[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000624968100103"]},"volume":29,"oa":1,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","project":[{"grant_number":"642841","name":"Distributed 3D Object Design","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"full_name":"Elek, Oskar","last_name":"Elek","first_name":"Oskar"},{"last_name":"Zhang","first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X"},{"full_name":"Sumin, Denis","first_name":"Denis","last_name":"Sumin"},{"first_name":"Karol","last_name":"Myszkowski","full_name":"Myszkowski, Karol"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wilkie, Alexander","last_name":"Wilkie","first_name":"Alexander"},{"full_name":"Křivánek, Jaroslav","last_name":"Křivánek","first_name":"Jaroslav"},{"first_name":"Tim","last_name":"Weyrich","full_name":"Weyrich, Tim"}],"date_created":"2021-03-14T23:01:33Z","publication_identifier":{"eissn":["1094-4087"]},"date_updated":"2025-03-31T15:58:16Z","intvolume":"        29","_id":"9241","year":"2021","date_published":"2021-03-01T00:00:00Z","title":"Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing","month":"03","scopus_import":"1","ec_funded":1,"status":"public","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","publisher":"The Optical Society","has_accepted_license":"1","ddc":["000"],"publication":"Optics Express","type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"BeBi"}],"file":[{"file_size":10873700,"content_type":"application/pdf","success":1,"file_id":"9269","date_updated":"2021-03-22T08:15:28Z","file_name":"2021_OpticsExpress_Elek.pdf","access_level":"open_access","checksum":"a9697ad83136c19ad87e46aa2db63cfd","creator":"dernst","relation":"main_file","date_created":"2021-03-22T08:15:28Z"}],"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.","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>","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>","short":"O. Elek, R. Zhang, D. Sumin, K. Myszkowski, B. Bickel, A. Wilkie, J. Křivánek, T. Weyrich, Optics Express 29 (2021) 7568–7588.","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."},"isi":1,"day":"01","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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.","issue":"5","doi":"10.1364/OE.406095","page":"7568-7588","file_date_updated":"2021-03-22T08:15:28Z"},{"department":[{"_id":"JoFi"}],"publication_status":"published","type":"journal_article","quality_controlled":"1","publication":"Physical Review A","publisher":"American Physical Society","article_number":"023708","doi":"10.1103/PhysRevA.103.023708","issue":"2","acknowledgement":"I thank Prof. Shabir Barzanjeh and Dr. Ulrich Vogl for the fruitful discussions.\r\n","day":"11","isi":1,"citation":{"mla":"Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” <i>Physical Review A</i>, vol. 103, no. 2, 023708, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">10.1103/PhysRevA.103.023708</a>.","ama":"Rueda Sanchez AR. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. <i>Physical Review A</i>. 2021;103(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">10.1103/PhysRevA.103.023708</a>","apa":"Rueda Sanchez, A. R. (2021). Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">https://doi.org/10.1103/PhysRevA.103.023708</a>","chicago":"Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” <i>Physical Review A</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">https://doi.org/10.1103/PhysRevA.103.023708</a>.","ista":"Rueda Sanchez AR. 2021. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. 103(2), 023708.","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.","short":"A.R. Rueda Sanchez, Physical Review A 103 (2021)."},"main_file_link":[{"url":"https://arxiv.org/abs/2010.05356","open_access":"1"}],"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"date_updated":"2023-08-07T14:11:18Z","date_created":"2021-03-14T23:01:33Z","author":[{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"}],"abstract":[{"lang":"eng","text":"In the recent years important experimental advances in resonant electro-optic modulators as high-efficiency sources for coherent frequency combs and as devices for quantum information transfer have been realized, where strong optical and microwave mode coupling were achieved. These features suggest electro-optic-based devices as candidates for entangled optical frequency comb sources. In the present work, I study the generation of entangled optical frequency combs in millimeter-sized resonant electro-optic modulators. These devices profit from the experimentally proven advantages such as nearly constant optical free spectral ranges over several gigahertz, and high optical and microwave quality factors. The generation of frequency multiplexed quantum channels with spectral bandwidth in the MHz range for conservative parameter values paves the way towards novel uses in long-distance hybrid quantum networks, quantum key distribution, enhanced optical metrology, and quantum computing."}],"arxiv":1,"oa_version":"Preprint","external_id":{"isi":["000617037900013"],"arxiv":["2010.05356"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":103,"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","status":"public","date_published":"2021-02-11T00:00:00Z","scopus_import":"1","month":"02","title":"Frequency-multiplexed hybrid optical entangled source based on the Pockels effect","intvolume":"       103","year":"2021","_id":"9242"},{"_id":"9243","year":"2021","intvolume":"        10","title":"Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins","month":"02","scopus_import":"1","date_published":"2021-02-24T00:00:00Z","ec_funded":1,"status":"public","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":10,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000627596400001"]},"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"author":[{"full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora","first_name":"Víctor M."},{"full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","last_name":"Baranova","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Peters, Katharina","first_name":"Katharina","last_name":"Peters"},{"first_name":"Eefjan","last_name":"Breukink","full_name":"Breukink, Eefjan"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"},{"first_name":"Waldemar","last_name":"Vollmer","full_name":"Vollmer, Waldemar"}],"date_created":"2021-03-14T23:01:33Z","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall synthesis","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"date_updated":"2024-10-22T10:04:21Z","publication_identifier":{"eissn":["2050-084X"]},"citation":{"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>","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>","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.","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>.","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.","short":"V.M. Hernández-Rocamora, N.S. Baranova, K. Peters, E. Breukink, M. Loose, W. Vollmer, ELife 10 (2021)."