[{"ddc":["004"],"type":"conference","publisher":"Curran Associates","article_processing_charge":"No","has_accepted_license":"1","date_created":"2023-02-20T08:21:50Z","arxiv":1,"citation":{"ama":"Scott JA, Yeo MX, Lampert C. Cross-client label propagation for transductive and semi-supervised federated learning. In: <i>Transactions in Machine Learning</i>. Curran Associates; 2023.","short":"J.A. Scott, M.X. Yeo, C. Lampert, in:, Transactions in Machine Learning, Curran Associates, 2023.","ieee":"J. A. Scott, M. X. Yeo, and C. Lampert, “Cross-client label propagation for transductive and semi-supervised federated learning,” in <i>Transactions in Machine Learning</i>, 2023.","chicago":"Scott, Jonathan A, Michelle X Yeo, and Christoph Lampert. “Cross-Client Label Propagation for Transductive and Semi-Supervised Federated Learning.” In <i>Transactions in Machine Learning</i>. Curran Associates, 2023.","mla":"Scott, Jonathan A., et al. “Cross-Client Label Propagation for Transductive and Semi-Supervised Federated Learning.” <i>Transactions in Machine Learning</i>, Curran Associates, 2023.","apa":"Scott, J. A., Yeo, M. X., &#38; Lampert, C. (2023). Cross-client label propagation for transductive and semi-supervised federated learning. In <i>Transactions in Machine Learning</i>. Curran Associates.","ista":"Scott JA, Yeo MX, Lampert C. 2023. Cross-client label propagation for transductive and semi-supervised federated learning. Transactions in Machine Learning. , TMLR, ."},"language":[{"iso":"eng"}],"publication_status":"published","OA_type":"green","alternative_title":["TMLR"],"oa":1,"external_id":{"arxiv":["2210.06434"]},"quality_controlled":"1","file":[{"date_created":"2025-02-04T08:30:05Z","relation":"main_file","checksum":"aa322ad91cbd229f5cafe6733a119bd1","success":1,"file_size":553717,"content_type":"application/pdf","creator":"dernst","file_id":"18990","file_name":"2023_TMLR_Scott.pdf","date_updated":"2025-02-04T08:30:05Z","access_level":"open_access"}],"author":[{"first_name":"Jonathan A","full_name":"Scott, Jonathan A","last_name":"Scott","id":"e499926b-f6e0-11ea-865d-9c63db0031e8"},{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","first_name":"Michelle X","last_name":"Yeo","orcid":"0009-0001-3676-4809"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"date_updated":"2025-02-04T08:32:19Z","corr_author":"1","abstract":[{"lang":"eng","text":"We present Cross-Client Label Propagation(XCLP), a new method for transductive federated learning. XCLP estimates a data graph jointly from the data of multiple clients and computes labels for the unlabeled data by propagating label information across the graph. To avoid clients having to share their data with anyone, XCLP employs two cryptographically secure protocols: secure Hamming distance computation and secure summation. We demonstrate two distinct applications of XCLP within federated learning. In the first, we use it in a one-shot way to predict labels for unseen test points. In the second, we use it to repeatedly pseudo-label unlabeled training data in a federated semi-supervised setting. Experiments on both real federated and standard benchmark datasets show that in both applications XCLP achieves higher classification accuracy than alternative approaches."}],"publication":"Transactions in Machine Learning","month":"11","license":"https://creativecommons.org/licenses/by/4.0/","related_material":{"link":[{"url":"https://github.com/jonnyascott/xclp","relation":"software"}]},"department":[{"_id":"ChLa"}],"_id":"12660","OA_place":"repository","file_date_updated":"2025-02-04T08:30:05Z","year":"2023","publication_identifier":{"issn":["2835-8856"]},"title":"Cross-client label propagation for transductive and semi-supervised federated learning","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"27","date_published":"2023-11-27T00:00:00Z","oa_version":"Preprint"},{"language":[{"iso":"eng"}],"pmid":1,"publication_status":"published","citation":{"chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>.","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>, vol. 24, 7, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>.","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7.","ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. 2023;24. doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","ieee":"L. Zhao <i>et al.</i>, “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” <i>Genome Biology</i>, vol. 24. Springer Nature, 2023."},"article_number":"7","external_id":{"pmid":["36639687"]},"oa":1,"intvolume":"        24","date_created":"2023-02-23T09:13:49Z","type":"journal_article","publisher":"Springer Nature","volume":24,"article_processing_charge":"No","publication_identifier":{"issn":["1474-760X"]},"title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","doi":"10.1186/s13059-022-02844-2","date_published":"2023-01-13T00:00:00Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"13","article_type":"original","quality_controlled":"1","author":[{"full_name":"Zhao, Long","first_name":"Long","last_name":"Zhao"},{"first_name":"Yiman","full_name":"Yang, Yiman","last_name":"Yang"},{"full_name":"Chen, Jinchao","first_name":"Jinchao","last_name":"Chen"},{"last_name":"Lin","first_name":"Xuelei","full_name":"Lin, Xuelei"},{"first_name":"Hao","full_name":"Zhang, Hao","last_name":"Zhang"},{"first_name":"Hao","full_name":"Wang, Hao","last_name":"Wang"},{"first_name":"Hongzhe","full_name":"Wang, Hongzhe","last_name":"Wang"},{"full_name":"Bie, Xiaomin","first_name":"Xiaomin","last_name":"Bie"},{"last_name":"Jiang","full_name":"Jiang, Jiafu","first_name":"Jiafu"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi"},{"last_name":"Fu","full_name":"Fu, Xiangdong","first_name":"Xiangdong"},{"last_name":"Zhang","full_name":"Zhang, Xiansheng","first_name":"Xiansheng"},{"last_name":"Du","full_name":"Du, Zhuo","first_name":"Zhuo"},{"full_name":"Xiao, Jun","first_name":"Jun","last_name":"Xiao"}],"extern":"1","date_updated":"2023-05-08T10:52:49Z","_id":"12668","scopus_import":"1","year":"2023","main_file_link":[{"url":"https://doi.org/10.1186/s13059-022-02844-2","open_access":"1"}],"abstract":[{"text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.","lang":"eng"}],"publication":"Genome Biology","month":"01","department":[{"_id":"XiFe"}]},{"intvolume":"        35","date_created":"2023-02-23T09:14:59Z","article_processing_charge":"No","type":"journal_article","publisher":"Oxford University Press","volume":35,"pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","citation":{"ista":"Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 35(6), koac346.","chicago":"Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>.","mla":"Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>, vol. 35, no. 6, koac346, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>.","apa":"Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth, L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>","short":"P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth, K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J. Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).","ama":"Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. 2023;35(6). doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>","ieee":"P. A. Manavella <i>et al.</i>, “Beyond transcription: compelling open questions in plant RNA biology,” <i>The Plant Cell</i>, vol. 35, no. 6. Oxford University Press, 2023."