[{"issue":"8","abstract":[{"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.","lang":"eng"}],"doi":"10.1016/j.jcss.2021.02.008","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Žikelić, Đorđe","last_name":"Žikelić","first_name":"Đorđe"}],"title":"Bidding mechanisms in graph games","_id":"9239","status":"public","publication_status":"published","publication_identifier":{"eissn":["1090-2724"],"issn":["0022-0000"]},"oa_version":"Preprint","day":"03","citation":{"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>","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.","short":"G. Avni, T.A. Henzinger, Đ. Žikelić, Journal of Computer and System Sciences 119 (2021) 133–144.","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>","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>.","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>."},"month":"03","volume":119,"article_processing_charge":"No","arxiv":1,"year":"2021","oa":1,"related_material":{"record":[{"id":"6884","status":"public","relation":"earlier_version"}]},"article_type":"original","page":"133-144","publication":"Journal of Computer and System Sciences","date_updated":"2023-08-07T14:08:34Z","date_published":"2021-03-03T00:00:00Z","external_id":{"isi":["000634149800009"],"arxiv":["1905.03835"]},"scopus_import":"1","date_created":"2021-03-14T23:01:32Z","department":[{"_id":"ToHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"intvolume":"       119","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.03835","open_access":"1"}],"publisher":"Elsevier"},{"oa_version":"Published Version","day":"25","citation":{"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>.","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>.","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.","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>","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.","short":"F. Cornalba, T. Shardlow, J. Zimmer, Journal of Differential Equations 284 (2021) 253–283."},"file_date_updated":"2021-03-22T07:18:01Z","ddc":["510"],"month":"05","has_accepted_license":"1","volume":284,"article_processing_charge":"Yes (via OA deal)","file":[{"file_name":"2021_JourDiffEquations_Cornalba.pdf","relation":"main_file","file_size":473310,"creator":"dernst","success":1,"date_updated":"2021-03-22T07:18:01Z","access_level":"open_access","content_type":"application/pdf","checksum":"c630b691fb9e716b02aa6103a9794ec8","file_id":"9267","date_created":"2021-03-22T07:18:01Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"5","abstract":[{"lang":"eng","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."}],"doi":"10.1016/j.jde.2021.02.048","author":[{"id":"2CEB641C-A400-11E9-A717-D712E6697425","first_name":"Federico","full_name":"Cornalba, Federico","last_name":"Cornalba"},{"last_name":"Shardlow","full_name":"Shardlow, Tony","first_name":"Tony"},{"first_name":"Johannes","last_name":"Zimmer","full_name":"Zimmer, Johannes"}],"title":"Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions","_id":"9240","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.","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"eissn":["1090-2732"],"issn":["0022-0396"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"external_id":{"isi":["000634823300010"]},"date_published":"2021-05-25T00:00:00Z","scopus_import":"1","date_created":"2021-03-14T23:01:32Z","department":[{"_id":"JuFi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       284","publisher":"Elsevier","year":"2021","oa":1,"article_type":"original","page":"253-283","publication":"Journal of Differential Equations","date_updated":"2023-08-07T14:08:05Z"},{"article_processing_charge":"No","volume":29,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"success":1,"date_updated":"2021-03-22T08:15:28Z","access_level":"open_access","checksum":"a9697ad83136c19ad87e46aa2db63cfd","content_type":"application/pdf","file_name":"2021_OpticsExpress_Elek.pdf","creator":"dernst","file_size":10873700,"relation":"main_file","file_id":"9269","date_created":"2021-03-22T08:15:28Z"}],"oa_version":"Published Version","month":"03","file_date_updated":"2021-03-22T08:15:28Z","ddc":["000"],"day":"01","citation":{"mla":"Elek, Oskar, et al. “Robust and Practical Measurement of Volume Transport Parameters in Solid Photo-Polymer Materials for 3D Printing.” <i>Optics Express</i>, vol. 29, no. 5, The Optical Society, 2021, pp. 7568–88, doi:<a href=\"https://doi.org/10.1364/OE.406095\">10.1364/OE.406095</a>.","chicago":"Elek, Oskar, Ran Zhang, Denis Sumin, Karol Myszkowski, Bernd Bickel, Alexander Wilkie, Jaroslav Křivánek, and Tim Weyrich. “Robust and Practical Measurement of Volume Transport Parameters in Solid Photo-Polymer Materials for 3D Printing.” <i>Optics Express</i>. The Optical Society, 2021. <a href=\"https://doi.org/10.1364/OE.406095\">https://doi.org/10.1364/OE.406095</a>.","ista":"Elek O, Zhang R, Sumin D, Myszkowski K, Bickel B, Wilkie A, Křivánek J, Weyrich T. 2021. Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing. Optics Express. 29(5), 7568–7588.","short":"O. Elek, R. Zhang, D. Sumin, K. Myszkowski, B. Bickel, A. Wilkie, J. Křivánek, T. Weyrich, Optics Express 29 (2021) 7568–7588.","ama":"Elek O, Zhang R, Sumin D, et al. Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing. <i>Optics Express</i>. 2021;29(5):7568-7588. doi:<a href=\"https://doi.org/10.1364/OE.406095\">10.1364/OE.406095</a>","apa":"Elek, O., Zhang, R., Sumin, D., Myszkowski, K., Bickel, B., Wilkie, A., … Weyrich, T. (2021). Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing. <i>Optics Express</i>. The Optical Society. <a href=\"https://doi.org/10.1364/OE.406095\">https://doi.org/10.1364/OE.406095</a>","ieee":"O. Elek <i>et al.</i>, “Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing,” <i>Optics Express</i>, vol. 29, no. 5. The Optical Society, pp. 7568–7588, 2021."},"ec_funded":1,"publication_status":"published","acknowledgement":"H2020 Marie Skłodowska-Curie Actions (642841); European Research Council (715767); Grantová Agentura České Republiky (16-08111S, 16-18964S); Univerzita Karlova v Praze (SVV-2017-260452); Engineering and Physical Sciences Research Council (EP/K023578/1).