},"isi":1,"day":"24","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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). ","doi":"10.7554/eLife.61525","article_number":"1-32","file_date_updated":"2021-03-22T07:36:08Z","has_accepted_license":"1","publisher":"eLife Sciences Publications","ddc":["570"],"publication":"eLife","quality_controlled":"1","type":"journal_article","publication_status":"published","file":[{"file_id":"9268","success":1,"file_size":2314698,"content_type":"application/pdf","relation":"main_file","date_created":"2021-03-22T07:36:08Z","file_name":"2021_eLife_HernandezRocamora.pdf","date_updated":"2021-03-22T07:36:08Z","checksum":"79897a09bfecd9914d39c4aea2841855","creator":"dernst","access_level":"open_access"}],"department":[{"_id":"MaLo"}]},{"scopus_import":"1","month":"02","title":"Derivation of the Landau–Pekar equations in a many-body mean-field limit","date_published":"2021-02-26T00:00:00Z","year":"2021","_id":"9246","intvolume":"       240","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","ec_funded":1,"oa_version":"Published Version","arxiv":1,"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"}],"volume":240,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["33785964"],"isi":["000622226200001"],"arxiv":["2001.03993"]},"pmid":1,"date_updated":"2025-06-12T06:35:22Z","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"date_created":"2021-03-14T23:01:34Z","author":[{"full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","last_name":"Leopold","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"}],"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s00205-021-01616-9","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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.","isi":1,"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>","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>","ista":"Leopold NK, Mitrouskas DJ, Seiringer R. 2021. Derivation of the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational Mechanics and Analysis. 240, 383–417.","chicago":"Leopold, Nikolai K, David Johannes Mitrouskas, and Robert Seiringer. “Derivation of the Landau–Pekar Equations in a Many-Body Mean-Field Limit.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00205-021-01616-9\">https://doi.org/10.1007/s00205-021-01616-9</a>.","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>.","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."},"file_date_updated":"2021-03-22T08:31:29Z","page":"383-417","ddc":["510"],"publication":"Archive for Rational Mechanics and Analysis","has_accepted_license":"1","publisher":"Springer Nature","file":[{"success":1,"file_id":"9270","content_type":"application/pdf","file_size":558006,"relation":"main_file","date_created":"2021-03-22T08:31:29Z","file_name":"2021_ArchRationalMechAnal_Leopold.pdf","date_updated":"2021-03-22T08:31:29Z","creator":"dernst","checksum":"23449e44dc5132501a5c86e70638800f","access_level":"open_access"}],"department":[{"_id":"RoSe"}],"quality_controlled":"1","publication_status":"published","type":"journal_article"},{"status":"public","article_type":"original","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"_id":"9252","year":"2021","intvolume":"        75","title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model","month":"05","scopus_import":"1","date_published":"2021-05-01T00:00:00Z","author":[{"full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep"},{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"date_created":"2021-03-20T08:22:10Z","date_updated":"2025-06-12T06:35:39Z","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"volume":75,"oa":1,"external_id":{"pmid":["33742441"],"isi":["000636966300001"]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","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"}],"page":"1030-1045","file_date_updated":"2021-08-11T13:39:19Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"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>.","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>","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>","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.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” <i>Evolution</i>, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.","short":"E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045."},"isi":1,"day":"01","acknowledgement":"We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1111/evo.14210","issue":"5","quality_controlled":"1","type":"journal_article","publication_status":"published","corr_author":"1","file":[{"success":1,"file_id":"9886","content_type":"application/pdf","file_size":734102,"relation":"main_file","date_created":"2021-08-11T13:39:19Z","date_updated":"2021-08-11T13:39:19Z","file_name":"2021_Evolution_Szep.pdf","checksum":"b90fb5767d623602046fed03725e16ca","creator":"kschuh","access_level":"open_access"}],"department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"13062","status":"public","relation":"research_data"}]},"has_accepted_license":"1","publisher":"Wiley","ddc":["570"],"publication":"Evolution"},{"status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"9253","year":"2021","scopus_import":"1","month":"03","title":"Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic","date_published":"2021-03-19T00:00:00Z","date_created":"2021-03-21T11:34:07Z","author":[{"full_name":"Heiler, Georg","first_name":"Georg","last_name":"Heiler"},{"first_name":"Tobias","last_name":"Reisch","full_name":"Reisch, Tobias"},{"full_name":"Hurt, Jan","last_name":"Hurt","first_name":"Jan"},{"last_name":"Forghani","first_name":"Mohammad","full_name":"Forghani, Mohammad"},{"full_name":"Omani, Aida","last_name":"Omani","first_name":"Aida"},{"first_name":"Allan","last_name":"Hanbury","full_name":"Hanbury, Allan"},{"id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","first_name":"Farid","last_name":"Karimipour","orcid":"0000-0001-6746-4174","full_name":"Karimipour, Farid"}],"date_updated":"2023-08-07T14:00:13Z","publication_identifier":{"isbn":["9781728162515"]},"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2008.10064"],"isi":["000662554703032"]},"oa_version":"Preprint","arxiv":1,"abstract":[{"text":"In March 2020, the Austrian government introduced a widespread lock-down in response to the COVID-19 pandemic. Based on subjective impressions and anecdotal evidence, Austrian public and private life came to a sudden halt. Here we assess the effect of the lock-down quantitatively for all regions in Austria and present an analysis of daily changes of human mobility throughout Austria using near-real-time anonymized mobile phone data. We describe an efficient data aggregation pipeline and analyze the mobility by quantifying mobile-phone traffic at specific point of interests (POIs), analyzing individual trajectories and investigating the cluster structure of the origin-destination graph. We found a reduction of commuters at Viennese metro stations of over 80% and the number of devices with a radius of gyration of less than 500 m almost doubled. The results of studying crowd-movement behavior highlight considerable changes in the structure of mobility networks, revealed by a higher modularity and an increase from 12 to 20 detected communities. We demonstrate the relevance of mobility data for epidemiological studies by showing a significant correlation of the outflow from the town of Ischgl (an early COVID-19 hotspot) and the reported COVID-19 cases with an 8-day time lag. This research indicates that mobile phone usage data permits the moment-by-moment quantification of mobility behavior for a whole country. We emphasize the need to improve the availability of such data in anonymized form to empower rapid response to combat COVID-19 and future pandemics.","lang":"eng"}],"conference":{"location":"Atlanta, GA, United States","end_date":"2020-12-13","name":"Big Data: International Conference on Big Data","start_date":"2020-12-10"},"page":"3123-3132","day":"19","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/2008.10064","open_access":"1"}],"citation":{"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.","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>","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>","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>.","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.","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>."