},"oa":1,"external_id":{"pmid":["36477566"]},"article_number":"koac346","keyword":["Cell Biology","Plant Science"],"extern":"1","author":[{"first_name":"Pablo A","full_name":"Manavella, Pablo A","last_name":"Manavella"},{"full_name":"Godoy Herz, Micaela A","first_name":"Micaela A","last_name":"Godoy Herz"},{"last_name":"Kornblihtt","full_name":"Kornblihtt, Alberto R","first_name":"Alberto R"},{"last_name":"Sorenson","first_name":"Reed","full_name":"Sorenson, Reed"},{"last_name":"Sieburth","full_name":"Sieburth, Leslie E","first_name":"Leslie E"},{"first_name":"Kentaro","full_name":"Nakaminami, Kentaro","last_name":"Nakaminami"},{"full_name":"Seki, Motoaki","first_name":"Motoaki","last_name":"Seki"},{"last_name":"Ding","full_name":"Ding, Yiliang","first_name":"Yiliang"},{"full_name":"Sun, Qianwen","first_name":"Qianwen","last_name":"Sun"},{"last_name":"Kang","first_name":"Hunseung","full_name":"Kang, Hunseung"},{"last_name":"Ariel","first_name":"Federico D","full_name":"Ariel, Federico D"},{"first_name":"Martin","full_name":"Crespi, Martin","last_name":"Crespi"},{"first_name":"Axel J","full_name":"Giudicatti, Axel J","last_name":"Giudicatti"},{"last_name":"Cai","first_name":"Qiang","full_name":"Cai, Qiang"},{"first_name":"Hailing","full_name":"Jin, Hailing","last_name":"Jin"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi"},{"last_name":"Qi","first_name":"Yijun","full_name":"Qi, Yijun"},{"first_name":"Craig S","full_name":"Pikaard, Craig S","last_name":"Pikaard"}],"article_type":"original","quality_controlled":"1","date_updated":"2023-10-04T09:48:43Z","_id":"12669","year":"2023","main_file_link":[{"url":"https://doi.org/10.1093/plcell/koac346","open_access":"1"}],"scopus_import":"1","month":"06","publication":"The Plant Cell","abstract":[{"lang":"eng","text":"The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader."}],"department":[{"_id":"XiFe"}],"publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"title":"Beyond transcription: compelling open questions in plant RNA biology","date_published":"2023-06-01T00:00:00Z","doi":"10.1093/plcell/koac346","oa_version":"Published Version","issue":"6","day":"01","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["2211-1247"]},"title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons","date_published":"2023-03-28T00:00:00Z","doi":"10.1016/j.celrep.2023.112132","oa_version":"Published Version","issue":"3","day":"28","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","corr_author":"1","author":[{"first_name":"David B.","full_name":"Lyons, David B.","last_name":"Lyons"},{"last_name":"Briffa","first_name":"Amy","full_name":"Briffa, Amy"},{"first_name":"Shengbo","full_name":"He, Shengbo","last_name":"He"},{"last_name":"Choi","first_name":"Jaemyung","full_name":"Choi, Jaemyung"},{"id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","last_name":"Hollwey","first_name":"Elizabeth","full_name":"Hollwey, Elizabeth"},{"full_name":"Colicchio, Jack","first_name":"Jack","last_name":"Colicchio"},{"first_name":"Ian","full_name":"Anderson, Ian","last_name":"Anderson"},{"full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"last_name":"Howard","full_name":"Howard, Martin","first_name":"Martin"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel"}],"article_type":"original","quality_controlled":"1","file":[{"date_created":"2023-05-11T10:41:42Z","relation":"main_file","checksum":"6cbc44fdb18bf18834c9e2a5b9c67123","success":1,"file_size":8401261,"content_type":"application/pdf","creator":"kschuh","file_id":"12941","file_name":"2023_CellReports_Lyons.pdf","date_updated":"2023-05-11T10:41:42Z","access_level":"open_access"}],"date_updated":"2025-04-14T07:57:43Z","_id":"12672","year":"2023","file_date_updated":"2023-05-11T10:41:42Z","scopus_import":"1","publication":"Cell Reports","month":"03","abstract":[{"text":"Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.","lang":"eng"}],"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"language":[{"iso":"eng"}],"publication_status":"published","citation":{"ista":"Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3), 112132.","apa":"Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">https://doi.org/10.1016/j.celrep.2023.112132</a>","mla":"Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” <i>Cell Reports</i>, vol. 42, no. 3, 112132, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">10.1016/j.celrep.2023.112132</a>.","chicago":"Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">https://doi.org/10.1016/j.celrep.2023.112132</a>.","short":"D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).","ama":"Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. <i>Cell Reports</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">10.1016/j.celrep.2023.112132</a>","ieee":"D. B. Lyons <i>et al.</i>, “Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons,” <i>Cell Reports</i>, vol. 42, no. 3. Elsevier, 2023."},"isi":1,"oa":1,"external_id":{"isi":["000944921600001"]},"article_number":"112132","project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746","call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin"}],"ddc":["580"],"intvolume":"        42","date_created":"2023-02-23T09:17:44Z","has_accepted_license":"1","ec_funded":1,"article_processing_charge":"Yes","publisher":"Elsevier","type":"journal_article","volume":42,"acknowledgement":"The authors would like to thank Jasper Rine for advice and mentorship to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from the Helen Hay Whitney Foundation to D.B.L."},{"publication_status":"published","language":[{"iso":"eng"}],"citation":{"short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. <i>Annual Review of Fluid Mechanics</i>. 2023;55(1):675-705. doi:<a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">10.1146/annurev-fluid-032822-025933</a>","ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” <i>Annual Review of Fluid Mechanics</i>, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705.","chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” <i>Annual Review of Fluid Mechanics</i>. Annual Reviews, 2023. <a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">https://doi.org/10.1146/annurev-fluid-032822-025933</a>.","mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” <i>Annual Review of Fluid Mechanics</i>, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:<a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">10.1146/annurev-fluid-032822-025933</a>.","apa":"Dubief, Y., Terrapon, V. E., &#38; Hof, B. (2023). Elasto-inertial turbulence. <i>Annual Review of Fluid Mechanics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">https://doi.org/10.1146/annurev-fluid-032822-025933</a>"},"external_id":{"isi":["000915418100026"]},"oa":1,"isi":1,"page":"675-705","intvolume":"        55","ddc":["530"],"date_created":"2023-02-26T23:01:01Z","has_accepted_license":"1","acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","article_processing_charge":"No","type":"journal_article","publisher":"Annual Reviews","volume":55,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Elasto-inertial turbulence","publication_identifier":{"eissn":["1545-4479"],"issn":["0066-4189"]},"oa_version":"Published Version","doi":"10.1146/annurev-fluid-032822-025933","date_published":"2023-01-19T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","day":"19","issue":"1","date_updated":"2023-08-01T13:19:47Z","article_type":"original","quality_controlled":"1","file":[{"file_name":"2023_AnnReviewFluidMech_Dubief.pdf","access_level":"open_access","date_updated":"2023-02-27T09:23:02Z","success":1,"relation":"main_file","date_created":"2023-02-27T09:23:02Z","checksum":"2666aa3af2a25252d35eb8681d3edff7","file_size":4036706,"content_type":"application/pdf","file_id":"12690","creator":"dernst"}],"author":[{"last_name":"Dubief","first_name":"Yves","full_name":"Dubief, Yves"},{"full_name":"Terrapon, Vincent E.","first_name":"Vincent E.","last_name":"Terrapon"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof"}],"file_date_updated":"2023-02-27T09:23:02Z","scopus_import":"1","year":"2023","_id":"12681","department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT."