[{"type":"preprint","abstract":[{"text":"We consider a model of the Riemann zeta function on the critical axis and study its maximum over intervals of length (log T)θ, where θ is either fixed or tends to zero at a suitable rate.\r\nIt is shown that the deterministic level of the maximum interpolates smoothly between the ones\r\nof log-correlated variables and of i.i.d. random variables, exhibiting a smooth transition ‘from\r\n3/4 to 1/4’ in the second order. This provides a natural context where extreme value statistics of\r\nlog-correlated variables with time-dependent variance and rate occur. A key ingredient of the\r\nproof is a precise upper tail tightness estimate for the maximum of the model on intervals of\r\nsize one, that includes a Gaussian correction. This correction is expected to be present for the\r\nRiemann zeta function and pertains to the question of the correct order of the maximum of\r\nthe zeta function in large intervals.","lang":"eng"}],"year":"2021","publication_status":"submitted","publication":"arXiv","_id":"9230","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2103.04817","open_access":"1"}],"status":"public","doi":"10.48550/arXiv.2103.04817","department":[{"_id":"LaEr"}],"date_created":"2021-03-09T11:08:15Z","date_updated":"2025-04-14T07:43:51Z","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"month":"03","oa":1,"date_published":"2021-03-08T00:00:00Z","ec_funded":1,"acknowledgement":"The research of L.-P. A. is supported in part by the grant NSF CAREER DMS-1653602. G. D. gratefully acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. The research of L. H. is supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through Project-ID 233630050 -TRR 146, Project-ID 443891315 within SPP 2265 and Project-ID 446173099.","author":[{"full_name":"Arguin, Louis-Pierre","last_name":"Arguin","first_name":"Louis-Pierre"},{"first_name":"Guillaume","last_name":"Dubach","full_name":"Dubach, Guillaume","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","orcid":"0000-0001-6892-8137"},{"first_name":"Lisa","last_name":"Hartung","full_name":"Hartung, Lisa"}],"language":[{"iso":"eng"}],"day":"08","title":"Maxima of a random model of the Riemann zeta function over intervals of varying length","citation":{"mla":"Arguin, Louis-Pierre, et al. “Maxima of a Random Model of the Riemann Zeta Function over Intervals of Varying Length.” <i>ArXiv</i>, 2103.04817, doi:<a href=\"https://doi.org/10.48550/arXiv.2103.04817\">10.48550/arXiv.2103.04817</a>.","ama":"Arguin L-P, Dubach G, Hartung L. Maxima of a random model of the Riemann zeta function over intervals of varying length. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2103.04817\">10.48550/arXiv.2103.04817</a>","ieee":"L.-P. Arguin, G. Dubach, and L. Hartung, “Maxima of a random model of the Riemann zeta function over intervals of varying length,” <i>arXiv</i>. .","chicago":"Arguin, Louis-Pierre, Guillaume Dubach, and Lisa Hartung. “Maxima of a Random Model of the Riemann Zeta Function over Intervals of Varying Length.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2103.04817\">https://doi.org/10.48550/arXiv.2103.04817</a>.","ista":"Arguin L-P, Dubach G, Hartung L. Maxima of a random model of the Riemann zeta function over intervals of varying length. arXiv, 2103.04817.","short":"L.-P. Arguin, G. Dubach, L. Hartung, ArXiv (n.d.).","apa":"Arguin, L.-P., Dubach, G., &#38; Hartung, L. (n.d.). Maxima of a random model of the Riemann zeta function over intervals of varying length. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2103.04817\">https://doi.org/10.48550/arXiv.2103.04817</a>"},"article_number":"2103.04817","arxiv":1,"external_id":{"arxiv":["2103.04817"]}},{"language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","citation":{"mla":"Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods for Solving Multivalued Variational Inequality Problems beyond Monotonicity.” <i>Networks and Spatial Economics</i>, vol. 21, no. 2, Springer Nature, 2021, pp. 291–323, doi:<a href=\"https://doi.org/10.1007/s11067-021-09517-w\">10.1007/s11067-021-09517-w</a>.","ama":"Izuchukwu C, Shehu Y. New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. <i>Networks and Spatial Economics</i>. 2021;21(2):291-323. doi:<a href=\"https://doi.org/10.1007/s11067-021-09517-w\">10.1007/s11067-021-09517-w</a>","ieee":"C. Izuchukwu and Y. Shehu, “New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity,” <i>Networks and Spatial Economics</i>, vol. 21, no. 2. Springer Nature, pp. 291–323, 2021.","chicago":"Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods for Solving Multivalued Variational Inequality Problems beyond Monotonicity.” <i>Networks and Spatial Economics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11067-021-09517-w\">https://doi.org/10.1007/s11067-021-09517-w</a>.","ista":"Izuchukwu C, Shehu Y. 2021. New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. Networks and Spatial Economics. 21(2), 291–323.","short":"C. Izuchukwu, Y. Shehu, Networks and Spatial Economics 21 (2021) 291–323.","apa":"Izuchukwu, C., &#38; Shehu, Y. (2021). New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. <i>Networks and Spatial Economics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11067-021-09517-w\">https://doi.org/10.1007/s11067-021-09517-w</a>"},"date_updated":"2024-11-04T13:52:33Z","ec_funded":1,"file":[{"checksum":"22b4253a2e5da843622a2df713784b4c","date_created":"2021-08-11T12:44:16Z","date_updated":"2021-08-11T12:44:16Z","file_size":834964,"creator":"kschuh","relation":"main_file","file_id":"9884","success":1,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_NetworksSpatialEconomics_Shehu.pdf"}],"month":"06","date_published":"2021-06-01T00:00:00Z","doi":"10.1007/s11067-021-09517-w","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"In this paper, we present two new inertial projection-type methods for solving multivalued variational inequality problems in finite-dimensional spaces. We establish the convergence of the sequence generated by these methods when the multivalued mapping associated with the problem is only required to be locally bounded without any monotonicity assumption. Furthermore, the inertial techniques that we employ in this paper are quite different from the ones used in most papers. Moreover, based on the weaker assumptions on the inertial factor in our methods, we derive several special cases of our methods. Finally, we present some experimental results to illustrate the profits that we gain by introducing the inertial extrapolation steps."}],"year":"2021","article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","external_id":{"isi":["000625002100001"]},"title":"New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity","issue":"2","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_created":"2021-03-10T12:18:47Z","quality_controlled":"1","acknowledgement":"The authors sincerely thank the Editor-in-Chief and anonymous referees for their careful reading, constructive comments and fruitful suggestions that help improve the manuscript. The research of the first author is supported by the National Research Foundation (NRF) South Africa (S& F-DSI/NRF Free Standing Postdoctoral Fellowship; Grant Number: 120784). The first author also acknowledges the financial support from DSI/NRF, South Africa Center of Excellence in Mathematical and Statistical Sciences (CoE-MaSS) Postdoctoral Fellowship. The second author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160). Open Access funding provided by Institute of Science and Technology (IST Austria).","author":[{"last_name":"Izuchukwu","full_name":"Izuchukwu, Chinedu","first_name":"Chinedu"},{"first_name":"Yekini","full_name":"Shehu, Yekini","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139"}],"oa":1,"keyword":["Computer Networks and Communications","Software","Artificial Intelligence"],"scopus_import":"1","oa_version":"Published Version","status":"public","ddc":["510"],"intvolume":"        21","department":[{"_id":"VlKo"}],"file_date_updated":"2021-08-11T12:44:16Z","isi":1,"volume":21,"page":"291-323","publication_identifier":{"issn":["1566-113X"],"eissn":["1572-9427"]},"type":"journal_article","has_accepted_license":"1","_id":"9234","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Networks and Spatial Economics"},{"intvolume":"       119","department":[{"_id":"ToHe"}],"isi":1,"scopus_import":"1","oa_version":"Preprint","status":"public","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6884"}]},"_id":"9239","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Journal of Computer and System Sciences","volume":119,"page":"133-144","publication_identifier":{"issn":["0022-0000"],"eissn":["1090-2724"]},"type":"journal_article","external_id":{"isi":["000634149800009"],"arxiv":["1905.03835"]},"arxiv":1,"title":"Bidding mechanisms in graph games","issue":"8","publisher":"Elsevier","quality_controlled":"1","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Đorđe","last_name":"Žikelić","full_name":"Žikelić, Đorđe"}],"oa":1,"date_created":"2021-03-14T23:01:32Z","doi":"10.1016/j.jcss.2021.02.008","article_type":"original","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.03835","open_access":"1"}],"article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","text":"A graph game proceeds as follows: two players move a token through a graph to produce a finite or infinite path, which determines the payoff of the game. We study bidding games in which in each turn, an auction determines which player moves the token. Bidding games were largely studied in combination with two variants of first-price auctions called “Richman” and “poorman” bidding. We study taxman bidding, which span the spectrum between the two. The game is parameterized by a constant : portion τ of the winning bid is paid to the other player, and portion  to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games: we unify, generalize, and simplify previous equivalences between bidding games and a class of stochastic games called random-turn games."}],"year":"2021","day":"03","citation":{"short":"G. Avni, T.A. Henzinger, Đ. Žikelić, Journal of Computer and System Sciences 119 (2021) 133–144.","apa":"Avni, G., Henzinger, T. A., &#38; Žikelić, Đ. (2021). Bidding mechanisms in graph games. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2021.02.008\">https://doi.org/10.1016/j.jcss.2021.02.008</a>","mla":"Avni, Guy, et al. “Bidding Mechanisms in Graph Games.” <i>Journal of Computer and System Sciences</i>, vol. 119, no. 8, Elsevier, 2021, pp. 133–44, doi:<a href=\"https://doi.org/10.1016/j.jcss.2021.02.008\">10.1016/j.jcss.2021.02.008</a>.","ama":"Avni G, Henzinger TA, Žikelić Đ. Bidding mechanisms in graph games. <i>Journal of Computer and System Sciences</i>. 2021;119(8):133-144. doi:<a href=\"https://doi.org/10.1016/j.jcss.2021.02.008\">10.1016/j.jcss.2021.02.008</a>","chicago":"Avni, Guy, Thomas A Henzinger, and Đorđe Žikelić. “Bidding Mechanisms in Graph Games.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jcss.2021.02.008\">https://doi.org/10.1016/j.jcss.2021.02.008</a>.","ieee":"G. Avni, T. A. Henzinger, and Đ. Žikelić, “Bidding mechanisms in graph games,” <i>Journal of Computer and System Sciences</i>, vol. 119, no. 8. Elsevier, pp. 133–144, 2021.","ista":"Avni G, Henzinger TA, Žikelić Đ. 2021. Bidding mechanisms in graph games. Journal of Computer and System Sciences. 119(8), 133–144."},"language":[{"iso":"eng"}],"month":"03","date_published":"2021-03-03T00:00:00Z","date_updated":"2025-07-10T11:53:57Z"},{"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"date_created":"2021-03-14T23:01:32Z","quality_controlled":"1","author":[{"orcid":"0000-0002-6269-5149","id":"2CEB641C-A400-11E9-A717-D712E6697425","last_name":"Cornalba","full_name":"Cornalba, Federico","first_name":"Federico"},{"first_name":"Tony","last_name":"Shardlow","full_name":"Shardlow, Tony"},{"first_name":"Johannes","last_name":"Zimmer","full_name":"Zimmer, Johannes"}],"acknowledgement":"All authors thank the anonymous referee for his/her careful reading of the manuscript and valuable suggestions. This paper was motivated by stimulating discussions at the First Berlin–Leipzig Workshop on Fluctuating Hydrodynamics in August 2019 with Ana Djurdjevac, Rupert Klein and Ralf Kornhuber. JZ gratefully acknowledges funding by a Royal Society Wolfson Research Merit Award. FC gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","oa":1,"publisher":"Elsevier","external_id":{"isi":["000634823300010"]},"issue":"5","title":"Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions","page":"253-283","volume":284,"publication_identifier":{"eissn":["1090-2732"],"issn":["0022-0396"]},"has_accepted_license":"1","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9240","publication":"Journal of Differential Equations","scopus_import":"1","status":"public","ddc":["510"],"oa_version":"Published Version","department":[{"_id":"JuFi"}],"intvolume":"       284","isi":1,"file_date_updated":"2021-03-22T07:18:01Z","date_updated":"2025-04-14T07:43:51Z","ec_funded":1,"file":[{"access_level":"open_access","date_created":"2021-03-22T07:18:01Z","checksum":"c630b691fb9e716b02aa6103a9794ec8","file_size":473310,"date_updated":"2021-03-22T07:18:01Z","creator":"dernst","file_id":"9267","relation":"main_file","success":1,"content_type":"application/pdf","file_name":"2021_JourDiffEquations_Cornalba.pdf"}],"date_published":"2021-05-25T00:00:00Z","month":"05","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"F. Cornalba, T. Shardlow, J. Zimmer, Journal of Differential Equations 284 (2021) 253–283.","apa":"Cornalba, F., Shardlow, T., &#38; Zimmer, J. (2021). Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2021.02.048\">https://doi.org/10.1016/j.jde.2021.02.048</a>","ama":"Cornalba F, Shardlow T, Zimmer J. Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. <i>Journal of Differential Equations</i>. 2021;284(5):253-283. doi:<a href=\"https://doi.org/10.1016/j.jde.2021.02.048\">10.1016/j.jde.2021.02.048</a>","mla":"Cornalba, Federico, et al. “Well-Posedness for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several Space Dimensions.” <i>Journal of Differential Equations</i>, vol. 284, no. 5, Elsevier, 2021, pp. 253–83, doi:<a href=\"https://doi.org/10.1016/j.jde.2021.02.048\">10.1016/j.jde.2021.02.048</a>.","ista":"Cornalba F, Shardlow T, Zimmer J. 2021. Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. Journal of Differential Equations. 284(5), 253–283.","ieee":"F. Cornalba, T. Shardlow, and J. Zimmer, “Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions,” <i>Journal of Differential Equations</i>, vol. 284, no. 5. Elsevier, pp. 253–283, 2021.","chicago":"Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “Well-Posedness for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several Space Dimensions.” <i>Journal of Differential Equations</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jde.2021.02.048\">https://doi.org/10.1016/j.jde.2021.02.048</a>."},"day":"25","publication_status":"published","year":"2021","abstract":[{"text":"A stochastic PDE, describing mesoscopic fluctuations in systems of weakly interacting inertial particles of finite volume, is proposed and analysed in any finite dimension . It is a regularised and inertial version of the Dean–Kawasaki model. A high-probability well-posedness theory for this model is developed. This theory improves significantly on the spatial scaling restrictions imposed in an earlier work of the same authors, which applied only to significantly larger particles in one dimension. The well-posedness theory now applies in d-dimensions when the particle-width ϵ is proportional to  for  and N is the number of particles. This scaling is optimal in a certain Sobolev norm. Key tools of the analysis are fractional Sobolev spaces, sharp bounds on Bessel functions, separability of the regularisation in the d-spatial dimensions, and use of the Faà di Bruno's formula.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","article_type":"original","doi":"10.1016/j.jde.2021.02.048"},{"isi":1,"department":[{"_id":"JoFi"}],"intvolume":"       103","status":"public","oa_version":"Preprint","scopus_import":"1","publication":"Physical Review A","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9242","type":"journal_article","volume":103,"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"issue":"2","title":"Frequency-multiplexed hybrid optical entangled source based on the Pockels effect","arxiv":1,"external_id":{"isi":["000617037900013"],"arxiv":["2010.05356"]},"publisher":"American Physical Society","oa":1,"author":[{"first_name":"Alfredo R","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"I thank Prof. Shabir Barzanjeh and Dr. Ulrich Vogl for the fruitful discussions.\r\n","quality_controlled":"1","date_created":"2021-03-14T23:01:33Z","main_file_link":[{"url":"https://arxiv.org/abs/2010.05356","open_access":"1"}],"article_type":"original","doi":"10.1103/PhysRevA.103.023708","article_processing_charge":"No","year":"2021","abstract":[{"lang":"eng","text":"In the recent years important experimental advances in resonant electro-optic modulators as high-efficiency sources for coherent frequency combs and as devices for quantum information transfer have been realized, where strong optical and microwave mode coupling were achieved. These features suggest electro-optic-based devices as candidates for entangled optical frequency comb sources. In the present work, I study the generation of entangled optical frequency combs in millimeter-sized resonant electro-optic modulators. These devices profit from the experimentally proven advantages such as nearly constant optical free spectral ranges over several gigahertz, and high optical and microwave quality factors. The generation of frequency multiplexed quantum channels with spectral bandwidth in the MHz range for conservative parameter values paves the way towards novel uses in long-distance hybrid quantum networks, quantum key distribution, enhanced optical metrology, and quantum computing."}],"publication_status":"published","citation":{"ieee":"A. R. Rueda Sanchez, “Frequency-multiplexed hybrid optical entangled source based on the Pockels effect,” <i>Physical Review A</i>, vol. 103, no. 2. American Physical Society, 2021.","chicago":"Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” <i>Physical Review A</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">https://doi.org/10.1103/PhysRevA.103.023708</a>.","ista":"Rueda Sanchez AR. 2021. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. 103(2), 023708.","mla":"Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” <i>Physical Review A</i>, vol. 103, no. 2, 023708, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">10.1103/PhysRevA.103.023708</a>.","ama":"Rueda Sanchez AR. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. <i>Physical Review A</i>. 2021;103(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">10.1103/PhysRevA.103.023708</a>","apa":"Rueda Sanchez, A. R. (2021). Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">https://doi.org/10.1103/PhysRevA.103.023708</a>","short":"A.R. Rueda Sanchez, Physical Review A 103 (2021)."},"day":"11","article_number":"023708","language":[{"iso":"eng"}],"date_published":"2021-02-11T00:00:00Z","month":"02","date_updated":"2023-08-07T14:11:18Z"},{"doi":"10.7554/eLife.61525","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials."}],"year":"2021","article_processing_charge":"No","language":[{"iso":"eng"}],"article_number":"1-32","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"24","citation":{"ieee":"V. M. Hernández-Rocamora, N. S. Baranova, K. Peters, E. Breukink, M. Loose, and W. Vollmer, “Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","chicago":"Hernández-Rocamora, Víctor M., Natalia S. Baranova, Katharina Peters, Eefjan Breukink, Martin Loose, and Waldemar Vollmer. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.61525\">https://doi.org/10.7554/eLife.61525</a>.","ista":"Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. 2021. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. eLife. 10, 1–32.","mla":"Hernández-Rocamora, Víctor M., et al. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” <i>ELife</i>, vol. 10, 1–32, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.61525\">10.7554/eLife.61525</a>.","ama":"Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.61525\">10.7554/eLife.61525</a>","apa":"Hernández-Rocamora, V. M., Baranova, N. S., Peters, K., Breukink, E., Loose, M., &#38; Vollmer, W. (2021). Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.61525\">https://doi.org/10.7554/eLife.61525</a>","short":"V.M. Hernández-Rocamora, N.S. Baranova, K. Peters, E. Breukink, M. Loose, W. Vollmer, ELife 10 (2021)."