\r\nWe are grateful to Stratasys Ltd. for access to the voxel-level print interface of the J750\r\nmachine.","status":"public","project":[{"grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"publication_identifier":{"eissn":["1094-4087"]},"doi":"10.1364/OE.406095","issue":"5","abstract":[{"text":"Volumetric light transport is a pervasive physical phenomenon, and therefore its accurate simulation is important for a broad array of disciplines. While suitable mathematical models for computing the transport are now available, obtaining the necessary material parameters needed to drive such simulations is a challenging task: direct measurements of these parameters from material samples are seldom possible. Building on the inverse scattering paradigm, we present a novel measurement approach which indirectly infers the transport parameters from extrinsic observations of multiple-scattered radiance. The novelty of the proposed approach lies in replacing structured illumination with a structured reflector bonded to the sample, and a robust fitting procedure that largely compensates for potential systematic errors in the calibration of the setup. We show the feasibility of our approach by validating simulations of complex 3D compositions of the measured materials against physical prints, using photo-polymer resins. As presented in this paper, our technique yields colorspace data suitable for accurate appearance reproduction in the area of 3D printing. Beyond that, and without fundamental changes to the basic measurement methodology, it could equally well be used to obtain spectral measurements that are useful for other application areas.","lang":"eng"}],"_id":"9241","author":[{"first_name":"Oskar","last_name":"Elek","full_name":"Elek, Oskar"},{"orcid":"0000-0002-3808-281X","first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Ran"},{"first_name":"Denis","last_name":"Sumin","full_name":"Sumin, Denis"},{"last_name":"Myszkowski","full_name":"Myszkowski, Karol","first_name":"Karol"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"full_name":"Wilkie, Alexander","last_name":"Wilkie","first_name":"Alexander"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"},{"first_name":"Tim","full_name":"Weyrich, Tim","last_name":"Weyrich"}],"title":"Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"intvolume":"        29","publisher":"The Optical Society","scopus_import":"1","date_created":"2021-03-14T23:01:33Z","external_id":{"isi":["000624968100103"]},"date_published":"2021-03-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BeBi"}],"article_type":"original","page":"7568-7588","date_updated":"2023-08-07T14:11:57Z","publication":"Optics Express","year":"2021","oa":1},{"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"American Physical Society","main_file_link":[{"url":"https://arxiv.org/abs/2010.05356","open_access":"1"}],"intvolume":"       103","date_created":"2021-03-14T23:01:33Z","scopus_import":"1","external_id":{"arxiv":["2010.05356"],"isi":["000617037900013"]},"date_published":"2021-02-11T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JoFi"}],"article_number":"023708","article_type":"original","date_updated":"2023-08-07T14:11:18Z","publication":"Physical Review A","year":"2021","oa":1,"volume":103,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","month":"02","citation":{"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>","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.","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>","ista":"Rueda Sanchez AR. 2021. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. 103(2), 023708.","short":"A.R. Rueda Sanchez, Physical Review A 103 (2021).","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>.","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>."},"day":"11","publication_status":"published","status":"public","acknowledgement":"I thank Prof. Shabir Barzanjeh and Dr. Ulrich Vogl for the fruitful discussions.\r\n","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"doi":"10.1103/PhysRevA.103.023708","abstract":[{"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.","lang":"eng"}],"issue":"2","_id":"9242","title":"Frequency-multiplexed hybrid optical entangled source based on the Pockels effect","author":[{"full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","orcid":"0000-0001-6249-5860"}]},{"citation":{"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>.","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>.","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>","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.","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>","short":"V.M. Hernández-Rocamora, N.S. Baranova, K. Peters, E. Breukink, M. Loose, W. Vollmer, ELife 10 (2021).","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."},"day":"24","month":"02","ddc":["570"],"file_date_updated":"2021-03-22T07:36:08Z","oa_version":"Published Version","file":[{"date_created":"2021-03-22T07:36:08Z","file_id":"9268","creator":"dernst","file_size":2314698,"relation":"main_file","file_name":"2021_eLife_HernandezRocamora.pdf","content_type":"application/pdf","checksum":"79897a09bfecd9914d39c4aea2841855","access_level":"open_access","date_updated":"2021-03-22T07:36:08Z","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":10,"article_processing_charge":"No","title":"Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins","author":[{"last_name":"Hernández-Rocamora","full_name":"Hernández-Rocamora, Víctor M.","first_name":"Víctor M."},{"orcid":"0000-0002-3086-9124","last_name":"Baranova","full_name":"Baranova, Natalia S.","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Peters, Katharina","last_name":"Peters","first_name":"Katharina"},{"last_name":"Breukink","full_name":"Breukink, Eefjan","first_name":"Eefjan"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vollmer, Waldemar","last_name":"Vollmer","first_name":"Waldemar"}],"_id":"9243","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."