}],"month":"01","publication":"Annual Review of Fluid Mechanics"},{"publisher":"Annual Reviews","volume":55,"article_processing_charge":"No","type":"journal_article","acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).","date_created":"2023-02-26T23:01:01Z","has_accepted_license":"1","project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"ddc":["530"],"intvolume":"        55","page":"575-602","isi":1,"external_id":{"isi":["000915418100023"]},"oa":1,"citation":{"short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602.","ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. <i>Annual Review of Fluid Mechanics</i>. 2023;55:575-602. doi:<a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">10.1146/annurev-fluid-120720-025957</a>","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” <i>Annual Review of Fluid Mechanics</i>, vol. 55. Annual Reviews, pp. 575–602, 2023.","ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” <i>Annual Review of Fluid Mechanics</i>. Annual Reviews, 2023. <a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">https://doi.org/10.1146/annurev-fluid-120720-025957</a>.","apa":"Avila, M., Barkley, D., &#38; Hof, B. (2023). Transition to turbulence in pipe flow. <i>Annual Review of Fluid Mechanics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">https://doi.org/10.1146/annurev-fluid-120720-025957</a>","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” <i>Annual Review of Fluid Mechanics</i>, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:<a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">10.1146/annurev-fluid-120720-025957</a>."},"language":[{"iso":"eng"}],"publication_status":"published","publication":"Annual Review of Fluid Mechanics","month":"01","abstract":[{"lang":"eng","text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed."}],"department":[{"_id":"BjHo"}],"_id":"12682","year":"2023","file_date_updated":"2023-02-27T09:35:52Z","scopus_import":"1","author":[{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"},{"last_name":"Barkley","full_name":"Barkley, Dwight","first_name":"Dwight"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","file":[{"date_updated":"2023-02-27T09:35:52Z","access_level":"open_access","file_name":"2023_AnnReviewFluidMech_Avila.pdf","file_size":4769537,"file_id":"12691","content_type":"application/pdf","creator":"dernst","relation":"main_file","date_created":"2023-02-27T09:35:52Z","checksum":"f99ef30f76cabc9e5e1946b380c16db4","success":1}],"quality_controlled":"1","date_updated":"2024-10-22T11:08:43Z","day":"19","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2023-01-19T00:00:00Z","doi":"10.1146/annurev-fluid-120720-025957","oa_version":"Published Version","publication_identifier":{"issn":["0066-4189"]},"title":"Transition to turbulence in pipe flow","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"_id":"12683","scopus_import":"1","file_date_updated":"2023-02-27T09:43:27Z","year":"2023","abstract":[{"lang":"eng","text":"We study the eigenvalue trajectories of a time dependent matrix Gt=H+itvv∗ for t≥0, where H is an N×N Hermitian random matrix and v is a unit vector. In particular, we establish that with high probability, an outlier can be distinguished at all times t>1+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices."}],"publication":"Electronic Communications in Probability","month":"02","department":[{"_id":"LaEr"}],"corr_author":"1","article_type":"original","quality_controlled":"1","file":[{"access_level":"open_access","date_updated":"2023-02-27T09:43:27Z","file_name":"2023_ElectCommProbability_Dubach.pdf","file_id":"12692","creator":"dernst","content_type":"application/pdf","file_size":479105,"success":1,"checksum":"a1c6f0a3e33688fd71309c86a9aad86e","relation":"main_file","date_created":"2023-02-27T09:43:27Z"}],"author":[{"id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","orcid":"0000-0001-6892-8137","last_name":"Dubach","full_name":"Dubach, Guillaume","first_name":"Guillaume"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","last_name":"Erdös"}],"date_updated":"2025-04-14T07:44:00Z","doi":"10.1214/23-ECP516","date_published":"2023-02-08T00:00:00Z","oa_version":"Published Version","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["1083-589X"]},"title":"Dynamics of a rank-one perturbation of a Hermitian matrix","has_accepted_license":"1","date_created":"2023-02-26T23:01:01Z","acknowledgement":"G. Dubach gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. L. Erdős is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","volume":28,"type":"journal_article","publisher":"Institute of Mathematical Statistics","article_processing_charge":"No","ec_funded":1,"intvolume":"        28","ddc":["510"],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"}],"isi":1,"oa":1,"external_id":{"isi":["000950650200005"],"arxiv":["2108.13694"]},"page":"1-13","publication_status":"published","language":[{"iso":"eng"}],"arxiv":1,"citation":{"ieee":"G. Dubach and L. Erdös, “Dynamics of a rank-one perturbation of a Hermitian matrix,” <i>Electronic Communications in Probability</i>, vol. 28. Institute of Mathematical Statistics, pp. 1–13, 2023.","ama":"Dubach G, Erdös L. Dynamics of a rank-one perturbation of a Hermitian matrix. <i>Electronic Communications in Probability</i>. 2023;28:1-13. doi:<a href=\"https://doi.org/10.1214/23-ECP516\">10.1214/23-ECP516</a>","short":"G. Dubach, L. Erdös, Electronic Communications in Probability 28 (2023) 1–13.","chicago":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/23-ECP516\">https://doi.org/10.1214/23-ECP516</a>.","apa":"Dubach, G., &#38; Erdös, L. (2023). Dynamics of a rank-one perturbation of a Hermitian matrix. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-ECP516\">https://doi.org/10.1214/23-ECP516</a>","mla":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” <i>Electronic Communications in Probability</i>, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–13, doi:<a href=\"https://doi.org/10.1214/23-ECP516\">10.1214/23-ECP516</a>.","ista":"Dubach G, Erdös L. 2023. Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. 28, 1–13."}},{"corr_author":"1","date_updated":"2025-04-14T13:55:29Z","file":[{"access_level":"open_access","date_updated":"2023-02-28T06:34:08Z","file_name":"Metzler_ReadMe.pdf","file_size":77070,"creator":"scremer","file_id":"12694","content_type":"application/pdf","success":1,"date_created":"2023-02-28T06:34:08Z","relation":"main_file","checksum":"c1565d655ca05601acfd84e0d12b8563"},{"date_updated":"2023-02-28T06:34:12Z","access_level":"open_access","file_name":"Metzler_RepositoryData.xlsx","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"12695","creator":"scremer","file_size":88001,"checksum":"75c4c4948563d6261cb7548f80d909f1","relation":"main_file","date_created":"2023-02-28T06:34:12Z","success":1}],"ddc":["570"],"author":[{"orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-02-28T06:38:37Z","has_accepted_license":"1","file_date_updated":"2023-02-28T06:34:12Z","year":"2023","_id":"12693","related_material":{"record":[{"id":"12696","status":"public","relation":"used_in_publication"}]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","department":[{"_id":"SyCr"}],"abstract":[{"text":"See Readme File for further information.","lang":"eng"}],"month":"02","article_processing_charge":"No","type":"research_data","publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"title":"Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ","citation":{"short":"S. Cremer, (2023).","ama":"Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12693\">10.15479/AT:ISTA:12693</a>","ieee":"S. Cremer, “Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males .” Institute of Science and Technology Austria, 2023.","ista":"Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12693\">10.15479/AT:ISTA:12693</a>.","chicago":"Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12693\">https://doi.org/10.15479/AT:ISTA:12693</a>.","apa":"Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12693\">https://doi.org/10.15479/AT:ISTA:12693</a>","mla":"Cremer, Sylvia. <i>Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males </i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12693\">10.15479/AT:ISTA:12693</a>."