},"date_updated":"2024-10-22T10:04:21Z","ec_funded":1,"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9268","relation":"main_file","date_updated":"2021-03-22T07:36:08Z","creator":"dernst","file_size":2314698,"checksum":"79897a09bfecd9914d39c4aea2841855","date_created":"2021-03-22T07:36:08Z","file_name":"2021_eLife_HernandezRocamora.pdf"}],"month":"02","date_published":"2021-02-24T00:00:00Z","scopus_import":"1","oa_version":"Published Version","ddc":["570"],"status":"public","intvolume":"        10","department":[{"_id":"MaLo"}],"isi":1,"file_date_updated":"2021-03-22T07:36:08Z","volume":10,"publication_identifier":{"eissn":["2050-084X"]},"type":"journal_article","has_accepted_license":"1","_id":"9243","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"eLife","publisher":"eLife Sciences Publications","external_id":{"isi":["000627596400001"]},"title":"Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins","project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall synthesis"}],"date_created":"2021-03-14T23:01:33Z","acknowledgement":"We thank Alexander Egan (Newcastle University) for purified proteins LpoB(sol) and LpoPPa(sol), Federico Corona (Newcastle University) for purified MepM, and Oliver Birkholz and Jacob Piehler (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for their help with PBP1B reconstitution into polymer-SLBs and initial guidance on single particle tracking. We also acknowledge Christian P Richter and Changjiang You (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for providing SLIMfast software and tris-DODA-NTA reagent, respectively. This work was funded by the BBSRC grant BB/R017409/1 (to WV), the European Research Council through grant ERC-2015-StG-679239 (to ML), and long-term fellowships HFSP LT 000824/2016-L4 and EMBO ALTF 1163–2015 (to NB). ","author":[{"first_name":"Víctor M.","full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora"},{"first_name":"Natalia S.","last_name":"Baranova","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Peters","full_name":"Peters, Katharina","first_name":"Katharina"},{"first_name":"Eefjan","full_name":"Breukink, Eefjan","last_name":"Breukink"},{"last_name":"Loose","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vollmer, Waldemar","last_name":"Vollmer","first_name":"Waldemar"}],"quality_controlled":"1","oa":1},{"article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","text":"Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models."}],"year":"2021","doi":"10.7554/eLife.60916","article_type":"original","ec_funded":1,"file":[{"file_name":"2021_eLife_Hankeova.pdf","content_type":"application/pdf","success":1,"file_id":"9271","relation":"main_file","file_size":9259690,"creator":"dernst","date_updated":"2021-03-22T08:50:33Z","checksum":"20ccf4dfe46c48cf986794c8bf4fd1cb","date_created":"2021-03-22T08:50:33Z","access_level":"open_access"}],"month":"02","date_published":"2021-02-26T00:00:00Z","date_updated":"2026-04-02T14:00:00Z","article_number":"e60916","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"26","citation":{"mla":"Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>, vol. 10, e60916, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>.","ama":"Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>","chicago":"Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>.","ieee":"S. Hankeova <i>et al.</i>, “DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 10, e60916.","short":"S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek, V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis, A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021).","apa":"Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek, A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>"},"language":[{"iso":"eng"}],"_id":"9244","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"eLife","volume":10,"publication_identifier":{"eissn":["2050-084X"]},"type":"journal_article","has_accepted_license":"1","intvolume":"        10","department":[{"_id":"EdHa"}],"isi":1,"file_date_updated":"2021-03-22T08:50:33Z","scopus_import":"1","oa_version":"Published Version","status":"public","ddc":["570"],"quality_controlled":"1","author":[{"first_name":"Simona","full_name":"Hankeova, Simona","last_name":"Hankeova"},{"last_name":"Salplachta","full_name":"Salplachta, Jakub","first_name":"Jakub"},{"full_name":"Zikmund, Tomas","last_name":"Zikmund","first_name":"Tomas"},{"first_name":"Michaela","last_name":"Kavkova","full_name":"Kavkova, Michaela"},{"first_name":"Noémi","full_name":"Van Hul, Noémi","last_name":"Van Hul"},{"first_name":"Adam","last_name":"Brinek","full_name":"Brinek, Adam"},{"last_name":"Smekalova","full_name":"Smekalova, Veronika","first_name":"Veronika"},{"first_name":"Jakub","last_name":"Laznovsky","full_name":"Laznovsky, Jakub"},{"first_name":"Feven","full_name":"Dawit, Feven","last_name":"Dawit"},{"first_name":"Josef","full_name":"Jaros, Josef","last_name":"Jaros"},{"last_name":"Bryja","full_name":"Bryja, Vítězslav","first_name":"Vítězslav"},{"full_name":"Lendahl, Urban","last_name":"Lendahl","first_name":"Urban"},{"full_name":"Ellis, Ewa","last_name":"Ellis","first_name":"Ewa"},{"full_name":"Nemeth, Antal","last_name":"Nemeth","first_name":"Antal"},{"full_name":"Fischler, Björn","last_name":"Fischler","first_name":"Björn"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"last_name":"Kaiser","full_name":"Kaiser, Jozef","first_name":"Jozef"},{"full_name":"Andersson, Emma Rachel","last_name":"Andersson","first_name":"Emma Rachel"}],"acknowledgement":"Work in ERA lab is supported by the Swedish Research Council, the Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated to this project. The funders have no role in the design or interpretation of the work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m Foundation Scholarship. We are grateful for support from Tornspiran foundation to NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II and CzechNanoLab Research Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged. JJ: The work was supported by the Grant Agency of Masaryk University (project no. MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise and help regarding bile duct cannulation and their laboratory hospitality. We also thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion. We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics (SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242. We thank Goncalo M Brito for all illustrations. This work was supported by the European Union (European Research Council Starting grant 851288 to E.H.).","oa":1,"pmid":1,"project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"date_created":"2021-03-14T23:01:34Z","external_id":{"isi":["000625357100001"],"pmid":["33635272"]},"title":"DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome","publisher":"eLife Sciences Publications"},{"article_type":"original","doi":"10.1007/s00205-021-01616-9","year":"2021","abstract":[{"text":"We consider the Fröhlich Hamiltonian in a mean-field limit where many bosonic particles weakly couple to the quantized phonon field. For large particle numbers and a suitably small coupling, we show that the dynamics of the system is approximately described by the Landau–Pekar equations. These describe a Bose–Einstein condensate interacting with a classical polarization field, whose dynamics is effected by the condensate, i.e., the back-reaction of the phonons that are created by the particles during the time evolution is of leading order.","lang":"eng"}],"publication_status":"published","article_processing_charge":"No","language":[{"iso":"eng"}],"citation":{"ama":"Leopold NK, Mitrouskas DJ, Seiringer R. Derivation of the Landau–Pekar equations in a many-body mean-field limit. <i>Archive for Rational Mechanics and Analysis</i>. 2021;240:383-417. doi:<a href=\"https://doi.org/10.1007/s00205-021-01616-9\">10.1007/s00205-021-01616-9</a>","mla":"Leopold, Nikolai K., et al. “Derivation of the Landau–Pekar Equations in a Many-Body Mean-Field Limit.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 240, Springer Nature, 2021, pp. 383–417, doi:<a href=\"https://doi.org/10.1007/s00205-021-01616-9\">10.1007/s00205-021-01616-9</a>.","ista":"Leopold NK, Mitrouskas DJ, Seiringer R. 2021. Derivation of the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational Mechanics and Analysis. 240, 383–417.","chicago":"Leopold, Nikolai K, David Johannes Mitrouskas, and Robert Seiringer. “Derivation of the Landau–Pekar Equations in a Many-Body Mean-Field Limit.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00205-021-01616-9\">https://doi.org/10.1007/s00205-021-01616-9</a>.","ieee":"N. K. Leopold, D. J. Mitrouskas, and R. Seiringer, “Derivation of the Landau–Pekar equations in a many-body mean-field limit,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 240. Springer Nature, pp. 383–417, 2021.","short":"N.K. Leopold, D.J. Mitrouskas, R. Seiringer, Archive for Rational Mechanics and Analysis 240 (2021) 383–417.","apa":"Leopold, N. K., Mitrouskas, D. J., &#38; Seiringer, R. (2021). Derivation of the Landau–Pekar equations in a many-body mean-field limit. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-021-01616-9\">https://doi.org/10.1007/s00205-021-01616-9</a>"},"day":"26","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-06-12T06:35:22Z","date_published":"2021-02-26T00:00:00Z","month":"02","file":[{"file_name":"2021_ArchRationalMechAnal_Leopold.pdf","access_level":"open_access","success":1,"content_type":"application/pdf","file_id":"9270","relation":"main_file","file_size":558006,"creator":"dernst","date_updated":"2021-03-22T08:31:29Z","checksum":"23449e44dc5132501a5c86e70638800f","date_created":"2021-03-22T08:31:29Z"}],"ec_funded":1,"ddc":["510"],"status":"public","oa_version":"Published Version","scopus_import":"1","file_date_updated":"2021-03-22T08:31:29Z","isi":1,"department":[{"_id":"RoSe"}],"intvolume":"       240","has_accepted_license":"1","type":"journal_article","page":"383-417","volume":240,"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"publication":"Archive for Rational Mechanics and Analysis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9246","publisher":"Springer Nature","title":"Derivation of the Landau–Pekar equations in a many-body mean-field limit","external_id":{"isi":["000622226200001"],"pmid":["33785964"],"arxiv":["2001.03993"]},"arxiv":1,"date_created":"2021-03-14T23:01:34Z","project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"pmid":1,"oa":1,"author":[{"first_name":"Nikolai K","last_name":"Leopold","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"acknowledgement":"Financial support by the European Research Council (ERC) under the\r\nEuropean Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo 694227; N.L and R.S.), the SNSF Eccellenza Project PCEFP2 181153 (N.L) and the\r\nDeutsche Forschungsgemeinschaft (DFG) through the Research TrainingGroup 1838: Spectral\r\nTheory and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. N.L.