},"doi":"10.1109/bigdata50022.2020.9378374","quality_controlled":"1","publication_status":"published","type":"conference","department":[{"_id":"HeEd"}],"publisher":"IEEE","publication":"2020 IEEE International Conference on Big Data"},{"file":[{"content_type":"application/pdf","file_size":1360271,"success":1,"file_id":"9274","file_name":"2021_NPJQuantumInformation_Pivoluska.pdf","date_updated":"2021-03-22T11:09:34Z","checksum":"26d3f2a2c8c8fa8c1002028326b45f64","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2021-03-22T11:09:34Z"}],"department":[{"_id":"FyKo"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","ddc":["530"],"publication":"npj Quantum Information","has_accepted_license":"1","publisher":"Springer Nature","file_date_updated":"2021-03-22T11:09:34Z","doi":"10.1038/s41534-021-00387-1","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).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"50","day":"15","isi":1,"citation":{"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>.","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.","apa":"Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia, N. H., … Aguilar, E. A. (2021). Semi-device-independent random number generation with flexible assumptions. <i>Npj Quantum Information</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41534-021-00387-1\">https://doi.org/10.1038/s41534-021-00387-1</a>","ama":"Pivoluska M, Plesch M, Farkas M, et al. Semi-device-independent random number generation with flexible assumptions. <i>npj Quantum Information</i>. 2021;7. doi:<a href=\"https://doi.org/10.1038/s41534-021-00387-1\">10.1038/s41534-021-00387-1</a>","mla":"Pivoluska, Matej, et al. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” <i>Npj Quantum Information</i>, vol. 7, 50, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41534-021-00387-1\">10.1038/s41534-021-00387-1</a>.","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).","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."},"date_updated":"2023-08-07T14:17:26Z","publication_identifier":{"eissn":["2056-6387"]},"date_created":"2021-03-21T23:01:19Z","author":[{"first_name":"Matej","last_name":"Pivoluska","full_name":"Pivoluska, Matej"},{"first_name":"Martin","last_name":"Plesch","full_name":"Plesch, Martin"},{"full_name":"Farkas, Máté","last_name":"Farkas","first_name":"Máté"},{"full_name":"Ruzickova, Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova","first_name":"Natalia"},{"full_name":"Flegel, Clara","first_name":"Clara","last_name":"Flegel"},{"full_name":"Valencia, Natalia Herrera","first_name":"Natalia Herrera","last_name":"Valencia"},{"full_name":"Mccutcheon, Will","first_name":"Will","last_name":"Mccutcheon"},{"last_name":"Malik","first_name":"Mehul","full_name":"Malik, Mehul"},{"first_name":"Edgar A.","last_name":"Aguilar","full_name":"Aguilar, Edgar A."}],"oa_version":"Published Version","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."}],"oa":1,"volume":7,"external_id":{"isi":["000629173100001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","month":"03","title":"Semi-device-independent random number generation with flexible assumptions","date_published":"2021-03-15T00:00:00Z","year":"2021","_id":"9255","intvolume":"         7"},{"date_updated":"2025-05-14T10:58:42Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"author":[{"orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"King, Ella M.","last_name":"King","first_name":"Ella M."},{"first_name":"Samuel S.","last_name":"Schoenholz","full_name":"Schoenholz, Samuel S."},{"full_name":"Cubuk, Ekin D.","last_name":"Cubuk","first_name":"Ekin D."},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."}],"date_created":"2021-03-21T23:01:20Z","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"oa":1,"volume":118,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"isi":["000627429100097"],"pmid":["33653960"]},"article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","title":"Designing self-assembling kinetics with differentiable statistical physics models","scopus_import":"1","month":"03","date_published":"2021-03-09T00:00:00Z","year":"2021","_id":"9257","intvolume":"       118","file":[{"content_type":"application/pdf","file_size":1047954,"file_id":"9278","success":1,"access_level":"open_access","creator":"dernst","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","file_name":"2021_PNAS_Goodrich.pdf","date_updated":"2021-03-22T12:23:54Z","date_created":"2021-03-22T12:23:54Z","relation":"main_file"}],"department":[{"_id":"CaGo"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","ddc":["530"],"publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","publisher":"National Academy of Sciences","file_date_updated":"2021-03-22T12:23:54Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"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.","doi":"10.1073/pnas.2024083118","issue":"10","article_number":"e2024083118","citation":{"mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>.","apa":"Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., &#38; Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>","ama":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(10). doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>","chicago":"Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>.","ista":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences of the United States of America. 118(10), e2024083118.","ieee":"C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 10. National Academy of Sciences, 2021.","short":"C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences of the United States of America 118 (2021)."},"isi":1,"day":"09"},{"department":[{"_id":"JoDa"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","publication":"Nature Methods","publisher":"Springer Nature","page":"226-228","issue":"3","doi":"10.1038/s41592-021-01087-6","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.","isi":1,"day":"01","citation":{"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.","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.","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>.","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>","ama":"Pinkard H, Stuurman N, Ivanov IE, et al. Pycro-Manager: Open-source software for customized and reproducible microscope control. <i>Nature Methods</i>. 