},"oa_version":"Published Version","oa":1,"doi":"10.15479/AT:ISTA:12693","date_published":"2023-02-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"28","contributor":[{"first_name":"Sina","last_name":"Metzler","contributor_type":"data_collector","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jessica","last_name":"Kirchner","id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3","contributor_type":"data_collector"},{"last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","contributor_type":"data_collector"}]},{"publication_identifier":{"issn":["2730-7182"]},"title":"Trade-offs between immunity and competitive ability in fighting ant males","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"LifeSc"}],"day":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2023-08-07T00:00:00Z","doi":"10.1186/s12862-023-02137-7","oa_version":"Published Version","author":[{"id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494","last_name":"Metzler","full_name":"Metzler, Sina","first_name":"Sina"},{"id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3","full_name":"Kirchner, Jessica","first_name":"Jessica","last_name":"Kirchner"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V","first_name":"Anna V"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"article_type":"original","quality_controlled":"1","file":[{"file_size":2004276,"content_type":"application/pdf","file_id":"14048","creator":"dernst","relation":"main_file","date_created":"2023-08-14T07:51:47Z","checksum":"95966dc7d242d2c85bdd4fe14233dbd8","success":1,"date_updated":"2023-08-14T07:51:47Z","access_level":"open_access","file_name":"2023_BMCEcology_Metzler.pdf"}],"date_updated":"2025-04-14T07:47:53Z","corr_author":"1","month":"08","publication":"BMC Ecology and Evolution","abstract":[{"lang":"eng","text":"Background: Fighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogen Metarhizium robertsii interfered with fighting success in Cardiocondyla obscurior ant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colony’s worker force.\r\nResults: We found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on.\r\nConclusions: Males of the ant C. obscurior have evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk."}],"department":[{"_id":"SyCr"}],"related_material":{"record":[{"id":"12693","status":"public","relation":"research_data"}]},"_id":"12696","year":"2023","scopus_import":"1","file_date_updated":"2023-08-14T07:51:47Z","citation":{"ama":"Metzler S, Kirchner J, Grasse AV, Cremer S. Trade-offs between immunity and competitive ability in fighting ant males. <i>BMC Ecology and Evolution</i>. 2023;23. doi:<a href=\"https://doi.org/10.1186/s12862-023-02137-7\">10.1186/s12862-023-02137-7</a>","short":"S. Metzler, J. Kirchner, A.V. Grasse, S. Cremer, BMC Ecology and Evolution 23 (2023).","ieee":"S. Metzler, J. Kirchner, A. V. Grasse, and S. Cremer, “Trade-offs between immunity and competitive ability in fighting ant males,” <i>BMC Ecology and Evolution</i>, vol. 23. Springer Nature, 2023.","apa":"Metzler, S., Kirchner, J., Grasse, A. V., &#38; Cremer, S. (2023). Trade-offs between immunity and competitive ability in fighting ant males. <i>BMC Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12862-023-02137-7\">https://doi.org/10.1186/s12862-023-02137-7</a>","mla":"Metzler, Sina, et al. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” <i>BMC Ecology and Evolution</i>, vol. 23, 37, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s12862-023-02137-7\">10.1186/s12862-023-02137-7</a>.","chicago":"Metzler, Sina, Jessica Kirchner, Anna V Grasse, and Sylvia Cremer. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” <i>BMC Ecology and Evolution</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s12862-023-02137-7\">https://doi.org/10.1186/s12862-023-02137-7</a>.","ista":"Metzler S, Kirchner J, Grasse AV, Cremer S. 2023. Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. 23, 37."},"language":[{"iso":"eng"}],"publication_status":"published","pmid":1,"isi":1,"oa":1,"external_id":{"pmid":["37550612"],"isi":["001042643600002"]},"article_number":"37","project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","name":"Epidemics in ant societies on a chip","call_identifier":"H2020"}],"ddc":["570"],"intvolume":"        23","publisher":"Springer Nature","ec_funded":1,"article_processing_charge":"Yes","type":"journal_article","volume":23,"acknowledgement":"We are thankful to Mike Bidochka for the fungal strain, Lukas Schrader for sharing the C. obscurior genome data for primer development, the Lab Support Facility of ISTA for general laboratory support and help with the permit approval procedures, and the Finca El Quinto for letting us collect ants on their property. We thank the Social Immunity Team at ISTA for help with ant collection and experimental help, in particular Elina Hanhimäki and Marta Gorecka for behavioural observation, and Elisabeth Naderlinger for spore load PCRs. We further thank the Social Immunity Team and Jürgen Heinze for continued discussion and comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology Austria (ISTA). This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 771402 to SC). ","date_created":"2023-02-28T07:38:17Z","has_accepted_license":"1"},{"keyword":["General Physics","Electrostatics","Triboelectricity","Soft Matter","Acoustic Levitation","Granular Materials"],"isi":1,"article_number":"098202","oa":1,"external_id":{"pmid":["36930925"],"isi":["000946178200008"],"arxiv":["2211.02488"]},"arxiv":1,"citation":{"ama":"Grosjean GM, Waitukaitis SR. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. <i>Physical Review Letters</i>. 2023;130(9). doi:<a href=\"https://doi.org/10.1103/physrevlett.130.098202\">10.1103/physrevlett.130.098202</a>","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media,” <i>Physical Review Letters</i>, vol. 130, no. 9. American Physical Society, 2023.","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.130.098202\">https://doi.org/10.1103/physrevlett.130.098202</a>.","apa":"Grosjean, G. M., &#38; Waitukaitis, S. R. (2023). Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.130.098202\">https://doi.org/10.1103/physrevlett.130.098202</a>","mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” <i>Physical Review Letters</i>, vol. 130, no. 9, 098202, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.130.098202\">10.1103/physrevlett.130.098202</a>.","ista":"Grosjean GM, Waitukaitis SR. 2023. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 130(9), 098202."