\r\ngratefully acknowledges support from the NCCRSwissMAP and would like to thank Simone\r\nRademacher and Benjamin Schlein for interesting discussions about the time-evolution of\r\nthe polaron at strong coupling. D.M. thanks Marcel Griesemer and Andreas Wünsch for\r\nextensive discussions about the Fröhlich polaron.","quality_controlled":"1"},{"publication_status":"published","year":"2021","abstract":[{"lang":"eng","text":"This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments."}],"article_processing_charge":"Yes (via OA deal)","article_type":"original","doi":"10.1111/evo.14210","date_updated":"2025-06-12T06:35:39Z","file":[{"date_created":"2021-08-11T13:39:19Z","checksum":"b90fb5767d623602046fed03725e16ca","file_size":734102,"creator":"kschuh","date_updated":"2021-08-11T13:39:19Z","relation":"main_file","file_id":"9886","success":1,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_Evolution_Szep.pdf"}],"date_published":"2021-05-01T00:00:00Z","month":"05","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"ama":"Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. <i>Evolution</i>. 2021;75(5):1030-1045. doi:<a href=\"https://doi.org/10.1111/evo.14210\">10.1111/evo.14210</a>","mla":"Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” <i>Evolution</i>, vol. 75, no. 5, Wiley, 2021, pp. 1030–45, doi:<a href=\"https://doi.org/10.1111/evo.14210\">10.1111/evo.14210</a>.","ista":"Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.","chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” <i>Evolution</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/evo.14210\">https://doi.org/10.1111/evo.14210</a>.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” <i>Evolution</i>, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.","short":"E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045.","apa":"Szep, E., Sachdeva, H., &#38; Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14210\">https://doi.org/10.1111/evo.14210</a>"},"day":"01","volume":75,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"page":"1030-1045","has_accepted_license":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9252","publication":"Evolution","scopus_import":"1","ddc":["570"],"corr_author":"1","status":"public","related_material":{"record":[{"id":"13062","status":"public","relation":"research_data"}]},"oa_version":"Published Version","department":[{"_id":"NiBa"}],"intvolume":"        75","isi":1,"file_date_updated":"2021-08-11T13:39:19Z","date_created":"2021-03-20T08:22:10Z","author":[{"first_name":"Eniko","full_name":"Szep, Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"acknowledgement":"We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper.","quality_controlled":"1","pmid":1,"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"oa":1,"publisher":"Wiley","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"isi":["000636966300001"],"pmid":["33742441"]},"issue":"5","title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model"},{"doi":"10.1109/bigdata50022.2020.9378374","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.10064"}],"publication_status":"published","year":"2021","abstract":[{"text":"In March 2020, the Austrian government introduced a widespread lock-down in response to the COVID-19 pandemic. Based on subjective impressions and anecdotal evidence, Austrian public and private life came to a sudden halt. Here we assess the effect of the lock-down quantitatively for all regions in Austria and present an analysis of daily changes of human mobility throughout Austria using near-real-time anonymized mobile phone data. We describe an efficient data aggregation pipeline and analyze the mobility by quantifying mobile-phone traffic at specific point of interests (POIs), analyzing individual trajectories and investigating the cluster structure of the origin-destination graph. We found a reduction of commuters at Viennese metro stations of over 80% and the number of devices with a radius of gyration of less than 500 m almost doubled. The results of studying crowd-movement behavior highlight considerable changes in the structure of mobility networks, revealed by a higher modularity and an increase from 12 to 20 detected communities. We demonstrate the relevance of mobility data for epidemiological studies by showing a significant correlation of the outflow from the town of Ischgl (an early COVID-19 hotspot) and the reported COVID-19 cases with an 8-day time lag. This research indicates that mobile phone usage data permits the moment-by-moment quantification of mobility behavior for a whole country. We emphasize the need to improve the availability of such data in anonymized form to empower rapid response to combat COVID-19 and future pandemics.","lang":"eng"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"citation":{"apa":"Heiler, G., Reisch, T., Hurt, J., Forghani, M., Omani, A., Hanbury, A., &#38; Karimipour, F. (2021). Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. In <i>2020 IEEE International Conference on Big Data</i> (pp. 3123–3132). Atlanta, GA, United States: IEEE. <a href=\"https://doi.org/10.1109/bigdata50022.2020.9378374\">https://doi.org/10.1109/bigdata50022.2020.9378374</a>","short":"G. Heiler, T. Reisch, J. Hurt, M. Forghani, A. Omani, A. Hanbury, F. Karimipour, in:, 2020 IEEE International Conference on Big Data, IEEE, 2021, pp. 3123–3132.","ista":"Heiler G, Reisch T, Hurt J, Forghani M, Omani A, Hanbury A, Karimipour F. 2021. Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. 2020 IEEE International Conference on Big Data. Big Data: International Conference on Big Data, 3123–3132.","ieee":"G. Heiler <i>et al.</i>, “Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic,” in <i>2020 IEEE International Conference on Big Data</i>, Atlanta, GA, United States, 2021, pp. 3123–3132.","chicago":"Heiler, Georg, Tobias Reisch, Jan Hurt, Mohammad Forghani, Aida Omani, Allan Hanbury, and Farid Karimipour. “Country-Wide Mobility Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In <i>2020 IEEE International Conference on Big Data</i>, 3123–32. IEEE, 2021. <a href=\"https://doi.org/10.1109/bigdata50022.2020.9378374\">https://doi.org/10.1109/bigdata50022.2020.9378374</a>.","ama":"Heiler G, Reisch T, Hurt J, et al. Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. In: <i>2020 IEEE International Conference on Big Data</i>. IEEE; 2021:3123-3132. doi:<a href=\"https://doi.org/10.1109/bigdata50022.2020.9378374\">10.1109/bigdata50022.2020.9378374</a>","mla":"Heiler, Georg, et al. “Country-Wide Mobility Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” <i>2020 IEEE International Conference on Big Data</i>, IEEE, 2021, pp. 3123–32, doi:<a href=\"https://doi.org/10.1109/bigdata50022.2020.9378374\">10.1109/bigdata50022.2020.9378374</a>."},"day":"19","date_updated":"2023-08-07T14:00:13Z","date_published":"2021-03-19T00:00:00Z","month":"03","scopus_import":"1","status":"public","oa_version":"Preprint","department":[{"_id":"HeEd"}],"isi":1,"publication_identifier":{"isbn":["9781728162515"]},"page":"3123-3132","type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9253","publication":"2020 IEEE International Conference on Big Data","publisher":"IEEE","conference":{"location":"Atlanta, GA, United States","start_date":"2020-12-10","end_date":"2020-12-13","name":"Big Data: International Conference on Big Data"},"external_id":{"arxiv":["2008.10064"],"isi":["000662554703032"]},"arxiv":1,"title":"Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic","date_created":"2021-03-21T11:34:07Z","author":[{"last_name":"Heiler","full_name":"Heiler, Georg","first_name":"Georg"},{"last_name":"Reisch","full_name":"Reisch, Tobias","first_name":"Tobias"},{"first_name":"Jan","last_name":"Hurt","full_name":"Hurt, Jan"},{"full_name":"Forghani, Mohammad","last_name":"Forghani","first_name":"Mohammad"},{"last_name":"Omani","full_name":"Omani, Aida","first_name":"Aida"},{"full_name":"Hanbury, Allan","last_name":"Hanbury","first_name":"Allan"},{"full_name":"Karimipour, Farid","last_name":"Karimipour","first_name":"Farid","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","orcid":"0000-0001-6746-4174"}],"quality_controlled":"1","oa":1},{"date_created":"2021-03-21T23:01:19Z","author":[{"last_name":"Hu","full_name":"Hu, Yangjie","first_name":"Yangjie"},{"first_name":"Moutasem","last_name":"Omary","full_name":"Omary, Moutasem"},{"first_name":"Yun","full_name":"Hu, Yun","last_name":"Hu"},{"first_name":"Ohad","last_name":"Doron","full_name":"Doron, Ohad"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","first_name":"Lukas","full_name":"Hörmayer, Lukas","last_name":"Hörmayer"},{"full_name":"Chen, Qingguo","last_name":"Chen","first_name":"Qingguo"},{"full_name":"Megides, Or","last_name":"Megides","first_name":"Or"},{"full_name":"Chekli, Ori","last_name":"Chekli","first_name":"Ori"},{"first_name":"Zhaojun","last_name":"Ding","full_name":"Ding, Zhaojun"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"first_name":"Yunde","full_name":"Zhao, Yunde","last_name":"Zhao"},{"first_name":"Ilan","full_name":"Tsarfaty, Ilan","last_name":"Tsarfaty"},{"full_name":"Shani, Eilon","last_name":"Shani","first_name":"Eilon"}],"acknowledgement":"This work was supported by grants from the Israel Science Foundation (2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.), the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships (to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF to I.T.).","quality_controlled":"1","pmid":1,"oa":1,"publisher":"Springer Nature","external_id":{"pmid":["33712581"],"isi":["000630419400048"]},"title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","volume":12,"publication_identifier":{"eissn":["2041-1723"]},"has_accepted_license":"1","type":"journal_article","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"9254","publication":"Nature Communications","scopus_import":"1","ddc":["580"],"status":"public","oa_version":"Published Version","department":[{"_id":"JiFr"}],"intvolume":"        12","isi":1,"file_date_updated":"2021-03-22T11:18:58Z","date_updated":"2026-04-02T13:57:40Z","file":[{"relation":"main_file","file_id":"9275","content_type":"application/pdf","success":1,"checksum":"e1022f3aee349853ded2b2b3e092362d","date_created":"2021-03-22T11:18:58Z","file_size":8602096,"date_updated":"2021-03-22T11:18:58Z","creator":"dernst","access_level":"open_access","file_name":"2021_NatureComm_Hu.pdf"}],"date_published":"2021-03-12T00:00:00Z","month":"03","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"1657","citation":{"short":"Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli, Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021).","apa":"Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021). Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-21802-3\">https://doi.org/10.1038/s41467-021-21802-3</a>","ama":"Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-21802-3\">10.1038/s41467-021-21802-3</a>","mla":"Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” <i>Nature Communications</i>, vol. 12, 1657, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-21802-3\">10.1038/s41467-021-21802-3</a>.","ista":"Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 12, 1657.","chicago":"Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-21802-3\">https://doi.org/10.1038/s41467-021-21802-3</a>.","ieee":"Y. Hu <i>et al.</i>, “Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021."},"day":"12","publication_status":"published","year":"2021","abstract":[{"lang":"eng","text":"Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms."}],"article_processing_charge":"No","article_type":"original","doi":"10.1038/s41467-021-21802-3"},{"author":[{"full_name":"Pivoluska, Matej","last_name":"Pivoluska","first_name":"Matej"},{"full_name":"Plesch, Martin","last_name":"Plesch","first_name":"Martin"},{"first_name":"Máté","last_name":"Farkas","full_name":"Farkas, Máté"},{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","first_name":"Natalia","full_name":"Ruzickova, Natalia","last_name":"Ruzickova"},{"first_name":"Clara","full_name":"Flegel, Clara","last_name":"Flegel"},{"full_name":"Valencia, Natalia Herrera","last_name":"Valencia","first_name":"Natalia Herrera"},{"full_name":"Mccutcheon, Will","last_name":"Mccutcheon","first_name":"Will"},{"full_name":"Malik, Mehul","last_name":"Malik","first_name":"Mehul"},{"full_name":"Aguilar, Edgar A.","last_name":"Aguilar","first_name":"Edgar A."}],"acknowledgement":"We would like to thank Robert Fickler for discussions about the experimental realization and Marek Sýs for running the NIST randomness test on the data we acquired in the experiment. We would like to thank Ugo Zanforlin, Gerald Buller, Daniel White, and Cristian Bonato for their help with the experiment. M. Pivoluska, M. Plesch, and M.M. acknowledge Czech-Austrian project MultiQUEST (I3053-N27 and GF17-33780L). M. Pivoluska and M. Plesch additionally acknowledge the support of VEGA project 2/0136/19. M.F. acknowledges support from the Polish NCN grant Sonata UMO-2014/14/E/ST2/00020, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program ERC AdG CERQUTE (grant agreement No 834266), the State Research Agency (AEI) TRANQI (PID2019-106888GB-I00/10.13039/501100011033), the Government of Spain (FIS2020-TRANQI; Severo Ochoa CEX2019-000910-S), Fundació Cellex, Fundació Mir-Puig, and Generalitat de Catalunya (CERCA, AGAUR). M.M., W.M., N.H.V., and C.F. acknowledge support from the QuantERA ERA-NET Co-fund (FWF Project I3773-N36) and the UK Engineering and Physical Sciences Research Council (EPSRC) (EP/P024114/1).","quality_controlled":"1","oa":1,"date_created":"2021-03-21T23:01:19Z","external_id":{"isi":["000629173100001"]},"title":"Semi-device-independent random number generation with flexible assumptions","publisher":"Springer Nature","_id":"9255","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"npj Quantum Information","publication_identifier":{"eissn":["2056-6387"]},"volume":7,"type":"journal_article","has_accepted_license":"1","intvolume":"         7","department":[{"_id":"FyKo"}],"isi":1,"file_date_updated":"2021-03-22T11:09:34Z","scopus_import":"1","oa_version":"Published Version","ddc":["530"],"status":"public","file":[{"file_name":"2021_NPJQuantumInformation_Pivoluska.pdf","content_type":"application/pdf","success":1,"relation":"main_file","file_id":"9274","creator":"dernst","date_updated":"2021-03-22T11:09:34Z","file_size":1360271,"checksum":"26d3f2a2c8c8fa8c1002028326b45f64","date_created":"2021-03-22T11:09:34Z","access_level":"open_access"}],"month":"03","date_published":"2021-03-15T00:00:00Z","date_updated":"2023-08-07T14:17:26Z","article_number":"50","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"15","citation":{"short":"M. Pivoluska, M. Plesch, M. Farkas, N. Ruzickova, C. Flegel, N.H. Valencia, W. Mccutcheon, M. Malik, E.A. Aguilar, Npj Quantum Information 7 (2021).","apa":"Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia, N. H., … Aguilar, E. A. (2021). Semi-device-independent random number generation with flexible assumptions. <i>Npj Quantum Information</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41534-021-00387-1\">https://doi.org/10.1038/s41534-021-00387-1</a>","ama":"Pivoluska M, Plesch M, Farkas M, et al. Semi-device-independent random number generation with flexible assumptions. <i>npj Quantum Information</i>. 2021;7. doi:<a href=\"https://doi.org/10.1038/s41534-021-00387-1\">10.1038/s41534-021-00387-1</a>","mla":"Pivoluska, Matej, et al. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” <i>Npj Quantum Information</i>, vol. 7, 50, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41534-021-00387-1\">10.1038/s41534-021-00387-1</a>.","ista":"Pivoluska M, Plesch M, Farkas M, Ruzickova N, Flegel C, Valencia NH, Mccutcheon W, Malik M, Aguilar EA. 2021. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 7, 50.","ieee":"M. Pivoluska <i>et al.</i>, “Semi-device-independent random number generation with flexible assumptions,” <i>npj Quantum Information</i>, vol. 7. Springer Nature, 2021.","chicago":"Pivoluska, Matej, Martin Plesch, Máté Farkas, Natalia Ruzickova, Clara Flegel, Natalia Herrera Valencia, Will Mccutcheon, Mehul Malik, and Edgar A. Aguilar. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” <i>Npj Quantum Information</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41534-021-00387-1\">https://doi.org/10.1038/s41534-021-00387-1</a>."},"language":[{"iso":"eng"}],"article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","text":"Our ability to trust that a random number is truly random is essential for fields as diverse as cryptography and fundamental tests of quantum mechanics. Existing solutions both come with drawbacks—device-independent quantum random number generators (QRNGs) are highly impractical and standard semi-device-independent QRNGs are limited to a specific physical implementation and level of trust. Here we propose a framework for semi-device-independent randomness certification, using a source of trusted vacuum in the form of a signal shutter. It employs a flexible set of assumptions and levels of trust, allowing it to be applied in a wide range of physical scenarios involving both quantum and classical entropy sources. We experimentally demonstrate our protocol with a photonic setup and generate secure random bits under three different assumptions with varying degrees of security and resulting data rates."}],"year":"2021","doi":"10.1038/s41534-021-00387-1","article_type":"original"},{"language":[{"iso":"eng"}],"citation":{"apa":"Napiórkowski, M. M., &#38; Seiringer, R. (2021). Free energy asymptotics of the quantum Heisenberg spin chain. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-021-01375-4\">https://doi.org/10.1007/s11005-021-01375-4</a>","short":"M.M. Napiórkowski, R. Seiringer, Letters in Mathematical Physics 111 (2021).","ieee":"M. M. Napiórkowski and R. Seiringer, “Free energy asymptotics of the quantum Heisenberg spin chain,” <i>Letters in Mathematical Physics</i>, vol. 111, no. 2. Springer Nature, 2021.","chicago":"Napiórkowski, Marcin M, and Robert Seiringer. “Free Energy Asymptotics of the Quantum Heisenberg Spin Chain.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11005-021-01375-4\">https://doi.org/10.1007/s11005-021-01375-4</a>.","ista":"Napiórkowski MM, Seiringer R. 2021. Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. 111(2), 31.","mla":"Napiórkowski, Marcin M., and Robert Seiringer. “Free Energy Asymptotics of the Quantum Heisenberg Spin Chain.” <i>Letters in Mathematical Physics</i>, vol. 111, no. 2, 31, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11005-021-01375-4\">10.1007/s11005-021-01375-4</a>.","ama":"Napiórkowski MM, Seiringer R. Free energy asymptotics of the quantum Heisenberg spin chain. <i>Letters in Mathematical Physics</i>. 2021;111(2). doi:<a href=\"https://doi.org/10.1007/s11005-021-01375-4\">10.1007/s11005-021-01375-4</a>"},"day":"09","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"31","date_updated":"2026-04-02T14:06:48Z","date_published":"2021-03-09T00:00:00Z","month":"03","file":[{"access_level":"open_access","creator":"dernst","date_updated":"2021-03-22T11:01:09Z","file_size":397962,"checksum":"687fef1525789c0950de90468dd81604","date_created":"2021-03-22T11:01:09Z","content_type":"application/pdf","success":1,"relation":"main_file","file_id":"9273","file_name":"2021_LettersMathPhysics_Napiorkowski.pdf"}],"article_type":"original","doi":"10.1007/s11005-021-01375-4","year":"2021","abstract":[{"lang":"eng","text":"We consider the ferromagnetic quantum Heisenberg model in one dimension, for any spin S≥1/2. We give upper and lower bounds on the free energy, proving that at low temperature it is asymptotically equal to the one of an ideal Bose gas of magnons, as predicted by the spin-wave approximation. The trial state used in the upper bound yields an analogous estimate also in the case of two spatial dimensions, which is believed to be sharp at low temperature."