}],"doi":"10.7554/eLife.61525","publication_identifier":{"eissn":["2050-084X"]},"project":[{"call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163"},{"grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425","name":"Reconstitution of bacterial cell wall sythesis"}],"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). ","publication_status":"published","status":"public","ec_funded":1,"department":[{"_id":"MaLo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000627596400001"]},"date_published":"2021-02-24T00:00:00Z","date_created":"2021-03-14T23:01:33Z","scopus_import":"1","publisher":"eLife Sciences Publications","intvolume":"        10","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","oa":1,"year":"2021","publication":"eLife","date_updated":"2023-08-07T14:10:50Z","article_number":"1-32","article_type":"original"},{"oa_version":"Published Version","citation":{"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>.","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>.","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.","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>","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).","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.","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>"},"day":"26","month":"02","ddc":["570"],"file_date_updated":"2021-03-22T08:50:33Z","pmid":1,"has_accepted_license":"1","volume":10,"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"9271","date_created":"2021-03-22T08:50:33Z","file_name":"2021_eLife_Hankeova.pdf","creator":"dernst","file_size":9259690,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"20ccf4dfe46c48cf986794c8bf4fd1cb","success":1,"date_updated":"2021-03-22T08:50:33Z"}],"abstract":[{"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.","lang":"eng"}],"doi":"10.7554/eLife.60916","title":"DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome","author":[{"first_name":"Simona","full_name":"Hankeova, Simona","last_name":"Hankeova"},{"first_name":"Jakub","last_name":"Salplachta","full_name":"Salplachta, Jakub"},{"last_name":"Zikmund","full_name":"Zikmund, Tomas","first_name":"Tomas"},{"first_name":"Michaela","full_name":"Kavkova, Michaela","last_name":"Kavkova"},{"first_name":"Noémi","last_name":"Van Hul","full_name":"Van Hul, Noémi"},{"first_name":"Adam","full_name":"Brinek, Adam","last_name":"Brinek"},{"first_name":"Veronika","last_name":"Smekalova","full_name":"Smekalova, Veronika"},{"full_name":"Laznovsky, Jakub","last_name":"Laznovsky","first_name":"Jakub"},{"first_name":"Feven","last_name":"Dawit","full_name":"Dawit, Feven"},{"last_name":"Jaros","full_name":"Jaros, Josef","first_name":"Josef"},{"first_name":"Vítězslav","last_name":"Bryja","full_name":"Bryja, Vítězslav"},{"last_name":"Lendahl","full_name":"Lendahl, Urban","first_name":"Urban"},{"first_name":"Ewa","full_name":"Ellis, Ewa","last_name":"Ellis"},{"last_name":"Nemeth","full_name":"Nemeth, Antal","first_name":"Antal"},{"last_name":"Fischler","full_name":"Fischler, Björn","first_name":"Björn"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaiser","full_name":"Kaiser, Jozef","first_name":"Jozef"},{"last_name":"Andersson","full_name":"Andersson, Emma Rachel","first_name":"Emma Rachel"}],"_id":"9244","publication_status":"published","status":"public","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.).","ec_funded":1,"publication_identifier":{"eissn":["2050084X"]},"project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"external_id":{"isi":["000625357100001"],"pmid":["33635272"]},"date_published":"2021-02-26T00:00:00Z","date_created":"2021-03-14T23:01:34Z","scopus_import":"1","department":[{"_id":"EdHa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"eLife Sciences Publications","intvolume":"        10","year":"2021","oa":1,"article_number":"e60916","article_type":"original","publication":"eLife","date_updated":"2023-08-07T14:12:54Z"},{"article_processing_charge":"No","volume":2218,"oa_version":"None","pmid":1,"month":"02","day":"20","citation":{"mla":"Xia, Peng, and Carl-Philipp J. Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, vol. 2218, Humana, 2021, pp. 117–28, doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>.","chicago":"Xia, Peng, and Carl-Philipp J Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” In <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, 2218:117–28. Humana, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>.","short":"P. Xia, C.-P.J. Heisenberg, in:, R. Dosch (Ed.), Germline Development in the Zebrafish, Humana, 2021, pp. 117–128.","ista":"Xia P, Heisenberg C-PJ. 2021.Quantifying tissue tension in the granulosa layer after laser surgery. In: Germline Development in the Zebrafish. Methods in Molecular Biology, vol. 2218, 117–128.","ama":"Xia P, Heisenberg C-PJ. Quantifying tissue tension in the granulosa layer after laser surgery. In: Dosch R, ed. <i>Germline Development in the Zebrafish</i>. Vol 2218. Humana; 2021:117-128. doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>","ieee":"P. Xia and C.-P. J. Heisenberg, “Quantifying tissue tension in the granulosa layer after laser surgery,” in <i>Germline Development in the Zebrafish</i>, vol. 2218, R. Dosch, Ed. Humana, 2021, pp. 117–128.","apa":"Xia, P., &#38; Heisenberg, C.-P. J. (2021). Quantifying tissue tension in the granulosa layer after laser surgery. In R. Dosch (Ed.), <i>Germline Development in the Zebrafish</i> (Vol. 2218, pp. 117–128). Humana. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>"},"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"We thank Prof. Masazumi Tada and Roland Dosch for providing transgenic zebrafish lines, the Heisenberg lab for technical assistance and feedback on the manuscript, and the Bioimaging and Fish facilities of IST Austria for continuous support. This work was funded by an ERC advanced grant (MECSPEC to C.-P.H.).","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"}],"publication_identifier":{"isbn":["978-1-0716-0969-9"],"eisbn":["978-1-0716-0970-5"],"issn":["1064-3745"],"eissn":["1940-6029"]},"doi":"10.1007/978-1-0716-0970-5_10","abstract":[{"text":"Tissue morphogenesis is driven by mechanical forces triggering cell movements and shape changes. Quantitatively measuring tension within tissues is of great importance for understanding the role of mechanical signals acting on the cell and tissue level during morphogenesis. Here we introduce laser ablation as a useful tool to probe tissue tension within the granulosa layer, an epithelial monolayer of somatic cells that surround the zebrafish female gamete during folliculogenesis. We describe in detail how to isolate follicles, mount samples, perform laser surgery, and analyze the data.","lang":"eng"}],"_id":"9245","editor":[{"full_name":"Dosch, Roland","last_name":"Dosch","first_name":"Roland"}],"author":[{"full_name":"Xia, Peng","last_name":"Xia","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","first_name":"Peng","orcid":"0000-0002-5419-7756"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"title":"Quantifying