},"publication_status":"published","language":[{"iso":"eng"}],"pmid":1,"acknowledgement":"We would like to thank Troy Shinbrot, Victor Lee and Daniele Foresti for helpful discussions. This project has received funding from the European Research Council Grant Agreement No. 949120 and from the the Marie Sk lodowska-Curie Grant Agreement No. 754411 under\r\nthe European Union’s Horizon 2020 research and innovation program.","ec_funded":1,"article_processing_charge":"No","publisher":"American Physical Society","volume":130,"type":"journal_article","date_created":"2023-02-28T12:14:46Z","has_accepted_license":"1","intvolume":"       130","project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"ddc":["530","537"],"issue":"9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"03","doi":"10.1103/physrevlett.130.098202","date_published":"2023-03-03T00:00:00Z","oa_version":"Preprint","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"title":"Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Models for same-material contact electrification in granular media often rely on a local charge-driving parameter whose spatial variations lead to a stochastic origin for charge exchange. Measuring the charge transfer from individual granular spheres after contacts with substrates of the same material, we find instead a “global” charging behavior, coherent over the sample’s whole surface. Cleaning and baking samples fully resets charging magnitude and direction, which indicates the underlying global parameter is not intrinsic to the material, but acquired from its history. Charging behavior is randomly and irreversibly affected by changes in relative humidity, hinting at a mechanism where adsorbates, in particular, water, are fundamental to the charge-transfer process."}],"publication":"Physical Review Letters","month":"03","related_material":{"record":[{"status":"public","id":"8101","relation":"research_paper"}]},"department":[{"_id":"ScWa"}],"_id":"12697","file_date_updated":"2023-02-28T12:37:54Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2211.02488","open_access":"1"}],"year":"2023","file":[{"file_size":2301864,"creator":"ggrosjea","file_id":"12698","content_type":"application/pdf","success":1,"date_created":"2023-02-28T12:20:27Z","relation":"main_file","checksum":"c4f2f6eea0408811f8f4898e15890355","access_level":"open_access","date_updated":"2023-02-28T12:20:27Z","file_name":"Main_Preprint.pdf"},{"access_level":"open_access","date_updated":"2023-02-28T12:20:55Z","file_name":"Suppl_info.pdf","creator":"ggrosjea","content_type":"application/pdf","file_id":"12699","file_size":1138625,"success":1,"checksum":"6af6ed6c97a977f923de4162294b43c4","relation":"main_file","date_created":"2023-02-28T12:20:55Z"},{"content_type":"video/mp4","creator":"ggrosjea","file_id":"12700","file_size":793449,"success":1,"checksum":"3f20365fb9515bdba3a111d912c8d8b4","relation":"main_file","date_created":"2023-02-28T12:37:54Z","access_level":"open_access","date_updated":"2023-02-28T12:37:54Z","file_name":"Suppl_vid1.mp4"},{"creator":"ggrosjea","content_type":"video/mp4","file_id":"12701","file_size":455925,"checksum":"90cecacbe0e2f9dea11f91a4ba20c32e","date_created":"2023-02-28T12:37:54Z","relation":"main_file","success":1,"date_updated":"2023-02-28T12:37:54Z","access_level":"open_access","file_name":"Suppl_vid2.mp4"}],"quality_controlled":"1","article_type":"original","author":[{"id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M","full_name":"Grosjean, Galien M","last_name":"Grosjean","orcid":"0000-0001-5154-417X"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"}],"date_updated":"2025-04-23T08:51:13Z","corr_author":"1"},{"corr_author":"1","date_updated":"2025-04-15T07:39:24Z","quality_controlled":"1","article_type":"original","file":[{"access_level":"open_access","date_updated":"2023-03-07T10:58:00Z","file_name":"2023_NatComm_Cheng.pdf","file_id":"12713","creator":"cchlebak","content_type":"application/pdf","file_size":1946443,"success":1,"checksum":"5ff61ad21511950c15abb73b18613883","date_created":"2023-03-07T10:58:00Z","relation":"main_file"}],"author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","full_name":"Cheng, Bingqing","first_name":"Bingqing","orcid":"0000-0002-3584-9632"},{"first_name":"Sebastien","full_name":"Hamel, Sebastien","last_name":"Hamel"},{"last_name":"Bethkenhagen","first_name":"Mandy","full_name":"Bethkenhagen, Mandy","orcid":"0000-0002-1838-2129","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f"}],"file_date_updated":"2023-03-07T10:58:00Z","scopus_import":"1","year":"2023","_id":"12702","department":[{"_id":"BiCh"}],"abstract":[{"lang":"eng","text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution."}],"month":"02","publication":"Nature Communications","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","publication_identifier":{"eissn":["2041-1723"]},"oa_version":"Published Version","doi":"10.1038/s41467-023-36841-1","date_published":"2023-02-27T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"27","intvolume":"        14","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"ddc":["540"],"has_accepted_license":"1","date_created":"2023-03-05T23:01:04Z","acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","publisher":"Springer Nature","type":"journal_article","article_processing_charge":"No","volume":14,"language":[{"iso":"eng"}],"pmid":1,"publication_status":"published","citation":{"short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-36841-1\">10.1038/s41467-023-36841-1</a>","ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-36841-1\">https://doi.org/10.1038/s41467-023-36841-1</a>.","apa":"Cheng, B., Hamel, S., &#38; Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-36841-1\">https://doi.org/10.1038/s41467-023-36841-1</a>","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” <i>Nature Communications</i>, vol. 14, 1104, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-36841-1\">10.1038/s41467-023-36841-1</a>."},"article_number":"1104","oa":1,"external_id":{"isi":["000939678300002"],"pmid":["36843123"]},"isi":1},{"department":[{"_id":"ToHe"}],"related_material":{"record":[{"id":"11366","status":"public","relation":"earlier_version"}]},"publication":"IEEE Robotics and Automation Letters","month":"03","abstract":[{"lang":"eng","text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice."}],"year":"2023","scopus_import":"1","file_date_updated":"2023-03-07T12:22:23Z","_id":"12704","date_updated":"2025-04-14T09:42:58Z","author":[{"full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","full_name":"Amini, Alexander","last_name":"Amini"},{"last_name":"Rus","full_name":"Rus, Daniela","first_name":"Daniela"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"quality_controlled":"1","article_type":"original","file":[{"file_size":944052,"creator":"cchlebak","content_type":"application/pdf","file_id":"12714","date_created":"2023-03-07T12:22:23Z","relation":"main_file","checksum":"5a75dcd326ea66685de2b1aaec259e85","success":1,"date_updated":"2023-03-07T12:22:23Z","access_level":"open_access","file_name":"2023_IEEERobAutLetters_Lechner.pdf"}],"day":"01","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","oa_version":"Published Version","date_published":"2023-03-01T00:00:00Z","doi":"10.1109/LRA.2023.3240930","title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","publication_identifier":{"eissn":["2377-3766"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","publisher":"Institute of Electrical and Electronics Engineers","article_processing_charge":"No","volume":8,"acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","has_accepted_license":"1","date_created":"2023-03-05T23:01:04Z","ddc":["000"],"intvolume":"         8","page":"1595-1602","oa":1,"external_id":{"arxiv":["2204.07373"],"isi":["000936534100012"]},"isi":1,"citation":{"chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>IEEE Robotics and Automation Letters</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/LRA.2023.3240930\">https://doi.org/10.1109/LRA.2023.3240930</a>.","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>IEEE Robotics and Automation Letters</i>, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:<a href=\"https://doi.org/10.1109/LRA.2023.3240930\">10.1109/LRA.2023.3240930</a>.","apa":"Lechner, M., Amini, A., Rus, D., &#38; Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>IEEE Robotics and Automation Letters</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/LRA.2023.3240930\">https://doi.org/10.1109/LRA.2023.3240930</a>","ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>IEEE Robotics and Automation Letters</i>. 