}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","issue":"2","title":"Free energy asymptotics of the quantum Heisenberg spin chain","external_id":{"pmid":["33785980"],"isi":["000626837400001"]},"date_created":"2021-03-21T23:01:19Z","pmid":1,"oa":1,"quality_controlled":"1","author":[{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski","first_name":"Marcin M"},{"first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"The work of MN was supported by the National Science Centre (NCN) Project Nr. 2016/21/D/ST1/02430. The work of RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227).\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","status":"public","ddc":["510"],"oa_version":"Published Version","scopus_import":"1","isi":1,"file_date_updated":"2021-03-22T11:01:09Z","department":[{"_id":"RoSe"}],"intvolume":"       111","has_accepted_license":"1","type":"journal_article","publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"volume":111,"publication":"Letters in Mathematical Physics","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"9256"},{"doi":"10.1073/pnas.2024083118","article_type":"original","abstract":[{"text":"The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems.","lang":"eng"}],"year":"2021","publication_status":"published","article_processing_charge":"No","language":[{"iso":"eng"}],"day":"09","citation":{"ama":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(10). doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>","mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>.","ista":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences of the United States of America. 118(10), e2024083118.","chicago":"Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>.","ieee":"C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 10. National Academy of Sciences, 2021.","short":"C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","apa":"Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., &#38; Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>"},"article_number":"e2024083118","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"date_updated":"2025-05-14T10:58:42Z","month":"03","date_published":"2021-03-09T00:00:00Z","file":[{"access_level":"open_access","date_created":"2021-03-22T12:23:54Z","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","file_size":1047954,"creator":"dernst","date_updated":"2021-03-22T12:23:54Z","relation":"main_file","file_id":"9278","success":1,"content_type":"application/pdf","file_name":"2021_PNAS_Goodrich.pdf"}],"oa_version":"Published Version","status":"public","ddc":["530"],"scopus_import":"1","file_date_updated":"2021-03-22T12:23:54Z","isi":1,"intvolume":"       118","department":[{"_id":"CaGo"}],"type":"journal_article","has_accepted_license":"1","volume":118,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","_id":"9257","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","title":"Designing self-assembling kinetics with differentiable statistical physics models","issue":"10","external_id":{"isi":["000627429100097"],"pmid":["33653960"]},"date_created":"2021-03-21T23:01:20Z","oa":1,"pmid":1,"author":[{"first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"first_name":"Ella M.","full_name":"King, Ella M.","last_name":"King"},{"first_name":"Samuel S.","last_name":"Schoenholz","full_name":"Schoenholz, Samuel S."},{"first_name":"Ekin D.","last_name":"Cubuk","full_name":"Cubuk, Ekin D."},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."}],"acknowledgement":"We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng, and Roy Frostig for helpful discussions. This material is based on work supported by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator of the Simons Foundation.","quality_controlled":"1"},{"_id":"9258","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Nature Methods","page":"226-228","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"volume":18,"type":"journal_article","intvolume":"        18","department":[{"_id":"JoDa"}],"isi":1,"scopus_import":"1","oa_version":"Published Version","status":"public","ddc":["570"],"author":[{"first_name":"Henry","full_name":"Pinkard, Henry","last_name":"Pinkard"},{"last_name":"Stuurman","full_name":"Stuurman, Nico","first_name":"Nico"},{"full_name":"Ivanov, Ivan E.","last_name":"Ivanov","first_name":"Ivan E."},{"first_name":"Nicholas M.","full_name":"Anthony, Nicholas M.","last_name":"Anthony"},{"first_name":"Wei","last_name":"Ouyang","full_name":"Ouyang, Wei"},{"full_name":"Li, Bin","last_name":"Li","first_name":"Bin"},{"first_name":"Bin","full_name":"Yang, Bin","last_name":"Yang"},{"first_name":"Mark A.","last_name":"Tsuchida","full_name":"Tsuchida, Mark A."},{"first_name":"Bryant","full_name":"Chhun, Bryant","last_name":"Chhun"},{"full_name":"Zhang, Grace","last_name":"Zhang","first_name":"Grace"},{"first_name":"Ryan","full_name":"Mei, Ryan","last_name":"Mei"},{"full_name":"Anderson, Michael","last_name":"Anderson","first_name":"Michael"},{"first_name":"Douglas P.","full_name":"Shepherd, Douglas P.","last_name":"Shepherd"},{"first_name":"Ian","last_name":"Hunt-Isaak","full_name":"Hunt-Isaak, Ian"},{"full_name":"Dunn, Raymond L.","last_name":"Dunn","first_name":"Raymond L."},{"orcid":"0000-0003-0201-2315","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","full_name":"Jahr, Wiebke","last_name":"Jahr"},{"full_name":"Kato, Saul","last_name":"Kato","first_name":"Saul"},{"last_name":"Royer","full_name":"Royer, Loïc A.","first_name":"Loïc A."},{"full_name":"Thiagarajah, Jay R.","last_name":"Thiagarajah","first_name":"Jay R."},{"last_name":"Eliceiri","full_name":"Eliceiri, Kevin W.","first_name":"Kevin W."},{"first_name":"Emma","last_name":"Lundberg","full_name":"Lundberg, Emma"},{"full_name":"Mehta, Shalin B.","last_name":"Mehta","first_name":"Shalin B."},{"first_name":"Laura","last_name":"Waller","full_name":"Waller, Laura"}],"quality_controlled":"1","acknowledgement":"We thank S. van der Walt and K. Marchuk for discussion during development. This project was funded by Packard Fellowship and Chan Zuckerberg Biohub Investigator Awards to L.W.; STROBE: A NSF Science and Technology Center; an NSF Graduate Research Fellowship awarded to H.P.; a Berkeley Institute for Data Science/UCSF Bakar Computational Health Sciences Institute Fellowship awarded to H.P. with support from the Koret Foundation, the Gordon and Betty Moore Foundation, and the Alfred P. Sloan Foundation to the University of California, Berkeley. K.W.E., B.L. and M.T. were funded by the Chan Zuckerberg Initiative and NIH grant P41GM135019.","oa":1,"pmid":1,"date_created":"2021-03-21T23:01:20Z","external_id":{"pmid":["33674797"],"isi":["000625600600007"]},"title":"Pycro-Manager: Open-source software for customized and reproducible microscope control","issue":"3","publisher":"Springer Nature","article_processing_charge":"No","publication_status":"published","year":"2021","doi":"10.1038/s41592-021-01087-6","article_type":"letter_note","main_file_link":[{"url":"https://doi.org/10.1038/s41592-021-01087-6","open_access":"1"}],"month":"03","date_published":"2021-03-01T00:00:00Z","date_updated":"2026-06-18T19:43:50Z","day":"01","citation":{"mla":"Pinkard, Henry, et al. “Pycro-Manager: Open-Source Software for Customized and Reproducible Microscope Control.” <i>Nature Methods</i>, vol. 18, no. 3, Springer Nature, 2021, pp. 226–28, doi:<a href=\"https://doi.org/10.1038/s41592-021-01087-6\">10.1038/s41592-021-01087-6</a>.","ama":"Pinkard H, Stuurman N, Ivanov IE, et al. Pycro-Manager: Open-source software for customized and reproducible microscope control. <i>Nature Methods</i>. 2021;18(3):226-228. doi:<a href=\"https://doi.org/10.1038/s41592-021-01087-6\">10.1038/s41592-021-01087-6</a>","chicago":"Pinkard, Henry, Nico Stuurman, Ivan E. Ivanov, Nicholas M. Anthony, Wei Ouyang, Bin Li, Bin Yang, et al. “Pycro-Manager: Open-Source Software for Customized and Reproducible Microscope Control.” <i>Nature Methods</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41592-021-01087-6\">https://doi.org/10.1038/s41592-021-01087-6</a>.","ieee":"H. Pinkard <i>et al.</i>, “Pycro-Manager: Open-source software for customized and reproducible microscope control,” <i>Nature Methods</i>, vol. 18, no. 3. Springer Nature, pp. 226–228, 2021.","ista":"Pinkard H, Stuurman N, Ivanov IE, Anthony NM, Ouyang W, Li B, Yang B, Tsuchida MA, Chhun B, Zhang G, Mei R, Anderson M, Shepherd DP, Hunt-Isaak I, Dunn RL, Jahr W, Kato S, Royer LA, Thiagarajah JR, Eliceiri KW, Lundberg E, Mehta SB, Waller L. 2021. Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. 18(3), 226–228.","short":"H. Pinkard, N. Stuurman, I.E. Ivanov, N.M. Anthony, W. Ouyang, B. Li, B. Yang, M.A. Tsuchida, B. Chhun, G. Zhang, R. Mei, M. Anderson, D.P. Shepherd, I. Hunt-Isaak, R.L. Dunn, W. Jahr, S. Kato, L.A. Royer, J.R. Thiagarajah, K.W. Eliceiri, E. Lundberg, S.B. Mehta, L. Waller, Nature Methods 18 (2021) 226–228.","apa":"Pinkard, H., Stuurman, N., Ivanov, I. E., Anthony, N. M., Ouyang, W., Li, B., … Waller, L. (2021). Pycro-Manager: Open-source software for customized and reproducible microscope control. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-021-01087-6\">https://doi.org/10.1038/s41592-021-01087-6</a>"},"language":[{"iso":"eng"}]},{"article_type":"original","doi":"10.3389/fimmu.2021.630002","year":"2021","abstract":[{"text":"Gradients of chemokines and growth factors guide migrating cells and morphogenetic processes. Migration of antigen-presenting dendritic cells from the interstitium into the lymphatic system is dependent on chemokine CCL21, which is secreted by endothelial cells of the lymphatic capillary, binds heparan sulfates and forms gradients decaying into the interstitium. Despite the importance of CCL21 gradients, and chemokine gradients in general, the mechanisms of gradient formation are unclear. Studies on fibroblast growth factors have shown that limited diffusion is crucial for gradient formation. Here, we used the mouse dermis as a model tissue to address the necessity of CCL21 anchoring to lymphatic capillary heparan sulfates in the formation of interstitial CCL21 gradients. Surprisingly, the absence of lymphatic endothelial heparan sulfates resulted only in a modest decrease of CCL21 levels at the lymphatic capillaries and did neither affect interstitial CCL21 gradient shape nor dendritic cell migration toward lymphatic capillaries. Thus, heparan sulfates at the level of the lymphatic endothelium are dispensable for the formation of a functional CCL21 gradient.","lang":"eng"}],"publication_status":"published","article_processing_charge":"No","language":[{"iso":"eng"}],"citation":{"ama":"Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. <i>Frontiers in Immunology</i>. 