2021;18(3):226-228. doi:<a href=\"https://doi.org/10.1038/s41592-021-01087-6\">10.1038/s41592-021-01087-6</a>","chicago":"Pinkard, Henry, Nico Stuurman, Ivan E. Ivanov, Nicholas M. Anthony, Wei Ouyang, Bin Li, Bin Yang, et al. “Pycro-Manager: Open-Source Software for Customized and Reproducible Microscope Control.” <i>Nature Methods</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41592-021-01087-6\">https://doi.org/10.1038/s41592-021-01087-6</a>.","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."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-021-01087-6"}],"date_updated":"2023-08-07T14:19:08Z","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"date_created":"2021-03-21T23:01:20Z","author":[{"last_name":"Pinkard","first_name":"Henry","full_name":"Pinkard, Henry"},{"full_name":"Stuurman, Nico","last_name":"Stuurman","first_name":"Nico"},{"last_name":"Ivanov","first_name":"Ivan E.","full_name":"Ivanov, Ivan E."},{"first_name":"Nicholas M.","last_name":"Anthony","full_name":"Anthony, Nicholas M."},{"first_name":"Wei","last_name":"Ouyang","full_name":"Ouyang, Wei"},{"full_name":"Li, Bin","last_name":"Li","first_name":"Bin"},{"first_name":"Bin","last_name":"Yang","full_name":"Yang, Bin"},{"first_name":"Mark A.","last_name":"Tsuchida","full_name":"Tsuchida, Mark A."},{"full_name":"Chhun, Bryant","last_name":"Chhun","first_name":"Bryant"},{"full_name":"Zhang, Grace","first_name":"Grace","last_name":"Zhang"},{"full_name":"Mei, Ryan","first_name":"Ryan","last_name":"Mei"},{"full_name":"Anderson, Michael","first_name":"Michael","last_name":"Anderson"},{"full_name":"Shepherd, Douglas P.","first_name":"Douglas P.","last_name":"Shepherd"},{"full_name":"Hunt-Isaak, Ian","last_name":"Hunt-Isaak","first_name":"Ian"},{"full_name":"Dunn, Raymond L.","last_name":"Dunn","first_name":"Raymond L."},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","first_name":"Wiebke","full_name":"Jahr, Wiebke"},{"first_name":"Saul","last_name":"Kato","full_name":"Kato, Saul"},{"first_name":"Loïc A.","last_name":"Royer","full_name":"Royer, Loïc A."},{"last_name":"Thiagarajah","first_name":"Jay R.","full_name":"Thiagarajah, Jay R."},{"first_name":"Kevin W.","last_name":"Eliceiri","full_name":"Eliceiri, Kevin W."},{"full_name":"Lundberg, Emma","first_name":"Emma","last_name":"Lundberg"},{"first_name":"Shalin B.","last_name":"Mehta","full_name":"Mehta, Shalin B."},{"full_name":"Waller, Laura","first_name":"Laura","last_name":"Waller"}],"oa_version":"Published Version","oa":1,"volume":18,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"external_id":{"isi":["000625600600007"],"pmid":["33674797"]},"article_processing_charge":"No","article_type":"letter_note","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","month":"03","title":"Pycro-Manager: Open-source software for customized and reproducible microscope control","date_published":"2021-03-01T00:00:00Z","_id":"9258","year":"2021","intvolume":"        18"},{"corr_author":"1","file":[{"content_type":"application/pdf","file_size":3740146,"success":1,"file_id":"9277","creator":"dernst","access_level":"open_access","checksum":"663f5a48375e42afa4bfef58d42ec186","file_name":"2021_FrontiersImmumo_Vaahtomeri.pdf","date_updated":"2021-03-22T12:08:26Z","date_created":"2021-03-22T12:08:26Z","relation":"main_file"}],"department":[{"_id":"MiSi"},{"_id":"Bio"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","ddc":["570"],"publication":"Frontiers in Immunology","has_accepted_license":"1","publisher":"Frontiers","file_date_updated":"2021-03-22T12:08:26Z","doi":"10.3389/fimmu.2021.630002","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.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"630002","day":"25","isi":1,"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>.","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>","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>","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>.","ista":"Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. 2021. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. 12, 630002.","ieee":"K. Vaahtomeri, C. Moussion, R. Hauschild, and M. K. Sixt, “Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium,” <i>Frontiers in Immunology</i>, vol. 12. Frontiers, 2021.","short":"K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology 12 (2021)."},"date_updated":"2025-04-14T07:42:07Z","publication_identifier":{"eissn":["1664-3224"]},"date_created":"2021-03-21T23:01:20Z","author":[{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari"},{"full_name":"Moussion, Christine","last_name":"Moussion","first_name":"Christine","id":"3356F664-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"project":[{"name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"Y 564-B12"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":12,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["33717158"],"isi":["000627134400001"]},"pmid":1,"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","ec_funded":1,"scopus_import":"1","month":"02","title":"Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium","date_published":"2021-02-25T00:00:00Z","_id":"9259","year":"2021","intvolume":"        12"},{"file_date_updated":"2021-03-22T12:41:26Z","page":"1071–1101","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.","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s00209-021-02695-w","citation":{"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>.","ista":"Browning TD, Yamagishi S. 2021. Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. Mathematische Zeitschrift. 299, 1071–1101.","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>.","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>","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>","short":"T.D. Browning, S. Yamagishi, Mathematische Zeitschrift 299 (2021) 1071–1101.","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."},"isi":1,"day":"05","file":[{"file_id":"9279","success":1,"file_size":492685,"content_type":"application/pdf","date_created":"2021-03-22T12:41:26Z","relation":"main_file","access_level":"open_access","creator":"dernst","checksum":"8ed9f49568806894744096dbbca0ad7b","date_updated":"2021-03-22T12:41:26Z","file_name":"2021_MathZeitschrift_Browning.pdf"}],"department":[{"_id":"TiBr"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","publication":"Mathematische Zeitschrift","ddc":["510"],"has_accepted_license":"1","publisher":"Springer Nature","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","title":"Arithmetic of higher-dimensional orbifolds and a mixed Waring problem","scopus_import":"1","month":"03","date_published":"2021-03-05T00:00:00Z","year":"2021","_id":"9260","intvolume":"       299","date_updated":"2025-04-14T09:25:44Z","publication_identifier":{"issn":["0025-5874"],"eissn":["1432-1823"]},"author":[{"last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177"},{"last_name":"Yamagishi","first_name":"Shuntaro","full_name":"Yamagishi, Shuntaro"}],"date_created":"2021-03-21T23:01:21Z","project":[{"_id":"26A8D266-B435-11E9-9278-68D0E5697425","name":"Between rational and integral