2023;8(3):1595-1602. doi:<a href=\"https://doi.org/10.1109/LRA.2023.3240930\">10.1109/LRA.2023.3240930</a>","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” <i>IEEE Robotics and Automation Letters</i>, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023."},"arxiv":1,"publication_status":"published","language":[{"iso":"eng"}]},{"_id":"12705","year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04810"}],"scopus_import":"1","publication":"Journal of Chemical Physics","month":"02","abstract":[{"text":"The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.","lang":"eng"}],"department":[{"_id":"AnSa"}],"author":[{"first_name":"Valerio","full_name":"Sorichetti, Valerio","last_name":"Sorichetti","orcid":"0000-0002-9645-6576","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b"},{"full_name":"Ninarello, Andrea","first_name":"Andrea","last_name":"Ninarello"},{"last_name":"Ruiz-Franco","full_name":"Ruiz-Franco, José","first_name":"José"},{"last_name":"Hugouvieux","full_name":"Hugouvieux, Virginie","first_name":"Virginie"},{"last_name":"Zaccarelli","full_name":"Zaccarelli, Emanuela","first_name":"Emanuela"},{"full_name":"Micheletti, Cristian","first_name":"Cristian","last_name":"Micheletti"},{"full_name":"Kob, Walter","first_name":"Walter","last_name":"Kob"},{"last_name":"Rovigatti","first_name":"Lorenzo","full_name":"Rovigatti, Lorenzo"}],"quality_controlled":"1","article_type":"original","date_updated":"2023-10-03T11:31:51Z","date_published":"2023-02-21T00:00:00Z","doi":"10.1063/5.0134271","oa_version":"Preprint","issue":"7","day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","date_created":"2023-03-05T23:01:05Z","volume":158,"article_processing_charge":"No","publisher":"American Institute of Physics","type":"journal_article","acknowledgement":"We thank Michael Lang for helpful discussions. We acknowledge financial support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC) and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir” French Government program, managed by the French National Research Agency (ANR). W.K. is a senior member of the Institut Universitaire de France.","intvolume":"       158","isi":1,"oa":1,"external_id":{"arxiv":["2211.04810"],"pmid":["36813705"],"isi":["000936943800002"]},"article_number":"074905","publication_status":"published","language":[{"iso":"eng"}],"pmid":1,"arxiv":1,"citation":{"short":"V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).","ama":"Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. <i>Journal of Chemical Physics</i>. 2023;158(7). doi:<a href=\"https://doi.org/10.1063/5.0134271\">10.1063/5.0134271</a>","ieee":"V. Sorichetti <i>et al.</i>, “Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks,” <i>Journal of Chemical Physics</i>, vol. 158, no. 7. American Institute of Physics, 2023.","ista":"Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.","chicago":"Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” <i>Journal of Chemical Physics</i>. American Institute of Physics, 2023. <a href=\"https://doi.org/10.1063/5.0134271\">https://doi.org/10.1063/5.0134271</a>.","mla":"Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” <i>Journal of Chemical Physics</i>, vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:<a href=\"https://doi.org/10.1063/5.0134271\">10.1063/5.0134271</a>.","apa":"Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli, E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. <i>Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0134271\">https://doi.org/10.1063/5.0134271</a>"}},{"publication_identifier":{"eissn":["1932-6203"]},"title":"Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"2","day":"27","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-02-27T00:00:00Z","doi":"10.1371/journal.pone.0279838","oa_version":"Published Version","author":[{"last_name":"Mckerral","full_name":"Mckerral, Jody C.","first_name":"Jody C."},{"id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Kleshnina, Maria","last_name":"Kleshnina"},{"full_name":"Ejov, Vladimir","first_name":"Vladimir","last_name":"Ejov"},{"full_name":"Bartle, Louise","first_name":"Louise","last_name":"Bartle"},{"last_name":"Mitchell","full_name":"Mitchell, James G.","first_name":"James G."},{"full_name":"Filar, Jerzy A.","first_name":"Jerzy A.","last_name":"Filar"}],"article_type":"original","file":[{"relation":"main_file","date_created":"2023-03-07T10:26:45Z","checksum":"798ed5739a4117b03173e5d56e0534c9","success":1,"file_size":1257003,"file_id":"12712","creator":"cchlebak","content_type":"application/pdf","file_name":"2023_PLOSOne_Mckerral.pdf","date_updated":"2023-03-07T10:26:45Z","access_level":"open_access"}],"quality_controlled":"1","date_updated":"2023-10-17T12:53:30Z","publication":"PLoS One","month":"02","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"}],"department":[{"_id":"KrCh"}],"_id":"12706","year":"2023","file_date_updated":"2023-03-07T10:26:45Z","scopus_import":"1","citation":{"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>","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.","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>.","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>","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>.","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."},"language":[{"iso":"eng"}],"pmid":1,"publication_status":"published","page":"e0279838","isi":1,"external_id":{"pmid":["36848357"],"isi":["000996122900022"]},"oa":1,"ddc":["000"],"intvolume":"        18","volume":18,"type":"journal_article","publisher":"Public Library of Science","article_processing_charge":"No","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.","date_created":"2023-03-05T23:01:05Z","has_accepted_license":"1"},{"ec_funded":1,"article_processing_charge":"No","publisher":"Bernoulli Society for Mathematical Statistics and Probability","type":"journal_article","volume":29,"date_created":"2023-03-05T23:01:05Z","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331"}],"intvolume":"        29","page":"1063-1079","isi":1,"oa":1,"external_id":{"isi":["000947270100008"],"arxiv":["2112.12093 "]},"arxiv":1,"citation":{"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>","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>.","ista":"Erdös L, Xu Y. 2023. Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. 29(2), 1063–1079.","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>","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."