"dernst","file_id":"12771","relation":"main_file"}],"ddc":["570"],"_id":"12758","issue":"3","publication_status":"published","external_id":{"isi":["000985134400106"]},"doi":"10.1371/journal.pone.0282689","file_date_updated":"2023-03-27T07:09:08Z","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":18,"publication":"PLoS ONE","day":"16","acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","has_accepted_license":"1","intvolume":"        18","date_published":"2023-03-16T00:00:00Z","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","article_number":"e0282689","oa":1,"citation":{"ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. 2023;18(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>","ieee":"M. A. Pak <i>et al.</i>, “Using AlphaFold to predict the impact of single mutations on protein stability and function,” <i>PLoS ONE</i>, vol. 18, no. 3. Public Library of Science, 2023.","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689.","short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>","chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>."},"date_created":"2023-03-26T22:01:07Z","quality_controlled":"1"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No","file_date_updated":"2023-03-27T06:51:09Z","doi":"10.1371/journal.pone.0277148","date_published":"2023-03-17T00:00:00Z","intvolume":"        18","has_accepted_license":"1","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","publication":"PLoS ONE","day":"17","volume":18,"title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","quality_controlled":"1","citation":{"ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” <i>PLoS ONE</i>, vol. 18, no. 3 March. Public Library of Science, 2023.","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. 2023;18(3 March). doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>","mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>.","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>.","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., &#38; Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>"},"acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2023-03-26T22:01:07Z","oa":1,"article_number":"e0277148","status":"public","author":[{"full_name":"Rothman, Jason Seth","last_name":"Rothman","first_name":"Jason Seth"},{"last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Holderith, Noemi","last_name":"Holderith","first_name":"Noemi"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"last_name":"Angus Silver","full_name":"Angus Silver, R.","first_name":"R."}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density."}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T13:46:39Z","article_type":"original","department":[{"_id":"PeJo"}],"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"V00739","call_identifier":"FWF","name":"Structural plasticity at mossy fiber-CA3 synapses","_id":"2696E7FE-B435-11E9-9278-68D0E5697425"}],"year":"2023","month":"03","publication_identifier":{"eissn":["1932-6203"]},"isi":1,"publication_status":"published","external_id":{"isi":["001024737400001"]},"_id":"12759","issue":"3 March","oa_version":"Published Version","file":[{"date_created":"2023-03-27T06:51:09Z","checksum":"2380331ec27cc87808826fc64419ac1c","success":1,"file_size":7290413,"date_updated":"2023-03-27T06:51:09Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"12770","creator":"dernst","file_name":"2023_PLoSOne_Rothman.pdf"}],"ddc":["570"],"type":"journal_article","publisher":"Public Library of Science"}]