2021;12. doi:<a href=\"https://doi.org/10.3389/fimmu.2021.630002\">10.3389/fimmu.2021.630002</a>","mla":"Vaahtomeri, Kari, et al. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” <i>Frontiers in Immunology</i>, vol. 12, 630002, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fimmu.2021.630002\">10.3389/fimmu.2021.630002</a>.","ista":"Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. 2021. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. 12, 630002.","ieee":"K. Vaahtomeri, C. Moussion, R. Hauschild, and M. K. Sixt, “Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium,” <i>Frontiers in Immunology</i>, vol. 12. Frontiers, 2021.","chicago":"Vaahtomeri, Kari, Christine Moussion, Robert Hauschild, and Michael K Sixt. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” <i>Frontiers in Immunology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fimmu.2021.630002\">https://doi.org/10.3389/fimmu.2021.630002</a>.","short":"K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology 12 (2021).","apa":"Vaahtomeri, K., Moussion, C., Hauschild, R., &#38; Sixt, M. K. (2021). Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. <i>Frontiers in Immunology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fimmu.2021.630002\">https://doi.org/10.3389/fimmu.2021.630002</a>"},"day":"25","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"630002","date_updated":"2025-04-14T07:42:07Z","date_published":"2021-02-25T00:00:00Z","month":"02","ec_funded":1,"file":[{"file_name":"2021_FrontiersImmumo_Vaahtomeri.pdf","access_level":"open_access","relation":"main_file","file_id":"9277","content_type":"application/pdf","success":1,"date_created":"2021-03-22T12:08:26Z","checksum":"663f5a48375e42afa4bfef58d42ec186","file_size":3740146,"date_updated":"2021-03-22T12:08:26Z","creator":"dernst"}],"status":"public","corr_author":"1","ddc":["570"],"oa_version":"Published Version","scopus_import":"1","isi":1,"file_date_updated":"2021-03-22T12:08:26Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"intvolume":"        12","has_accepted_license":"1","type":"journal_article","volume":12,"publication_identifier":{"eissn":["1664-3224"]},"publication":"Frontiers in Immunology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9259","publisher":"Frontiers","title":"Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium","external_id":{"pmid":["33717158"],"isi":["000627134400001"]},"date_created":"2021-03-21T23:01:20Z","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"Y 564-B12","call_identifier":"FWF"}],"pmid":1,"oa":1,"quality_controlled":"1","acknowledgement":"This work was supported by Sigrid Juselius fellowship (KV), University of Helsinki 3-year research grant (KV), Academy of Finland Research fellow funding (315710, to KV), the European Research Council (ERC CoG 724373 to MS), and by the Austrian Science foundation (FWF) (Y564-B12 START award to MS).\r\nTaija Mäkinen is acknowledged for providing Prox1CreERT2 transgenic mice and Yu Yamaguchi for providing the conditional Ext1 mouse strain.","author":[{"orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri"},{"first_name":"Christine","last_name":"Moussion","full_name":"Moussion, Christine","id":"3356F664-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"}]},{"date_created":"2021-03-22T07:14:03Z","quality_controlled":"1","acknowledgement":"We thank the Synchrotron SOLEIL, the European Synchrotron Radiation Facility (ESRF), and the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INBS-05. We are particularly grateful to A. Clavier and A. Campalans for help in setting up and performing the cell penetration assays. Funding: Research was funded by the French Centre National de Recherche Scientifique (CNRS), the Commissariat à l’Energie Atomique (CEA), University of Bordeaux, University Paris-Saclay, and the Synchrotron Soleil. The project was supported by the ANR 2007 BREAKABOUND (JC-07-216078), 2011 BIPBIP (ANR-10-BINF-0003), 2012 CHAPINHIB (ANR-12-BSV5-0022-01), 2015 CHIPSET (ANR-15-CE11-008-01), 2015 HIMPP2I (ANR-15-CE07-0010), and the program labeled by the ARC foundation 2016 PGA1*20160203953). M.B. was supported by Canceropole (Paris, France) and a grant for young researchers from La Ligue contre le Cancer. J.M. was supported by La Ligue contre le Cancer.","author":[{"first_name":"Johanne","full_name":"Mbianda, Johanne","last_name":"Mbianda"},{"first_name":"May M","last_name":"Bakail","full_name":"Bakail, May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","orcid":"0000-0002-9592-1587"},{"full_name":"André, Christophe","last_name":"André","first_name":"Christophe"},{"first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle","last_name":"Moal"},{"first_name":"Marie E.","full_name":"Perrin, Marie E.","last_name":"Perrin"},{"first_name":"Guillaume","full_name":"Pinna, Guillaume","last_name":"Pinna"},{"last_name":"Guerois","full_name":"Guerois, Raphaël","first_name":"Raphaël"},{"first_name":"Francois","full_name":"Becher, Francois","last_name":"Becher"},{"last_name":"Legrand","full_name":"Legrand, Pierre","first_name":"Pierre"},{"first_name":"Seydou","last_name":"Traoré","full_name":"Traoré, Seydou"},{"full_name":"Douat, Céline","last_name":"Douat","first_name":"Céline"},{"last_name":"Guichard","full_name":"Guichard, Gilles","first_name":"Gilles"},{"first_name":"Françoise","last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise"}],"pmid":1,"oa":1,"publisher":"American Association for the Advancement of Science","license":"https://creativecommons.org/licenses/by-nc/4.0/","external_id":{"isi":["000633443000011"],"pmid":["33741589"]},"issue":"12","title":"Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity","publication_identifier":{"issn":["2375-2548"]},"volume":7,"has_accepted_license":"1","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9262","publication":"Science Advances","ddc":["570"],"status":"public","oa_version":"Published Version","department":[{"_id":"CampIT"}],"intvolume":"         7","isi":1,"file_date_updated":"2021-03-22T12:49:00Z","date_updated":"2023-08-07T14:20:26Z","file":[{"file_name":"2021_ScienceAdv_Mbianda.pdf","access_level":"open_access","checksum":"737624cd0e630ffa7c52797a690500e3","date_created":"2021-03-22T12:49:00Z","creator":"dernst","date_updated":"2021-03-22T12:49:00Z","file_size":837156,"relation":"main_file","file_id":"9280","content_type":"application/pdf","success":1}],"date_published":"2021-03-19T00:00:00Z","month":"03","language":[{"iso":"eng"}],"article_number":"eabd9153","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"citation":{"ama":"Mbianda J, Bakail MM, André C, et al. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. <i>Science Advances</i>. 2021;7(12). doi:<a href=\"https://doi.org/10.1126/sciadv.abd9153\">10.1126/sciadv.abd9153</a>","mla":"Mbianda, Johanne, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” <i>Science Advances</i>, vol. 7, no. 12, eabd9153, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abd9153\">10.1126/sciadv.abd9153</a>.","ista":"Mbianda J, Bakail MM, André C, Moal G, Perrin ME, Pinna G, Guerois R, Becher F, Legrand P, Traoré S, Douat C, Guichard G, Ochsenbein F. 2021. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. 7(12), eabd9153.","ieee":"J. Mbianda <i>et al.</i>, “Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity,” <i>Science Advances</i>, vol. 7, no. 12. American Association for the Advancement of Science, 2021.","chicago":"Mbianda, Johanne, May M Bakail, Christophe André, Gwenaëlle Moal, Marie E. Perrin, Guillaume Pinna, Raphaël Guerois, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” <i>Science Advances</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/sciadv.abd9153\">https://doi.org/10.1126/sciadv.abd9153</a>.","short":"J. Mbianda, M.M. Bakail, C. André, G. Moal, M.E. Perrin, G. Pinna, R. Guerois, F. Becher, P. Legrand, S. Traoré, C. Douat, G. Guichard, F. Ochsenbein, Science Advances 7 (2021).","apa":"Mbianda, J., Bakail, M. M., André, C., Moal, G., Perrin, M. E., Pinna, G., … Ochsenbein, F. (2021). Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abd9153\">https://doi.org/10.1126/sciadv.abd9153</a>"},"day":"19","publication_status":"published","year":"2021","abstract":[{"text":"Sequence-specific oligomers with predictable folding patterns, i.e., foldamers, provide new opportunities to mimic α-helical peptides and design inhibitors of protein-protein interactions. One major hurdle of this strategy is to retain the correct orientation of key side chains involved in protein surface recognition. Here, we show that the structural plasticity of a foldamer backbone may notably contribute to the required spatial adjustment for optimal interaction with the protein surface. By using oligoureas as α helix mimics, we designed a foldamer/peptide hybrid inhibitor of histone chaperone ASF1, a key regulator of chromatin dynamics. The crystal structure of its complex with ASF1 reveals a notable plasticity of the urea backbone, which adapts to the ASF1 surface to maintain the same binding interface. One additional benefit of generating ASF1 ligands with nonpeptide oligourea segments is the resistance to proteolysis in human plasma, which was highly improved compared to the cognate α-helical peptide.","lang":"eng"}],"article_processing_charge":"No","article_type":"original","doi":"10.1126/sciadv.abd9153"},{"publication_status":"submitted","year":"2021","type":"preprint","abstract":[{"text":"We comment on two formal proofs of Fermat's sum of two squares theorem, written using the Mathematical Components libraries of the Coq proof assistant. The first one follows Zagier's celebrated one-sentence proof; the second follows David Christopher's recent new proof relying on partition-theoretic arguments. Both formal proofs rely on a general property of involutions of finite sets, of independent interest. The proof technique consists for the most part of automating recurrent tasks (such as case distinctions and computations on natural numbers) via ad hoc tactics.