tissue tension in the granulosa layer after laser surgery","type":"book_chapter","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"      2218","publisher":"Humana","scopus_import":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_created":"2021-03-14T23:01:34Z","date_published":"2021-02-20T00:00:00Z","external_id":{"pmid":["33606227"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"}],"page":"117-128","date_updated":"2022-06-03T10:57:55Z","publication":"Germline Development in the Zebrafish","keyword":["Tissue tension","Morphogenesis","Laser ablation","Zebrafish folliculogenesis","Granulosa cells"],"alternative_title":["Methods in Molecular Biology"],"year":"2021"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"9270","date_created":"2021-03-22T08:31:29Z","file_name":"2021_ArchRationalMechAnal_Leopold.pdf","file_size":558006,"relation":"main_file","creator":"dernst","success":1,"date_updated":"2021-03-22T08:31:29Z","access_level":"open_access","content_type":"application/pdf","checksum":"23449e44dc5132501a5c86e70638800f"}],"arxiv":1,"has_accepted_license":"1","article_processing_charge":"No","volume":240,"day":"26","citation":{"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>","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.","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.","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>.","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>."},"file_date_updated":"2021-03-22T08:31:29Z","ddc":["510"],"month":"02","oa_version":"Published Version","publication_identifier":{"eissn":["14320673"],"issn":["00039527"]},"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"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.","publication_status":"published","status":"public","ec_funded":1,"author":[{"orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K"},{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"title":"Derivation of the Landau–Pekar equations in a many-body mean-field limit","_id":"9246","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"}],"doi":"10.1007/s00205-021-01616-9","intvolume":"       240","publisher":"Springer Nature","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-02-26T00:00:00Z","external_id":{"isi":["000622226200001"],"arxiv":["2001.03993"]},"scopus_import":"1","date_created":"2021-03-14T23:01:34Z","publication":"Archive for Rational Mechanics and Analysis","date_updated":"2023-08-07T14:12:27Z","article_type":"original","page":"383-417","oa":1,"year":"2021"},{"article_processing_charge":"No","volume":13,"has_accepted_license":"1","file":[{"access_level":"open_access","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","content_type":"application/pdf","date_updated":"2021-09-16T22:30:03Z","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","relation":"main_file","file_size":1811448,"creator":"dernst","embargo":"2021-09-15","file_id":"9276","date_created":"2021-03-22T11:46:00Z"}],"oa_version":"Submitted Version","ddc":["540"],"file_date_updated":"2021-09-16T22:30:03Z","month":"03","pmid":1,"day":"15","citation":{"chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>.","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. 2021;13(5):465-471. doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","ieee":"Y. K. Petit <i>et al.</i>, “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” <i>Nature Chemistry</i>, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>"},"publication_status":"published","status":"public","acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"doi":"10.1038/s41557-021-00643-z","issue":"5","abstract":[{"lang":"eng","text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate."}],"_id":"9250","author":[{"first_name":"Yann K.","full_name":"Petit, Yann K.","last_name":"Petit"},{"last_name":"Mourad","full_name":"Mourad, Eléonore","first_name":"Eléonore"},{"last_name":"Prehal","full_name":"Prehal, Christian","first_name":"Christian"},{"full_name":"Leypold, Christian","last_name":"Leypold","first_name":"Christian"},{"full_name":"Windischbacher, Andreas","last_name":"Windischbacher","first_name":"Andreas"},{"first_name":"Daniel","full_name":"Mijailovic, Daniel","last_name":"Mijailovic"},{"first_name":"Christian","full_name":"Slugovc, Christian","last_name":"Slugovc"},{"full_name":"Borisov, Sergey M.","last_name":"Borisov","first_name":"Sergey M."},{"first_name":"Egbert","full_name":"Zojer, Egbert","last_name":"Zojer"},{"full_name":"Brutti, Sergio","last_name":"Brutti","first_name":"Sergio"},{"full_name":"Fontaine, Olivier","last_name":"Fontaine","first_name":"Olivier"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"}],"title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"intvolume":"        13","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"M-Shop"}],"scopus_import":"1","date_created":"2021-03-16T11:12:20Z","external_id":{"pmid":["33723377"],"isi":["000629296400001"]},"date_published":"2021-03-15T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"StFr"}],"article_type":"original","page":"465-471","date_updated":"2023-09-05T15:34:44Z","publication":"Nature Chemistry","keyword":["General Chemistry","General Chemical Engineering"],"year":"2021","oa":1},{"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"year":"2021","oa":1,"article_type":"original","page":"1030-1045","related_material":{"record":[{"id":"13062","status":"public","relation":"research_data"}]},"date_updated":"2023-09-05T15:44:06Z","publication":"Evolution","scopus_import":"1","date_created":"2021-03-20T08:22:10Z","date_published":"2021-05-01T00:00:00Z","external_id":{"isi":["000636966300001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"intvolume":"        75","publisher":"Wiley","doi":"10.1111/evo.14210","issue":"5","abstract":[{"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.","lang":"eng"}],"_id":"9252","author":[{"last_name":"Szep","full_name":"Szep, Eniko","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model","status":"public","acknowledgement":"We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper.","publication_status":"published","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2021-08-11T13:39:19Z","month":"05","ddc":["570"],"day":"01","citation":{"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>.","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>.","ista":"Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.","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>","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>","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."