points","grant_number":"EP-P026710-2"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"oa":1,"volume":299,"external_id":{"isi":["000625573800002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_published":"2021-03-19T00:00:00Z","title":"Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity","month":"03","intvolume":"         7","year":"2021","_id":"9262","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","status":"public","abstract":[{"text":"Sequence-specific oligomers with predictable folding patterns, i.e., foldamers, provide new opportunities to mimic α-helical peptides and design inhibitors of protein-protein interactions. One major hurdle of this strategy is to retain the correct orientation of key side chains involved in protein surface recognition. Here, we show that the structural plasticity of a foldamer backbone may notably contribute to the required spatial adjustment for optimal interaction with the protein surface. By using oligoureas as α helix mimics, we designed a foldamer/peptide hybrid inhibitor of histone chaperone ASF1, a key regulator of chromatin dynamics. The crystal structure of its complex with ASF1 reveals a notable plasticity of the urea backbone, which adapts to the ASF1 surface to maintain the same binding interface. One additional benefit of generating ASF1 ligands with nonpeptide oligourea segments is the resistance to proteolysis in human plasma, which was highly improved compared to the cognate α-helical peptide.","lang":"eng"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"external_id":{"pmid":["33741589"],"isi":["000633443000011"]},"volume":7,"oa":1,"publication_identifier":{"issn":["2375-2548"]},"date_updated":"2023-08-07T14:20:26Z","author":[{"full_name":"Mbianda, Johanne","first_name":"Johanne","last_name":"Mbianda"},{"orcid":"0000-0002-9592-1587","full_name":"Bakail, May M","first_name":"May M","last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E"},{"full_name":"André, Christophe","first_name":"Christophe","last_name":"André"},{"full_name":"Moal, Gwenaëlle","first_name":"Gwenaëlle","last_name":"Moal"},{"first_name":"Marie E.","last_name":"Perrin","full_name":"Perrin, Marie E."},{"full_name":"Pinna, Guillaume","first_name":"Guillaume","last_name":"Pinna"},{"full_name":"Guerois, Raphaël","first_name":"Raphaël","last_name":"Guerois"},{"last_name":"Becher","first_name":"Francois","full_name":"Becher, Francois"},{"last_name":"Legrand","first_name":"Pierre","full_name":"Legrand, Pierre"},{"last_name":"Traoré","first_name":"Seydou","full_name":"Traoré, Seydou"},{"full_name":"Douat, Céline","last_name":"Douat","first_name":"Céline"},{"full_name":"Guichard, Gilles","last_name":"Guichard","first_name":"Gilles"},{"full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein","first_name":"Françoise"}],"date_created":"2021-03-22T07:14:03Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","article_number":"eabd9153","tmp":{"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)","short":"CC BY-NC (4.0)"},"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.","issue":"12","doi":"10.1126/sciadv.abd9153","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>.","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.","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>.","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>","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>","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).","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."},"isi":1,"day":"19","file_date_updated":"2021-03-22T12:49:00Z","publication":"Science Advances","ddc":["570"],"publisher":"American Association for the Advancement of Science","has_accepted_license":"1","department":[{"_id":"CampIT"}],"file":[{"checksum":"737624cd0e630ffa7c52797a690500e3","access_level":"open_access","creator":"dernst","date_updated":"2021-03-22T12:49:00Z","file_name":"2021_ScienceAdv_Mbianda.pdf","date_created":"2021-03-22T12:49:00Z","relation":"main_file","file_size":837156,"content_type":"application/pdf","success":1,"file_id":"9280"}],"type":"journal_article","publication_status":"published","quality_controlled":"1"},{"author":[{"full_name":"Dubach, Guillaume","orcid":"0000-0001-6892-8137","last_name":"Dubach","first_name":"Guillaume","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E"},{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","first_name":"Fabian","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177"}],"date_created":"2021-03-23T05:38:48Z","type":"preprint","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"submitted","date_updated":"2025-04-15T06:26:12Z","corr_author":"1","department":[{"_id":"LaEr"},{"_id":"ToHe"}],"oa":1,"related_material":{"record":[{"relation":"other","status":"public","id":"9946"}]},"external_id":{"arxiv":["2103.11389"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"publication":"arXiv","ec_funded":1,"status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"9281","year":"2021","citation":{"mla":"Dubach, Guillaume, and Fabian Mühlböck. “Formal Verification of Zagier’s One-Sentence Proof.” <i>ArXiv</i>, 2103.11389, doi:<a href=\"https://doi.org/10.48550/arXiv.2103.11389\">10.48550/arXiv.2103.11389</a>.","ama":"Dubach G, Mühlböck F. Formal verification of Zagier’s one-sentence proof. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2103.11389\">10.48550/arXiv.2103.11389</a>","apa":"Dubach, G., &#38; Mühlböck, F. (n.d.). Formal verification of Zagier’s one-sentence proof. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2103.11389\">https://doi.org/10.48550/arXiv.2103.11389</a>","ista":"Dubach G, Mühlböck F. Formal verification of Zagier’s one-sentence proof. arXiv, 2103.11389.","chicago":"Dubach, Guillaume, and Fabian Mühlböck. “Formal Verification of Zagier’s One-Sentence Proof.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2103.11389\">https://doi.org/10.48550/arXiv.2103.11389</a>.","ieee":"G. Dubach and F. Mühlböck, “Formal verification of Zagier’s one-sentence proof,” <i>arXiv</i>. .","short":"G. Dubach, F. Mühlböck, ArXiv (n.d.)."},"main_file_link":[{"url":"https://arxiv.org/abs/2103.11389","open_access":"1"}],"day":"21","title":"Formal verification of Zagier's one-sentence proof","doi":"10.48550/arXiv.2103.11389","month":"03","date_published":"2021-03-21T00:00:00Z","article_number":"2103.11389"},{"publication_identifier":{"issn":["2053-1583"]},"date_updated":"2021-12-01T10:36:56Z","author":[{"last_name":"Nauman","first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846"},{"full_name":"Kiem, Do Hoon","first_name":"Do Hoon","last_name":"Kiem"},{"last_name":"Lee","first_name":"Sungmin","full_name":"Lee, Sungmin"},{"last_name":"Son","first_name":"Suhan","full_name":"Son, Suhan"},{"full_name":"Park, J-G","first_name":"J-G","last_name":"Park"},{"full_name":"Kang, Woun","first_name":"Woun","last_name":"Kang"},{"full_name":"Han, Myung Joon","first_name":"Myung Joon","last_name":"Han"},{"first_name":"Youn Jung","last_name":"Jo","full_name":"Jo, Youn Jung"}],"date_created":"2021-03-23T07:10:17Z","abstract":[{"lang":"eng","text":"Several Ising-type magnetic van der Waals (vdW) materials exhibit stable magnetic ground states. Despite these clear experimental demonstrations, a complete theoretical and microscopic understanding of their magnetic anisotropy is still lacking. In particular, the validity limit of identifying their one-dimensional (1-D) Ising nature has remained uninvestigated in a quantitative way. Here we performed the complete mapping of magnetic anisotropy for a prototypical Ising vdW magnet FePS3 for the first time. Combining torque magnetometry measurements with their magnetostatic model analysis and the relativistic density functional total energy calculations, we successfully constructed the three-dimensional (3-D) mappings of the magnetic anisotropy in terms of magnetic torque and energy. The results not only quantitatively confirm that the easy axis is perpendicular to the ab plane, but also reveal the anisotropies within the ab, ac, and bc planes. Our approach can be applied to the detailed quantitative study of magnetism in vdW materials."