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","_id":"9281","publication":"arXiv","doi":"10.48550/arXiv.2103.11389","status":"public","related_material":{"record":[{"relation":"other","id":"9946","status":"public"}]},"corr_author":"1","main_file_link":[{"url":"https://arxiv.org/abs/2103.11389","open_access":"1"}],"oa_version":"Preprint","department":[{"_id":"LaEr"},{"_id":"ToHe"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-04-15T06:26:12Z","date_created":"2021-03-23T05:38:48Z","author":[{"orcid":"0000-0001-6892-8137","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Guillaume","full_name":"Dubach, Guillaume","last_name":"Dubach"},{"orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian","last_name":"Mühlböck","first_name":"Fabian"}],"ec_funded":1,"date_published":"2021-03-21T00:00:00Z","oa":1,"month":"03","language":[{"iso":"eng"}],"arxiv":1,"external_id":{"arxiv":["2103.11389"]},"article_number":"2103.11389","citation":{"chicago":"Dubach, Guillaume, and Fabian Mühlböck. “Formal Verification of Zagier’s One-Sentence Proof.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2103.11389\">https://doi.org/10.48550/arXiv.2103.11389</a>.","ieee":"G. Dubach and F. Mühlböck, “Formal verification of Zagier’s one-sentence proof,” <i>arXiv</i>. .","ista":"Dubach G, Mühlböck F. Formal verification of Zagier’s one-sentence proof. arXiv, 2103.11389.","mla":"Dubach, Guillaume, and Fabian Mühlböck. “Formal Verification of Zagier’s One-Sentence Proof.” <i>ArXiv</i>, 2103.11389, doi:<a href=\"https://doi.org/10.48550/arXiv.2103.11389\">10.48550/arXiv.2103.11389</a>.","ama":"Dubach G, Mühlböck F. Formal verification of Zagier’s one-sentence proof. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2103.11389\">10.48550/arXiv.2103.11389</a>","apa":"Dubach, G., &#38; Mühlböck, F. (n.d.). Formal verification of Zagier’s one-sentence proof. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2103.11389\">https://doi.org/10.48550/arXiv.2103.11389</a>","short":"G. Dubach, F. Mühlböck, ArXiv (n.d.)."},"day":"21","title":"Formal verification of Zagier's one-sentence proof"},{"day":"08","citation":{"chicago":"Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>.","ieee":"A. A. Nagy-Staron <i>et al.</i>, “Local genetic context shapes the function of a gene regulatory network,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory network. eLife. 10, e65993.","mla":"Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>, vol. 10, e65993, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>.","ama":"Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>","apa":"Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., &#38; Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>","short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021)."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e65993","language":[{"iso":"eng"}],"month":"03","date_published":"2021-03-08T00:00:00Z","ec_funded":1,"file":[{"file_name":"elife-65993-v2.pdf","relation":"main_file","file_id":"9284","content_type":"application/pdf","success":1,"checksum":"3c2f44058c2dd45a5a1027f09d263f8e","date_created":"2021-03-23T10:12:58Z","creator":"bkavcic","date_updated":"2021-03-23T10:12:58Z","file_size":1390469,"access_level":"open_access"}],"date_updated":"2025-06-12T06:36:17Z","doi":"10.7554/elife.65993","article_type":"original","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs."}],"year":"2021","publication_status":"published","title":"Local genetic context shapes the function of a gene regulatory network","external_id":{"pmid":["33683203"],"isi":["000631050900001"]},"publisher":"eLife Sciences Publications","oa":1,"keyword":["Genetics and Molecular Biology"],"pmid":1,"quality_controlled":"1","author":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1391-8377","first_name":"Anna A","last_name":"Nagy-Staron","full_name":"Nagy-Staron, Anna A"},{"first_name":"Kathrin","full_name":"Tomasek, Kathrin","last_name":"Tomasek","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Caroline","last_name":"Caruso Carter","full_name":"Caruso Carter, Caroline"},{"first_name":"Elisabeth","full_name":"Sonnleitner, Elisabeth","last_name":"Sonnleitner"},{"last_name":"Kavcic","full_name":"Kavcic, Bor","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixão","full_name":"Paixão, Tiago","first_name":"Tiago"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}],"acknowledgement":"We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau, G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and members of the Guet lab for comments. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377 (ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG).","date_created":"2021-03-23T10:11:46Z","project":[{"call_identifier":"FP7","grant_number":"628377","name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","_id":"2517526A-B435-11E9-9278-68D0E5697425"},{"_id":"268BFA92-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03901","name":"Cybergenetic circuits to test composability of gene networks"}],"file_date_updated":"2021-03-23T10:12:58Z","isi":1,"intvolume":"        10","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"oa_version":"Published Version","status":"public","ddc":["570"],"corr_author":"1","related_material":{"record":[{"relation":"research_data","id":"8951","status":"public"}]},"scopus_import":"1","publication":"eLife","_id":"9283","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","has_accepted_license":"1","publication_identifier":{"issn":["2050-084X"]},"volume":10},{"date_updated":"2026-06-18T19:44:45Z","month":"03","date_published":"2021-03-17T00:00:00Z","language":[{"iso":"eng"}],"day":"17","citation":{"ista":"El Houari I, Van Beirs C, Arents H, Han H, Chanoca A, Opdenacker D, Pollier J, Storme V, Steenackers W, Quareshy M, Napier R, Beeckman T, Friml J, De Rybel B, Boerjan W, Vanholme B. 2021. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. 230(6), 2275–2291.","ieee":"I. El Houari <i>et al.</i>, “Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport,” <i>New Phytologist</i>, vol. 230, no. 6. Wiley, pp. 2275–2291, 2021.","chicago":"El Houari, I, C Van Beirs, HE Arents, Huibin Han, A Chanoca, D Opdenacker, J Pollier, et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17349\">https://doi.org/10.1111/nph.17349</a>.","ama":"El Houari I, Van Beirs C, Arents H, et al. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. <i>New Phytologist</i>. 2021;230(6):2275-2291. doi:<a href=\"https://doi.org/10.1111/nph.17349\">10.1111/nph.17349</a>","mla":"El Houari, I., et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” <i>New Phytologist</i>, vol. 230, no. 6, Wiley, 2021, pp. 2275–91, doi:<a href=\"https://doi.org/10.1111/nph.17349\">10.1111/nph.17349</a>.","apa":"El Houari, I., Van Beirs, C., Arents, H., Han, H., Chanoca, A., Opdenacker, D., … Vanholme, B. (2021). Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17349\">https://doi.org/10.1111/nph.17349</a>","short":"I. El Houari, C. Van Beirs, H. Arents, H. Han, A. Chanoca, D. Opdenacker, J. Pollier, V. Storme, W. Steenackers, M. Quareshy, R. Napier, T. Beeckman, J. Friml, B. De Rybel, W. Boerjan, B. Vanholme, New Phytologist 230 (2021) 2275–2291."},"publication_status":"published","abstract":[{"lang":"eng","text":"• The phenylpropanoid pathway serves a central role in plant metabolism, providing numerous compounds involved in diverse physiological processes. Most carbon entering the pathway is incorporated into lignin. Although several phenylpropanoid pathway mutants show seedling growth arrest, the role for lignin in seedling growth and development is unexplored.\r\n• We use complementary pharmacological and genetic approaches to block CINNAMATE‐4‐HYDROXYLASE (C4H) functionality in Arabidopsis seedlings and a set of molecular and biochemical techniques to investigate the underlying phenotypes.\r\n• Blocking C4H resulted in reduced lateral rooting and increased adventitious rooting apically in the hypocotyl. These phenotypes coincided with an inhibition in auxin transport. The upstream accumulation in cis‐cinnamic acid was found to likely cause polar auxin transport inhibition. Conversely, a downstream depletion in lignin perturbed phloem‐mediated auxin transport. Restoring lignin deposition effectively reestablished phloem transport and, accordingly, auxin homeostasis.\r\n• Our results show that the accumulation of bioactive intermediates and depletion in lignin jointly cause the aberrant phenotypes upon blocking C4H, and demonstrate that proper deposition of lignin is essential for the establishment of auxin distribution in seedlings. Our data position the phenylpropanoid pathway and lignin in a new physiological framework, consolidating their importance in plant growth and development."}],"year":"2021","article_processing_charge":"No","doi":"10.1111/nph.17349","article_type":"original","main_file_link":[{"url":"https://biblio.ugent.be/publication/8703799/file/8703800.pdf","open_access":"1"}],"date_created":"2021-03-26T12:09:01Z","quality_controlled":"1","author":[{"first_name":"I","last_name":"El Houari","full_name":"El Houari, I"},{"full_name":"Van Beirs, C","last_name":"Van Beirs","first_name":"C"},{"first_name":"HE","last_name":"Arents","full_name":"Arents, HE"},{"first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chanoca","full_name":"Chanoca, A","first_name":"A"},{"first_name":"D","last_name":"Opdenacker","full_name":"Opdenacker, D"},{"first_name":"J","last_name":"Pollier","full_name":"Pollier, J"},{"first_name":"V","last_name":"Storme","full_name":"Storme, V"},{"first_name":"W","full_name":"Steenackers, W","last_name":"Steenackers"},{"first_name":"M","last_name":"Quareshy","full_name":"Quareshy, M"},{"last_name":"Napier","full_name":"Napier, R","first_name":"R"},{"last_name":"Beeckman","full_name":"Beeckman, T","first_name":"T"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"full_name":"De Rybel, B","last_name":"De Rybel","first_name":"B"},{"full_name":"Boerjan, W","last_name":"Boerjan","first_name":"W"},{"first_name":"B","full_name":"Vanholme, B","last_name":"Vanholme"}],"oa":1,"pmid":1,"publisher":"Wiley","external_id":{"isi":["000639552400001"],"pmid":["33728703"]},"title":"Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport","issue":"6","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"page":"2275-2291","volume":230,"type":"journal_article","_id":"9288","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"New Phytologist","scopus_import":"1","oa_version":"Published Version","status":"public","ddc":["580"],"intvolume":"       230","department":[{"_id":"JiFr"}],"isi":1}]