},"volume":75,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file":[{"date_created":"2021-08-11T13:39:19Z","file_id":"9886","relation":"main_file","creator":"kschuh","file_size":734102,"file_name":"2021_Evolution_Szep.pdf","date_updated":"2021-08-11T13:39:19Z","success":1,"content_type":"application/pdf","checksum":"b90fb5767d623602046fed03725e16ca","access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"}},{"arxiv":1,"article_processing_charge":"No","month":"03","citation":{"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>.","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>.","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.","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.","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>","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."},"day":"19","oa_version":"Preprint","conference":{"name":"Big Data: International Conference on Big Data","end_date":"2020-12-13","start_date":"2020-12-10","location":"Atlanta, GA, United States"},"publication_identifier":{"isbn":["9781728162515"]},"status":"public","publication_status":"published","_id":"9253","title":"Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic","author":[{"full_name":"Heiler, Georg","last_name":"Heiler","first_name":"Georg"},{"full_name":"Reisch, Tobias","last_name":"Reisch","first_name":"Tobias"},{"full_name":"Hurt, Jan","last_name":"Hurt","first_name":"Jan"},{"first_name":"Mohammad","full_name":"Forghani, Mohammad","last_name":"Forghani"},{"full_name":"Omani, Aida","last_name":"Omani","first_name":"Aida"},{"last_name":"Hanbury","full_name":"Hanbury, Allan","first_name":"Allan"},{"orcid":"0000-0001-6746-4174","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","first_name":"Farid","full_name":"Karimipour, Farid","last_name":"Karimipour"}],"doi":"10.1109/bigdata50022.2020.9378374","abstract":[{"lang":"eng","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."}],"publisher":"IEEE","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.10064"}],"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"HeEd"}],"date_created":"2021-03-21T11:34:07Z","scopus_import":"1","date_published":"2021-03-19T00:00:00Z","external_id":{"arxiv":["2008.10064"],"isi":["000662554703032"]},"date_updated":"2023-08-07T14:00:13Z","publication":"2020 IEEE International Conference on Big Data","page":"3123-3132","oa":1,"year":"2021"},{"ddc":["580"],"file_date_updated":"2021-03-22T11:18:58Z","month":"03","pmid":1,"day":"12","citation":{"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>.","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>.","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>","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.","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).","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.","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>"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"creator":"dernst","relation":"main_file","file_size":8602096,"file_name":"2021_NatureComm_Hu.pdf","content_type":"application/pdf","checksum":"e1022f3aee349853ded2b2b3e092362d","access_level":"open_access","date_updated":"2021-03-22T11:18:58Z","success":1,"date_created":"2021-03-22T11:18:58Z","file_id":"9275"}],"article_processing_charge":"No","volume":12,"has_accepted_license":"1","_id":"9254","author":[{"first_name":"Yangjie","full_name":"Hu, Yangjie","last_name":"Hu"},{"last_name":"Omary","full_name":"Omary, Moutasem","first_name":"Moutasem"},{"full_name":"Hu, Yun","last_name":"Hu","first_name":"Yun"},{"full_name":"Doron, Ohad","last_name":"Doron","first_name":"Ohad"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","full_name":"Hörmayer, Lukas","last_name":"Hörmayer"},{"full_name":"Chen, Qingguo","last_name":"Chen","first_name":"Qingguo"},{"first_name":"Or","last_name":"Megides","full_name":"Megides, Or"},{"first_name":"Ori","last_name":"Chekli","full_name":"Chekli, Ori"},{"first_name":"Zhaojun","full_name":"Ding, Zhaojun","last_name":"Ding"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"Yunde","full_name":"Zhao, Yunde","last_name":"Zhao"},{"last_name":"Tsarfaty","full_name":"Tsarfaty, Ilan","first_name":"Ilan"},{"last_name":"Shani","full_name":"Shani, Eilon","first_name":"Eilon"}],"title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","doi":"10.1038/s41467-021-21802-3","abstract":[{"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.","lang":"eng"}],"publication_identifier":{"eissn":["20411723"]},"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.).","publication_status":"published","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"scopus_import":"1","date_created":"2021-03-21T23:01:19Z","external_id":{"pmid":["33712581"],"isi":["000630419400048"]},"date_published":"2021-03-12T00:00:00Z","intvolume":"        12","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"oa":1,"year":"2021","date_updated":"2023-08-07T14:17:55Z","publication":"Nature Communications","article_type":"original","article_number":"1657"},{"doi":"10.1038/s41534-021-00387-1","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."}],"_id":"9255","title":"Semi-device-independent random number generation with flexible assumptions","author":[{"full_name":"Pivoluska, Matej","last_name":"Pivoluska","first_name":"Matej"},{"first_name":"Martin","full_name":"Plesch, Martin","last_name":"Plesch"},{"first_name":"Máté","full_name":"Farkas, Máté","last_name":"Farkas"},{"last_name":"Ruzickova","full_name":"Ruzickova, Natalia","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"},{"last_name":"Flegel","full_name":"Flegel, Clara","first_name":"Clara"},{"first_name":"Natalia Herrera","last_name":"Valencia","full_name":"Valencia, Natalia Herrera"},{"last_name":"Mccutcheon","full_name":"Mccutcheon, Will","first_name":"Will"},{"first_name":"Mehul","last_name":"Malik","full_name":"Malik, Mehul"},{"first_name":"Edgar A.","last_name":"Aguilar","full_name":"Aguilar, Edgar A."