}],"arxiv":1,"oa_version":"Preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["2103.09029"]},"volume":8,"oa":1,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","status":"public","date_published":"2021-04-06T00:00:00Z","title":"Complete mapping of magnetic anisotropy for prototype Ising van der Waals FePS3","extern":"1","month":"04","intvolume":"         8","year":"2021","_id":"9282","department":[{"_id":"KiMo"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","publication":"2D Materials","publisher":"IOP Publishing","keyword":["Mechanical Engineering","General Materials Science","Mechanics of Materials","General Chemistry","Condensed Matter Physics"],"article_number":"035011","issue":"3","doi":"10.1088/2053-1583/abeed3","main_file_link":[{"url":"https://arxiv.org/abs/2103.09029","open_access":"1"}],"citation":{"short":"M. Nauman, D.H. Kiem, S. Lee, S. Son, J.-G. Park, W. Kang, M.J. Han, Y.J. Jo, 2D Materials 8 (2021).","ieee":"M. Nauman <i>et al.</i>, “Complete mapping of magnetic anisotropy for prototype Ising van der Waals FePS3,” <i>2D Materials</i>, vol. 8, no. 3. IOP Publishing, 2021.","chicago":"Nauman, Muhammad, Do Hoon Kiem, Sungmin Lee, Suhan Son, J-G Park, Woun Kang, Myung Joon Han, and Youn Jung Jo. “Complete Mapping of Magnetic Anisotropy for Prototype Ising van Der Waals FePS3.” <i>2D Materials</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/2053-1583/abeed3\">https://doi.org/10.1088/2053-1583/abeed3</a>.","ista":"Nauman M, Kiem DH, Lee S, Son S, Park J-G, Kang W, Han MJ, Jo YJ. 2021. Complete mapping of magnetic anisotropy for prototype Ising van der Waals FePS3. 2D Materials. 8(3), 035011.","apa":"Nauman, M., Kiem, D. H., Lee, S., Son, S., Park, J.-G., Kang, W., … Jo, Y. J. (2021). Complete mapping of magnetic anisotropy for prototype Ising van der Waals FePS3. <i>2D Materials</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2053-1583/abeed3\">https://doi.org/10.1088/2053-1583/abeed3</a>","ama":"Nauman M, Kiem DH, Lee S, et al. Complete mapping of magnetic anisotropy for prototype Ising van der Waals FePS3. <i>2D Materials</i>. 2021;8(3). doi:<a href=\"https://doi.org/10.1088/2053-1583/abeed3\">10.1088/2053-1583/abeed3</a>","mla":"Nauman, Muhammad, et al. “Complete Mapping of Magnetic Anisotropy for Prototype Ising van Der Waals FePS3.” <i>2D Materials</i>, vol. 8, no. 3, 035011, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/2053-1583/abeed3\">10.1088/2053-1583/abeed3</a>."},"day":"06"},{"corr_author":"1","file":[{"content_type":"application/pdf","file_size":1390469,"success":1,"file_id":"9284","date_updated":"2021-03-23T10:12:58Z","file_name":"elife-65993-v2.pdf","access_level":"open_access","checksum":"3c2f44058c2dd45a5a1027f09d263f8e","creator":"bkavcic","relation":"main_file","date_created":"2021-03-23T10:12:58Z"}],"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","ddc":["570"],"publication":"eLife","related_material":{"record":[{"relation":"research_data","id":"8951","status":"public"}]},"has_accepted_license":"1","publisher":"eLife Sciences Publications","keyword":["Genetics and Molecular Biology"],"file_date_updated":"2021-03-23T10:12:58Z","doi":"10.7554/elife.65993","acknowledgement":"We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau, G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and members of the Guet lab for comments. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377 (ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e65993","day":"08","isi":1,"citation":{"mla":"Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>, vol. 10, e65993, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>.","ista":"Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory network. eLife. 10, e65993.","chicago":"Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>.","ama":"Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>","apa":"Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., &#38; Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>","short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).","ieee":"A. A. Nagy-Staron <i>et al.</i>, “Local genetic context shapes the function of a gene regulatory network,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021."},"date_updated":"2025-06-12T06:36:17Z","publication_identifier":{"issn":["2050-084X"]},"date_created":"2021-03-23T10:11:46Z","author":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A"},{"orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","last_name":"Tomasek"},{"last_name":"Caruso Carter","first_name":"Caroline","full_name":"Caruso Carter, Caroline"},{"full_name":"Sonnleitner, Elisabeth","first_name":"Elisabeth","last_name":"Sonnleitner"},{"first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor"},{"full_name":"Paixão, Tiago","first_name":"Tiago","last_name":"Paixão"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"project":[{"_id":"2517526A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","grant_number":"628377"},{"name":"Cybergenetic circuits to test composability of gene networks","grant_number":"I03901","_id":"268BFA92-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"Published Version","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs.","lang":"eng"}],"oa":1,"volume":10,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000631050900001"],"pmid":["33683203"]},"pmid":1,"article_processing_charge":"Yes","article_type":"original","language":[{"iso":"eng"}],"status":"public","ec_funded":1,"scopus_import":"1","month":"03","title":"Local genetic context shapes the function of a gene regulatory network","date_published":"2021-03-08T00:00:00Z","year":"2021","_id":"9283","intvolume":"        10"},{"intvolume":"        33","year":"2021","_id":"9285","date_published":"2021-02-01T00:00:00Z","title":"Justifying Kubo’s formula for gapped systems at zero temperature: A brief review and some new results","month":"02","scopus_import":"1","extern":"1","status":"public","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2002.08669"]},"volume":33,"oa":1,"abstract":[{"lang":"eng","text":"We first review the problem of a rigorous justification of Kubo’s formula for transport coefficients in gapped extended Hamiltonian quantum systems at zero temperature. In particular, the theoretical understanding of the quantum Hall effect rests on the validity of Kubo’s formula for such systems, a connection that we review briefly as well. We then highlight an approach to linear response theory based on non-equilibrium almost-stationary states (NEASS) and on a corresponding adiabatic theorem for such systems that was recently proposed and worked out by one of us in [51] for interacting fermionic systems on finite lattices. In the second part of our paper, we show how to lift the results of [51] to infinite systems by taking a thermodynamic limit."