},"language":[{"iso":"eng"}],"publication_status":"published","month":"05","publication":"Bernoulli","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"}],"department":[{"_id":"LaEr"}],"_id":"12707","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2112.12093"}],"year":"2023","scopus_import":"1","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László","first_name":"László"},{"id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","first_name":"Yuanyuan","full_name":"Xu, Yuanyuan","last_name":"Xu","orcid":"0000-0003-1559-1205"}],"quality_controlled":"1","article_type":"original","date_updated":"2025-04-14T07:57:19Z","corr_author":"1","issue":"2","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2023-05-01T00:00:00Z","doi":"10.3150/22-BEJ1490","oa_version":"Preprint","publication_identifier":{"issn":["1350-7265"]},"title":"Small deviation estimates for the largest eigenvalue of Wigner matrices"},{"intvolume":"        19","project":[{"grant_number":"802960","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"ddc":["540"],"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).","article_processing_charge":"No","type":"journal_article","ec_funded":1,"publisher":"Royal Society of Chemistry","volume":19,"has_accepted_license":"1","date_created":"2023-03-05T23:01:06Z","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.","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>.","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>","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>.","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.","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.","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>"},"publication_status":"published","pmid":1,"language":[{"iso":"eng"}],"page":"1695-1704","isi":1,"external_id":{"isi":["000940388100001"],"pmid":["36779972"],"arxiv":["2204.10059"]},"oa":1,"file":[{"access_level":"open_access","date_updated":"2023-03-07T09:19:41Z","file_name":"2023_SoftMatter_Araujo.pdf","creator":"cchlebak","file_id":"12711","content_type":"application/pdf","file_size":3581939,"success":1,"checksum":"af95aa18b9b01e32fb8f13477c0e2687","date_created":"2023-03-07T09:19:41Z","relation":"main_file"}],"quality_controlled":"1","article_type":"original","author":[{"last_name":"Araújo","first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M."},{"full_name":"Janssen, Liesbeth M.C.","first_name":"Liesbeth M.C.","last_name":"Janssen"},{"first_name":"Thomas","full_name":"Barois, Thomas","last_name":"Barois"},{"full_name":"Boffetta, Guido","first_name":"Guido","last_name":"Boffetta"},{"first_name":"Itai","full_name":"Cohen, Itai","last_name":"Cohen"},{"last_name":"Corbetta","first_name":"Alessandro","full_name":"Corbetta, Alessandro"},{"first_name":"Olivier","full_name":"Dauchot, Olivier","last_name":"Dauchot"},{"last_name":"Dijkstra","full_name":"Dijkstra, Marjolein","first_name":"Marjolein"},{"first_name":"William M.","full_name":"Durham, William M.","last_name":"Durham"},{"last_name":"Dussutour","full_name":"Dussutour, Audrey","first_name":"Audrey"},{"last_name":"Garnier","full_name":"Garnier, Simon","first_name":"Simon"},{"last_name":"Gelderblom","full_name":"Gelderblom, Hanneke","first_name":"Hanneke"},{"first_name":"Ramin","full_name":"Golestanian, Ramin","last_name":"Golestanian"},{"full_name":"Isa, Lucio","first_name":"Lucio","last_name":"Isa"},{"full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H.","last_name":"Koenderink"},{"full_name":"Löwen, Hartmut","first_name":"Hartmut","last_name":"Löwen"},{"first_name":"Ralf","full_name":"Metzler, Ralf","last_name":"Metzler"},{"last_name":"Polin","first_name":"Marco","full_name":"Polin, Marco"},{"full_name":"Royall, C. Patrick","first_name":"C. Patrick","last_name":"Royall"},{"orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Anupam","full_name":"Sengupta, Anupam","last_name":"Sengupta"},{"last_name":"Sykes","full_name":"Sykes, Cécile","first_name":"Cécile"},{"last_name":"Trianni","first_name":"Vito","full_name":"Trianni, Vito"},{"last_name":"Tuval","full_name":"Tuval, Idan","first_name":"Idan"},{"first_name":"Nicolas","full_name":"Vogel, Nicolas","last_name":"Vogel"},{"full_name":"Yeomans, Julia M.","first_name":"Julia M.","last_name":"Yeomans"},{"first_name":"Iker","full_name":"Zuriguel, Iker","last_name":"Zuriguel"},{"first_name":"Alvaro","full_name":"Marin, Alvaro","last_name":"Marin"},{"full_name":"Volpe, Giorgio","first_name":"Giorgio","last_name":"Volpe"}],"date_updated":"2025-04-23T08:48:51Z","abstract":[{"text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.","lang":"eng"}],"publication":"Soft Matter","month":"02","department":[{"_id":"AnSa"}],"_id":"12708","file_date_updated":"2023-03-07T09:19:41Z","scopus_import":"1","year":"2023","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"title":"Steering self-organisation through confinement","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"06","doi":"10.1039/d2sm01562e","date_published":"2023-02-06T00:00:00Z","oa_version":"Published Version"},{"title":"Computing the multicover bifiltration","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","doi":"10.1007/s00454-022-00476-8","date_published":"2023-09-01T00:00:00Z","date_updated":"2025-07-10T12:01:57Z","file":[{"success":1,"relation":"main_file","date_created":"2023-03-07T14:40:14Z","checksum":"71ce7e59f7ee4620acc704fecca620c2","file_size":1359323,"content_type":"application/pdf","file_id":"12715","creator":"cchlebak","file_name":"2023_DisCompGeo_Corbet.pdf","access_level":"open_access","date_updated":"2023-03-07T14:40:14Z"}],"article_type":"original","quality_controlled":"1","author":[{"last_name":"Corbet","first_name":"René","full_name":"Corbet, René"},{"orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","full_name":"Lesnick, Michael","last_name":"Lesnick"},{"first_name":"Georg F","full_name":"Osang, Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9605"}]},"department":[{"_id":"HeEd"}],"abstract":[{"lang":"eng","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."}],"month":"09","publication":"Discrete and Computational Geometry","scopus_import":"1","file_date_updated":"2023-03-07T14:40:14Z","year":"2023","_id":"12709","citation":{"short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, Discrete and Computational Geometry 70 (2023) 376–405.","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>","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.","ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2023. Computing the multicover bifiltration. Discrete and Computational Geometry. 70, 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>."},"arxiv":1,"publication_status":"published","language":[{"iso":"eng"}],"pmid":1,"page":"376-405","external_id":{"arxiv":["2103.07823"],"isi":["000936496800001"],"pmid":["37581017"]},"oa":1,"isi":1,"intvolume":"        70","ddc":["000"],"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.","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","type":"journal_article","volume":70,"date_created":"2023-03-05T23:01:06Z","has_accepted_license":"1"},{"file_date_updated":"2023-09-26T10:51:56Z","scopus_import":"1","year":"2023","_id":"12710","department":[{"_id":"EdHa"}],"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."}],"month":"03","publication":"Advanced Materials","date_updated":"2023-09-26T10:56:46Z","file":[{"success":1,"date_created":"2023-09-26T10:51:56Z","relation":"main_file","checksum":"5c04d68130e97a0ecd1ca27fbc15a246","file_size":2898063,"creator":"dernst","file_id":"14373","content_type":"application/pdf","file_name":"2023_AdvancedMaterials_Schamberger.pdf","access_level":"open_access","date_updated":"2023-09-26T10:51:56Z"}],"quality_controlled":"1","article_type":"review","author":[{"last_name":"Schamberger","full_name":"Schamberger, Barbara","first_name":"Barbara"},{"first_name":"Ricardo","full_name":"Ziege, Ricardo","last_name":"Ziege"},{"full_name":"Anselme, Karine","first_name":"Karine","last_name":"Anselme"},{"last_name":"Ben Amar","full_name":"Ben Amar, Martine","first_name":"Martine"},{"first_name":"Michał","full_name":"Bykowski, Michał","last_name":"Bykowski"},{"first_name":"André P.G.","full_name":"Castro, André P.G.","last_name":"Castro"},{"last_name":"Cipitria","full_name":"Cipitria, Amaia","first_name":"Amaia"},{"first_name":"Rhoslyn A.","full_name":"Coles, Rhoslyn A.","last_name":"Coles"},{"full_name":"Dimova, Rumiana","first_name":"Rumiana","last_name":"Dimova"},{"full_name":"Eder, Michaela","first_name":"Michaela","last_name":"Eder"},{"full_name":"Ehrig, Sebastian","first_name":"Sebastian","last_name":"Ehrig"},{"full_name":"Escudero, Luis M.","first_name":"Luis M.","last_name":"Escudero"},{"last_name":"Evans","full_name":"Evans, Myfanwy E.","first_name":"Myfanwy E."