}],"status":"public","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).","publication_status":"published","publication_identifier":{"eissn":["2056-6387"]},"oa_version":"Published Version","month":"03","file_date_updated":"2021-03-22T11:09:34Z","ddc":["530"],"citation":{"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.","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).","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>","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.","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>","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>.","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>."},"day":"15","article_processing_charge":"No","volume":7,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2021-03-22T11:09:34Z","file_id":"9274","relation":"main_file","file_size":1360271,"creator":"dernst","file_name":"2021_NPJQuantumInformation_Pivoluska.pdf","content_type":"application/pdf","checksum":"26d3f2a2c8c8fa8c1002028326b45f64","access_level":"open_access","date_updated":"2021-03-22T11:09:34Z","success":1}],"year":"2021","oa":1,"article_number":"50","article_type":"original","date_updated":"2023-08-07T14:17:26Z","publication":"npj Quantum Information","date_created":"2021-03-21T23:01:19Z","scopus_import":"1","date_published":"2021-03-15T00:00:00Z","external_id":{"isi":["000629173100001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"FyKo"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Springer Nature","intvolume":"         7"},{"intvolume":"       111","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"RoSe"}],"scopus_import":"1","date_created":"2021-03-21T23:01:19Z","date_published":"2021-03-09T00:00:00Z","external_id":{"isi":["000626837400001"]},"date_updated":"2023-08-07T14:17:00Z","publication":"Letters in Mathematical Physics","article_type":"original","article_number":"31","oa":1,"year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"creator":"dernst","file_size":397962,"relation":"main_file","file_name":"2021_LettersMathPhysics_Napiorkowski.pdf","date_updated":"2021-03-22T11:01:09Z","success":1,"content_type":"application/pdf","checksum":"687fef1525789c0950de90468dd81604","access_level":"open_access","date_created":"2021-03-22T11:01:09Z","file_id":"9273"}],"volume":111,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","month":"03","ddc":["510"],"file_date_updated":"2021-03-22T11:01:09Z","day":"09","citation":{"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>","short":"M.M. Napiórkowski, R. Seiringer, Letters in Mathematical Physics 111 (2021).","ista":"Napiórkowski MM, Seiringer R. 2021. Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. 111(2), 31.","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.","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>","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>.","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>."},"oa_version":"Published Version","publication_identifier":{"issn":["03779017"],"eissn":["15730530"]},"publication_status":"published","status":"public","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).","_id":"9256","author":[{"full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"title":"Free energy asymptotics of the quantum Heisenberg spin chain","doi":"10.1007/s11005-021-01375-4","issue":"2","abstract":[{"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.","lang":"eng"}]},{"file_date_updated":"2021-03-22T12:23:54Z","ddc":["530"],"pmid":1,"month":"03","day":"09","citation":{"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</i>, vol. 118, no. 10. National Academy of Sciences, 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</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>","short":"C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences 118 (2021).","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</i>. 2021;118(10). 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. 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</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/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</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>."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"date_created":"2021-03-22T12:23:54Z","file_id":"9278","date_updated":"2021-03-22T12:23:54Z","success":1,"checksum":"5be8da2b1c0757feb1057f1a515cf9e0","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":1047954,"creator":"dernst","file_name":"2021_PNAS_Goodrich.pdf"}],"volume":118,"article_processing_charge":"No","has_accepted_license":"1","_id":"9257","author":[{"orcid":"0000-0002-1307-5074","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"King","full_name":"King, Ella M.","first_name":"Ella M."},{"first_name":"Samuel S.","last_name":"Schoenholz","full_name":"Schoenholz, Samuel S."},{"first_name":"Ekin D.","last_name":"Cubuk","full_name":"Cubuk, Ekin D."},{"last_name":"Brenner","full_name":"Brenner, Michael P.","first_name":"Michael P."}],"title":"Designing self-assembling kinetics with differentiable statistical physics models","doi":"10.1073/pnas.2024083118","issue":"10","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"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"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.","publication_status":"published","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CaGo"}],"scopus_import":"1","date_created":"2021-03-21T23:01:20Z","external_id":{"pmid":["33653960"],"isi":["000627429100097"]},"date_published":"2021-03-09T00:00:00Z","intvolume":"       118","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"oa":1,"year":"2021","date_updated":"2023-08-07T14:19:34Z","publication":"Proceedings of the National Academy of Sciences","article_type":"original","article_number":"e2024083118"},{"volume":18,"article_processing_charge":"No","oa_version":"Published Version","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>.","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>.","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.","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>","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.","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>","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."