}],"oa_version":"Preprint","arxiv":1,"author":[{"orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha","first_name":"Sven Joscha","last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"},{"full_name":"Teufel, Stefan","first_name":"Stefan","last_name":"Teufel"}],"date_created":"2021-03-26T11:29:46Z","publication_identifier":{"issn":["0129-055X","1793-6659"]},"date_updated":"2023-02-23T13:53:59Z","citation":{"ieee":"S. J. Henheik and S. Teufel, “Justifying Kubo’s formula for gapped systems at zero temperature: A brief review and some new results,” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 01. World Scientific Publishing, 2021.","short":"S.J. Henheik, S. Teufel, Reviews in Mathematical Physics 33 (2021).","apa":"Henheik, S. J., &#38; Teufel, S. (2021). Justifying Kubo’s formula for gapped systems at zero temperature: A brief review and some new results. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0129055x20600041\">https://doi.org/10.1142/s0129055x20600041</a>","ama":"Henheik SJ, Teufel S. Justifying Kubo’s formula for gapped systems at zero temperature: A brief review and some new results. <i>Reviews in Mathematical Physics</i>. 2021;33(01). doi:<a href=\"https://doi.org/10.1142/s0129055x20600041\">10.1142/s0129055x20600041</a>","chicago":"Henheik, Sven Joscha, and Stefan Teufel. “Justifying Kubo’s Formula for Gapped Systems at Zero Temperature: A Brief Review and Some New Results.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2021. <a href=\"https://doi.org/10.1142/s0129055x20600041\">https://doi.org/10.1142/s0129055x20600041</a>.","ista":"Henheik SJ, Teufel S. 2021. Justifying Kubo’s formula for gapped systems at zero temperature: A brief review and some new results. Reviews in Mathematical Physics. 33(01), 2060004.","mla":"Henheik, Sven Joscha, and Stefan Teufel. “Justifying Kubo’s Formula for Gapped Systems at Zero Temperature: A Brief Review and Some New Results.” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 01, 2060004, World Scientific Publishing, 2021, doi:<a href=\"https://doi.org/10.1142/s0129055x20600041\">10.1142/s0129055x20600041</a>."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.08669"}],"day":"01","article_number":"2060004","doi":"10.1142/s0129055x20600041","issue":"01","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"publisher":"World Scientific Publishing","has_accepted_license":"1","publication":"Reviews in Mathematical Physics","ddc":["500"],"type":"journal_article","publication_status":"published","quality_controlled":"1"},{"publication":"New Phytologist","publisher":"Wiley","department":[{"_id":"JiFr"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","doi":"10.1111/nph.17349","issue":"6","day":"17","isi":1,"citation":{"ieee":"I. El Houari <i>et al.</i>, “Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport,” <i>New Phytologist</i>, vol. 230, no. 6. Wiley, pp. 2275–2291, 2021.","short":"I. El Houari, C. Van Beirs, H. Arents, H. Han, A. Chanoca, D. Opdenacker, J. Pollier, V. Storme, W. Steenackers, M. Quareshy, R. Napier, T. Beeckman, J. Friml, B. De Rybel, W. Boerjan, B. Vanholme, New Phytologist 230 (2021) 2275–2291.","mla":"El Houari, I., et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” <i>New Phytologist</i>, vol. 230, no. 6, Wiley, 2021, pp. 2275–91, doi:<a href=\"https://doi.org/10.1111/nph.17349\">10.1111/nph.17349</a>.","apa":"El Houari, I., Van Beirs, C., Arents, H., Han, H., Chanoca, A., Opdenacker, D., … Vanholme, B. (2021). Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17349\">https://doi.org/10.1111/nph.17349</a>","ama":"El Houari I, Van Beirs C, Arents H, et al. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. <i>New Phytologist</i>. 2021;230(6):2275-2291. doi:<a href=\"https://doi.org/10.1111/nph.17349\">10.1111/nph.17349</a>","chicago":"El Houari, I, C Van Beirs, HE Arents, Huibin Han, A Chanoca, D Opdenacker, J Pollier, et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17349\">https://doi.org/10.1111/nph.17349</a>.","ista":"El Houari I, Van Beirs C, Arents H, Han H, Chanoca A, Opdenacker D, Pollier J, Storme V, Steenackers W, Quareshy M, Napier R, Beeckman T, Friml J, De Rybel B, Boerjan W, Vanholme B. 2021. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. 230(6), 2275–2291."},"main_file_link":[{"url":"https://biblio.ugent.be/publication/8703799/file/8703800.pdf","open_access":"1"}],"page":"2275-2291","oa_version":"Published Version","abstract":[{"text":"• The phenylpropanoid pathway serves a central role in plant metabolism, providing numerous compounds involved in diverse physiological processes. Most carbon entering the pathway is incorporated into lignin. Although several phenylpropanoid pathway mutants show seedling growth arrest, the role for lignin in seedling growth and development is unexplored.\r\n• We use complementary pharmacological and genetic approaches to block CINNAMATE‐4‐HYDROXYLASE (C4H) functionality in Arabidopsis seedlings and a set of molecular and biochemical techniques to investigate the underlying phenotypes.\r\n• Blocking C4H resulted in reduced lateral rooting and increased adventitious rooting apically in the hypocotyl. These phenotypes coincided with an inhibition in auxin transport. The upstream accumulation in cis‐cinnamic acid was found to likely cause polar auxin transport inhibition. Conversely, a downstream depletion in lignin perturbed phloem‐mediated auxin transport. Restoring lignin deposition effectively reestablished phloem transport and, accordingly, auxin homeostasis.\r\n• Our results show that the accumulation of bioactive intermediates and depletion in lignin jointly cause the aberrant phenotypes upon blocking C4H, and demonstrate that proper deposition of lignin is essential for the establishment of auxin distribution in seedlings. Our data position the phenylpropanoid pathway and lignin in a new physiological framework, consolidating their importance in plant growth and development.","lang":"eng"}],"volume":230,"oa":1,"pmid":1,"external_id":{"pmid":["33728703"],"isi":["000639552400001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-05T15:46:55Z","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"date_created":"2021-03-26T12:09:01Z","author":[{"full_name":"El Houari, I","last_name":"El Houari","first_name":"I"},{"last_name":"Van Beirs","first_name":"C","full_name":"Van Beirs, C"},{"first_name":"HE","last_name":"Arents","full_name":"Arents, HE"},{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"last_name":"Chanoca","first_name":"A","full_name":"Chanoca, A"},{"full_name":"Opdenacker, D","last_name":"Opdenacker","first_name":"D"},{"first_name":"J","last_name":"Pollier","full_name":"Pollier, J"},{"last_name":"Storme","first_name":"V","full_name":"Storme, V"},{"last_name":"Steenackers","first_name":"W","full_name":"Steenackers, W"},{"full_name":"Quareshy, M","last_name":"Quareshy","first_name":"M"},{"full_name":"Napier, R","first_name":"R","last_name":"Napier"},{"full_name":"Beeckman, T","first_name":"T","last_name":"Beeckman"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"},{"last_name":"De