},{"full_name":"Fernandes, Paulo R.","first_name":"Paulo R.","last_name":"Fernandes"},{"first_name":"Peter","full_name":"Fratzl, Peter","last_name":"Fratzl"},{"first_name":"Liesbet","full_name":"Geris, Liesbet","last_name":"Geris"},{"last_name":"Gierlinger","full_name":"Gierlinger, Notburga","first_name":"Notburga"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Iglič","first_name":"Aleš","full_name":"Iglič, Aleš"},{"last_name":"Kirkensgaard","full_name":"Kirkensgaard, Jacob J.K.","first_name":"Jacob J.K."},{"full_name":"Kollmannsberger, Philip","first_name":"Philip","last_name":"Kollmannsberger"},{"last_name":"Kowalewska","full_name":"Kowalewska, Łucja","first_name":"Łucja"},{"first_name":"Nicholas A.","full_name":"Kurniawan, Nicholas A.","last_name":"Kurniawan"},{"last_name":"Papantoniou","first_name":"Ioannis","full_name":"Papantoniou, Ioannis"},{"first_name":"Laurent","full_name":"Pieuchot, Laurent","last_name":"Pieuchot"},{"last_name":"Pires","full_name":"Pires, Tiago H.V.","first_name":"Tiago H.V."},{"first_name":"Lars D.","full_name":"Renner, Lars D.","last_name":"Renner"},{"full_name":"Sageman-Furnas, Andrew O.","first_name":"Andrew O.","last_name":"Sageman-Furnas"},{"last_name":"Schröder-Turk","full_name":"Schröder-Turk, Gerd E.","first_name":"Gerd E."},{"last_name":"Sengupta","first_name":"Anupam","full_name":"Sengupta, Anupam"},{"first_name":"Vikas R.","full_name":"Sharma, Vikas R.","last_name":"Sharma"},{"first_name":"Antonio","full_name":"Tagua, Antonio","last_name":"Tagua"},{"first_name":"Caterina","full_name":"Tomba, Caterina","last_name":"Tomba"},{"last_name":"Trepat","full_name":"Trepat, Xavier","first_name":"Xavier"},{"full_name":"Waters, Sarah L.","first_name":"Sarah L.","last_name":"Waters"},{"full_name":"Yeo, Edwina F.","first_name":"Edwina F.","last_name":"Yeo"},{"last_name":"Roschger","full_name":"Roschger, Andreas","first_name":"Andreas"},{"last_name":"Bidan","first_name":"Cécile M.","full_name":"Bidan, Cécile M."},{"first_name":"John W.C.","full_name":"Dunlop, John W.C.","last_name":"Dunlop"}],"oa_version":"Published Version","doi":"10.1002/adma.202206110","date_published":"2023-03-29T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"29","issue":"13","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"date_created":"2023-03-05T23:01:06Z","has_accepted_license":"1","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.","type":"journal_article","publisher":"Wiley","volume":35,"article_processing_charge":"No","intvolume":"        35","ddc":["570"],"article_number":"2206110","oa":1,"external_id":{"isi":["000941068900001"],"pmid":["36461812"]},"isi":1,"pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","citation":{"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.","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>","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>"}},{"ddc":["570"],"intvolume":"        15","type":"journal_article","volume":15,"article_processing_charge":"No","publisher":"Springer Nature","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.","date_created":"2023-03-12T23:01:02Z","has_accepted_license":"1","citation":{"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.","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>.","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>","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).","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>","ieee":"E. Bernabeu <i>et al.</i>, “Refining epigenetic prediction of chronological and biological age,” <i>Genome Medicine</i>, vol. 15. Springer Nature, 2023."},"pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","isi":1,"oa":1,"external_id":{"isi":["000940286600001"],"pmid":["36855161"]},"article_number":"12","author":[{"first_name":"Elena","full_name":"Bernabeu, Elena","last_name":"Bernabeu"},{"last_name":"Mccartney","full_name":"Mccartney, Daniel L.","first_name":"Daniel L."},{"full_name":"Gadd, Danni A.","first_name":"Danni A.","last_name":"Gadd"},{"last_name":"Hillary","full_name":"Hillary, Robert F.","first_name":"Robert F."},{"first_name":"Ake T.","full_name":"Lu, Ake T.","last_name":"Lu"},{"first_name":"Lee","full_name":"Murphy, Lee","last_name":"Murphy"},{"last_name":"Wrobel","first_name":"Nicola","full_name":"Wrobel, Nicola"},{"full_name":"Campbell, Archie","first_name":"Archie","last_name":"Campbell"},{"full_name":"Harris, Sarah E.","first_name":"Sarah E.","last_name":"Harris"},{"last_name":"Liewald","full_name":"Liewald, David","first_name":"David"},{"first_name":"Caroline","full_name":"Hayward, Caroline","last_name":"Hayward"},{"full_name":"Sudlow, Cathie","first_name":"Cathie","last_name":"Sudlow"},{"last_name":"Cox","first_name":"Simon R.","full_name":"Cox, Simon R."},{"full_name":"Evans, Kathryn L.","first_name":"Kathryn L.","last_name":"Evans"},{"last_name":"Horvath","first_name":"Steve","full_name":"Horvath, Steve"},{"last_name":"Mcintosh","first_name":"Andrew M.","full_name":"Mcintosh, Andrew M."},{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"last_name":"Vallejos","full_name":"Vallejos, Catalina A.","first_name":"Catalina A."},{"last_name":"Marioni","first_name":"Riccardo E.","full_name":"Marioni, Riccardo E."}],"article_type":"original","quality_controlled":"1","file":[{"access_level":"open_access","date_updated":"2023-03-14T10:29:47Z","file_name":"2023_GenomeMed_Bernabeu.pdf","file_size":4275987,"file_id":"12722","creator":"cchlebak","content_type":"application/pdf","success":1,"date_created":"2023-03-14T10:29:47Z","relation":"main_file","checksum":"833b837910c4db42fb5f0f34125f77a7"}],"date_updated":"2025-04-23T08:49:38Z","month":"02","publication":"Genome Medicine","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"}],"department":[{"_id":"MaRo"}],"_id":"12719","year":"2023","file_date_updated":"2023-03-14T10:29:47Z","scopus_import":"1","publication_identifier":{"eissn":["1756-994X"]},"title":"Refining epigenetic prediction of chronological and biological age","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2023-02-28T00:00:00Z","doi":"10.1186/s13073-023-01161-y","oa_version":"Published Version"},{"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2023-03-01T00:00:00Z","doi":"10.1007/978-1-0716-3004-4_3","oa_version":"Submitted Version","publication_identifier":{"isbn":["978-1-0716-3003-7"],"eissn":["1940-6029"],"eisbn":["978-1-0716-3004-4"],"issn":["1064-3745"]},"place":"New York, NY, United States","title":"Molecular Cloning Using In Vivo DNA Assembly","publication":"DNA Manipulation and Analysis","month":"03","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"}],"department":[{"_id":"PeJo"}],"_id":"12720","OA_place":"repository","main_file_link":[{"url":"https://zaguan.unizar.es/record/125930/files/texto_completo.pdf","open_access":"1"}],"year":"2023","scopus_import":"1","author":[{"last_name":"Arroyo-Urea","first_name":"Sandra","full_name":"Arroyo-Urea, Sandra"},{"last_name":"Watson","first_name":"Jake","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"last_name":"García-Nafría","full_name":"García-Nafría, Javier","first_name":"Javier"}],"quality_controlled":"1","date_updated":"2025-06-25T05:56:45Z","OA_type":"green","page":"33-44","alternative_title":["Methods in Molecular Biology"],"series_title":"MIMB","external_id":{"pmid":["36853454"]},"oa":1,"citation":{"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.","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>","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.","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>.","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>."},"pmid":1,"publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Springer Nature","volume":2633,"type":"book_chapter","date_created":"2023-03-12T23:01:02Z","intvolume":"      2633","editor":[{"last_name":"Scarlett","first_name":"Garry","full_name":"Scarlett, Garry"}]}]