},"month":"03","pmid":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.","status":"public","publication_status":"published","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"issue":"3","doi":"10.1038/s41592-021-01087-6","author":[{"full_name":"Pinkard, Henry","last_name":"Pinkard","first_name":"Henry"},{"first_name":"Nico","last_name":"Stuurman","full_name":"Stuurman, Nico"},{"first_name":"Ivan E.","full_name":"Ivanov, Ivan E.","last_name":"Ivanov"},{"first_name":"Nicholas M.","last_name":"Anthony","full_name":"Anthony, Nicholas M."},{"last_name":"Ouyang","full_name":"Ouyang, Wei","first_name":"Wei"},{"first_name":"Bin","full_name":"Li, Bin","last_name":"Li"},{"first_name":"Bin","last_name":"Yang","full_name":"Yang, Bin"},{"last_name":"Tsuchida","full_name":"Tsuchida, Mark A.","first_name":"Mark A."},{"first_name":"Bryant","last_name":"Chhun","full_name":"Chhun, Bryant"},{"first_name":"Grace","last_name":"Zhang","full_name":"Zhang, Grace"},{"full_name":"Mei, Ryan","last_name":"Mei","first_name":"Ryan"},{"full_name":"Anderson, Michael","last_name":"Anderson","first_name":"Michael"},{"first_name":"Douglas P.","last_name":"Shepherd","full_name":"Shepherd, Douglas P."},{"first_name":"Ian","last_name":"Hunt-Isaak","full_name":"Hunt-Isaak, Ian"},{"full_name":"Dunn, Raymond L.","last_name":"Dunn","first_name":"Raymond L."},{"full_name":"Jahr, Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke"},{"full_name":"Kato, Saul","last_name":"Kato","first_name":"Saul"},{"full_name":"Royer, Loïc A.","last_name":"Royer","first_name":"Loïc A."},{"first_name":"Jay R.","last_name":"Thiagarajah","full_name":"Thiagarajah, Jay R."},{"first_name":"Kevin W.","full_name":"Eliceiri, Kevin W.","last_name":"Eliceiri"},{"first_name":"Emma","last_name":"Lundberg","full_name":"Lundberg, Emma"},{"first_name":"Shalin B.","last_name":"Mehta","full_name":"Mehta, Shalin B."},{"first_name":"Laura","full_name":"Waller, Laura","last_name":"Waller"}],"title":"Pycro-Manager: Open-source software for customized and reproducible microscope control","_id":"9258","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":"        18","main_file_link":[{"url":"https://doi.org/10.1038/s41592-021-01087-6","open_access":"1"}],"publisher":"Springer Nature","date_published":"2021-03-01T00:00:00Z","external_id":{"pmid":["33674797"],"isi":["000625600600007"]},"scopus_import":"1","date_created":"2021-03-21T23:01:20Z","department":[{"_id":"JoDa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"letter_note","page":"226-228","publication":"Nature Methods","date_updated":"2023-08-07T14:19:08Z","year":"2021","oa":1},{"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"}],"doi":"10.3389/fimmu.2021.630002","author":[{"orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Moussion, Christine","last_name":"Moussion","id":"3356F664-F248-11E8-B48F-1D18A9856A87","first_name":"Christine"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"title":"Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium","_id":"9259","status":"public","publication_status":"published","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.","ec_funded":1,"publication_identifier":{"eissn":["1664-3224"]},"project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","day":"25","citation":{"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>.","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).","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>","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.","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>","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."},"pmid":1,"month":"02","ddc":["570"],"file_date_updated":"2021-03-22T12:08:26Z","has_accepted_license":"1","volume":12,"article_processing_charge":"No","file":[{"file_name":"2021_FrontiersImmumo_Vaahtomeri.pdf","relation":"main_file","file_size":3740146,"creator":"dernst","access_level":"open_access","checksum":"663f5a48375e42afa4bfef58d42ec186","content_type":"application/pdf","success":1,"date_updated":"2021-03-22T12:08:26Z","file_id":"9277","date_created":"2021-03-22T12:08:26Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","oa":1,"article_type":"original","article_number":"630002","publication":"Frontiers in Immunology","date_updated":"2023-08-07T14:18:26Z","date_published":"2021-02-25T00:00:00Z","external_id":{"pmid":["33717158"],"isi":["000627134400001"]},"scopus_import":"1","date_created":"2021-03-21T23:01:20Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        12","publisher":"Frontiers"},{"oa_version":"Published Version","day":"05","citation":{"short":"T.D. Browning, S. Yamagishi, Mathematische Zeitschrift 299 (2021) 1071–1101.","ama":"Browning TD, Yamagishi S. Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. <i>Mathematische Zeitschrift</i>. 2021;299:1071–1101. doi:<a href=\"https://doi.org/10.1007/s00209-021-02695-w\">10.1007/s00209-021-02695-w</a>","ista":"Browning TD, Yamagishi S. 2021. Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. Mathematische Zeitschrift. 299, 1071–1101.","apa":"Browning, T. D., &#38; Yamagishi, S. (2021). Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. <i>Mathematische Zeitschrift</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00209-021-02695-w\">https://doi.org/10.1007/s00209-021-02695-w</a>","ieee":"T. D. Browning and S. Yamagishi, “Arithmetic of higher-dimensional orbifolds and a mixed Waring problem,” <i>Mathematische Zeitschrift</i>, vol. 299. Springer Nature, pp. 1071–1101, 2021.","mla":"Browning, Timothy D., and Shuntaro Yamagishi. “Arithmetic of Higher-Dimensional Orbifolds and a Mixed Waring Problem.” <i>Mathematische Zeitschrift</i>, vol. 299, Springer Nature, 2021, pp. 1071–1101, doi:<a href=\"https://doi.org/10.1007/s00209-021-02695-w\">10.1007/s00209-021-02695-w</a>.","chicago":"Browning, Timothy D, and Shuntaro Yamagishi. “Arithmetic of Higher-Dimensional Orbifolds and a Mixed Waring Problem.” <i>Mathematische Zeitschrift</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00209-021-02695-w\">https://doi.org/10.1007/s00209-021-02695-w</a>."},"month":"03","file_date_updated":"2021-03-22T12:41:26Z","ddc":["510"],"has_accepted_license":"1","article_processing_charge":"No","volume":299,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"9279","date_created":"2021-03-22T12:41:26Z","access_level":"open_access","content_type":"application/pdf","checksum":"8ed9f49568806894744096dbbca0ad7b","success":1,"date_updated":"2021-03-22T12:41:26Z","file_name":"2021_MathZeitschrift_Browning.pdf","file_size":492685,"creator":"dernst","relation":"main_file"}],"abstract":[{"text":"We study the density of rational points on a higher-dimensional orbifold (Pn−1,Δ) when Δ is a Q-divisor involving hyperplanes. This allows us to address a question of Tanimoto about whether the set of rational points on such an orbifold constitutes a thin set. Our approach relies on the Hardy–Littlewood circle method to first study an asymptotic version of Waring’s problem for mixed powers. In doing so we make crucial use of the recent resolution of the main conjecture in Vinogradov’s mean value theorem, due to Bourgain–Demeter–Guth and Wooley.","lang":"eng"}],"doi":"10.1007/s00209-021-02695-w","author":[{"orcid":"0000-0002-8314-0177","last_name":"Browning","full_name":"Browning, Timothy D","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shuntaro","full_name":"Yamagishi, Shuntaro","last_name":"Yamagishi"}],"title":"Arithmetic of higher-dimensional orbifolds and a mixed Waring problem","_id":"9260","status":"public","acknowledgement":"While working on this paper the authors were both supported by EPSRC grant EP/P026710/1, and the second author received additional support from the NWO Veni Grant 016.Veni.192.047. Thanks are due to Marta Pieropan, Arne Smeets and Sho Tanimoto for useful conversations related to this topic, and to the anonymous referee for numerous helpful suggestions.","publication_status":"published","publication_identifier":{"issn":["0025-5874"],"eissn":["1432-1823"]},"project":[{"name":"Between rational and integral points","grant_number":"EP-P026710-2","_id":"26A8D266-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000625573800002"]},"date_published":"2021-03-05T00:00:00Z","scopus_import":"1","date_created":"2021-03-21T23:01:21Z","department":[{"_id":"TiBr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":"       299","publisher":"Springer Nature","year":"2021","oa":1,"article_type":"original","page":"1071–1101","publication":"Mathematische Zeitschrift","date_updated":"2023-08-07T14:20:00Z"},{"date_created":"2021-03-22T07:14:03Z","date_published":"2021-03-19T00:00:00Z","external_id":{"pmid":["33741589"],"isi":["000633443000011"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CampIT"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"American Association for the Advancement of Science","intvolume":"         7","year":"2021","oa":1,"article_number":"eabd9153","article_type":"original","date_updated":"2023-08-07T14:20:26Z","publication":"Science Advances","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","month":"03","pmid":1,"file_date_updated":"2021-03-22T12:49:00Z","ddc":["570"],"citation":{"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>.","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>.","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.","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>","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>","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).","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."},"day":"19","volume":7,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"file_name":"2021_ScienceAdv_Mbianda.pdf","file_size":837156,"relation":"main_file","creator":"dernst","success":1,"date_updated":"2021-03-22T12:49:00Z","access_level":"open_access","content_type":"application/pdf","checksum":"737624cd0e630ffa7c52797a690500e3","file_id":"9280","date_created":"2021-03-22T12:49:00Z"}],"doi":"10.1126/sciadv.abd9153","abstract":[{"lang":"eng","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."}],"issue":"12","_id":"9262","title":"Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity","author":[{"first_name":"Johanne","full_name":"Mbianda, Johanne","last_name":"Mbianda"},{"full_name":"Bakail, May M","last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","orcid":"0000-0002-9592-1587"},{"first_name":"Christophe","last_name":"André","full_name":"André, Christophe"},{"full_name":"Moal, Gwenaëlle","last_name":"Moal","first_name":"Gwenaëlle"},{"last_name":"Perrin","full_name":"Perrin, Marie E.","first_name":"Marie E."},{"full_name":"Pinna, Guillaume","last_name":"Pinna","first_name":"Guillaume"},{"first_name":"Raphaël","full_name":"Guerois, Raphaël","last_name":"Guerois"},{"first_name":"Francois","last_name":"Becher","full_name":"Becher, Francois"},{"first_name":"Pierre","full_name":"Legrand, Pierre","last_name":"Legrand"},{"first_name":"Seydou","last_name":"Traoré","full_name":"Traoré, Seydou"},{"last_name":"Douat","full_name":"Douat, Céline","first_name":"Céline"},{"last_name":"Guichard","full_name":"Guichard, Gilles","first_name":"Gilles"},{"first_name":"Françoise","last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise"}],"publication_status":"published","status":"public","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.","publication_identifier":{"issn":["2375-2548"]}},{"date_created":"2021-03-23T05:38:48Z","oa_version":"Preprint","external_id":{"arxiv":["2103.11389"]},"date_published":"2021-03-21T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","citation":{"ista":"Dubach G, Mühlböck F. Formal verification of Zagier’s one-sentence proof. arXiv, 2103.11389.","short":"G. Dubach, F. Mühlböck, ArXiv (n.d.).","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>","ieee":"G. Dubach and F. Mühlböck, “Formal verification of Zagier’s one-sentence proof,” <i>arXiv</i>. .","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>.","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>."},"day":"21","department":[{"_id":"LaEr"},{"_id":"ToHe"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.11389"}],"arxiv":1,"doi":"10.48550/arXiv.2103.11389","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"}],"year":"2021","_id":"9281","oa":1,"title":"Formal verification of Zagier's one-sentence proof","author":[{"first_name":"Guillaume","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","last_name":"Dubach","full_name":"Dubach, Guillaume","orcid":"0000-0001-6892-8137"},{"orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian"}],"article_number":"2103.11389","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"other","id":"9946"}]},"status":"public","publication_status":"submitted","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"date_updated":"2023-05-03T10:26:45Z","publication":"arXiv"}]