Rybel","first_name":"B","full_name":"De Rybel, B"},{"full_name":"Boerjan, W","first_name":"W","last_name":"Boerjan"},{"full_name":"Vanholme, B","last_name":"Vanholme","first_name":"B"}],"scopus_import":"1","month":"03","title":"Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport","date_published":"2021-03-17T00:00:00Z","year":"2021","_id":"9288","intvolume":"       230","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public"},{"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"date_updated":"2025-04-14T07:45:00Z","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc"},{"full_name":"Van Gelderen, K","last_name":"Van Gelderen","first_name":"K"},{"first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang"},{"full_name":"Naramoto, S","last_name":"Naramoto","first_name":"S"},{"first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"full_name":"Domjan, David","orcid":"0000-0003-2267-106X","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","last_name":"Domjan","first_name":"David"},{"first_name":"L","last_name":"Vcelarova","full_name":"Vcelarova, L"},{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"de Koning, E","last_name":"de Koning","first_name":"E"},{"full_name":"van Dop, M","first_name":"M","last_name":"van Dop"},{"full_name":"Rademacher, E","last_name":"Rademacher","first_name":"E"},{"full_name":"Janson, S","last_name":"Janson","first_name":"S"},{"full_name":"Wei, X","first_name":"X","last_name":"Wei"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"first_name":"B","last_name":"De Rybel","full_name":"De Rybel, B"},{"first_name":"R","last_name":"Offringa","full_name":"Offringa, R"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"date_created":"2021-03-26T12:09:33Z","abstract":[{"lang":"eng","text":"Polar subcellular localization of the PIN exporters of the phytohormone auxin is a key determinant of directional, intercellular auxin transport and thus a central topic of both plant cell and developmental biology. Arabidopsis mutants lacking PID, a kinase that phosphorylates PINs, or the MAB4/MEL proteins of unknown molecular function display PIN polarity defects and phenocopy pin mutants, but mechanistic insights into how these factors convey PIN polarity are missing. Here, by combining protein biochemistry with quantitative live-cell imaging, we demonstrate that PINs, MAB4/MELs, and AGC kinases interact in the same complex at the plasma membrane. MAB4/MELs are recruited to the plasma membrane by the PINs and in concert with the AGC kinases maintain PIN polarity through limiting lateral diffusion-based escape of PINs from the polar domain. The PIN-MAB4/MEL-PID protein complex has self-reinforcing properties thanks to positive feedback between AGC kinase-mediated PIN phosphorylation and MAB4/MEL recruitment. We thus uncover the molecular mechanism by which AGC kinases and MAB4/MEL proteins regulate PIN localization and plant development."}],"oa_version":"Published Version","external_id":{"isi":["000653077800004"],"pmid":["33705718"]},"pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"volume":31,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","ec_funded":1,"status":"public","date_published":"2021-03-10T00:00:00Z","title":"AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells","scopus_import":"1","month":"03","intvolume":"        31","year":"2021","_id":"9290","department":[{"_id":"JiFr"}],"file":[{"content_type":"application/pdf","file_size":4324371,"file_id":"9303","success":1,"file_name":"2021_CurrentBiology_Glanc.pdf","date_updated":"2021-04-01T10:53:42Z","access_level":"open_access","creator":"dernst","checksum":"b1723040ecfd8c81194185472eb62546","relation":"main_file","date_created":"2021-04-01T10:53:42Z"}],"corr_author":"1","type":"journal_article","publication_status":"published","quality_controlled":"1","publication":"Current Biology","ddc":["580"],"publisher":"Elsevier","has_accepted_license":"1","file_date_updated":"2021-04-01T10:53:42Z","page":"1918-1930","acknowledgement":"We acknowledge Ben Scheres, Christian Luschnig, and Claus Schwechheimer for sharing published material. We thank Monika Hrtyan and Dorota Jaworska at IST Austria and Gerda Lamers and Ward de Winter at IBL Netherlands for technical assistance; Corinna Hartinger, Jakub Hajný, Lesia Rodriguez, Mingyue Li, and Lindy Abas for experimental support; and the Bioimaging Facility at IST Austria and the Bioimaging Core at VIB for imaging support. We are grateful to Christian Luschnig, Lindy Abas, and Roman Pleskot for valuable discussions. We also acknowledge the EMBO for supporting M.G. with a long-term fellowship ( ALTF 1005-2019 ) during the finalization and revision of this manuscript in the laboratory of B.D.R., and we thank R. Pierik for allowing K.V.G. to work on this manuscript during a postdoc in his laboratory at Utrecht University. This work was supported by grants from the European Research Council under the European Union’s Seventh Framework Programme (ERC grant agreements 742985 to J.F., 714055 to B.D.R., and 803048 to M.F.), the Austrian Science Fund (FWF; I 3630-B25 to J.F.), Chemical Sciences (partly) financed by the Dutch Research Council (NWO-CW TOP 700.58.301 to R.O.), the Dutch Research Council (NWO-VICI 865.17.002 to R. Pierik), Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology, Japan (KAKENHI grant 17K17595 to S.N.), the Ministry of Education, Youth and Sports of the Czech Republic (MŠMT project NPUI-LO1417 ), and a China Scholarship Council (to X.W.).","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.cub.2021.02.028","acknowledged_ssus":[{"_id":"Bio"}],"issue":"9","citation":{"chicago":"Glanc, Matous, K Van Gelderen, Lukas Hörmayer, Shutang Tan, S Naramoto, Xixi Zhang, David Domjan, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.02.028\">https://doi.org/10.1016/j.cub.2021.02.028</a>.","ista":"Glanc M, Van Gelderen K, Hörmayer L, Tan S, Naramoto S, Zhang X, Domjan D, Vcelarova L, Hauschild R, Johnson AJ, de Koning E, van Dop M, Rademacher E, Janson S, Wei X, Molnar G, Fendrych M, De Rybel B, Offringa R, Friml J. 2021. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 31(9), 1918–1930.","apa":"Glanc, M., Van Gelderen, K., Hörmayer, L., Tan, S., Naramoto, S., Zhang, X., … Friml, J. (2021). AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2021.02.028\">https://doi.org/10.1016/j.cub.2021.02.028</a>","ama":"Glanc M, Van Gelderen K, Hörmayer L, et al. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. <i>Current Biology</i>. 2021;31(9):1918-1930. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.028\">10.1016/j.cub.2021.02.028</a>","mla":"Glanc, Matous, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” <i>Current Biology</i>, vol. 31, no. 9, Elsevier, 2021, pp. 1918–30, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.028\">10.1016/j.cub.2021.02.028</a>.","short":"M. Glanc, K. Van Gelderen, L. Hörmayer, S. Tan, S. Naramoto, X. Zhang, D. Domjan, L. Vcelarova, R. Hauschild, A.J. Johnson, E. de Koning, M. van Dop, E. Rademacher, S. Janson, X. Wei, G. Molnar, M. Fendrych, B. De Rybel, R. Offringa, J. Friml, Current Biology 31 (2021) 1918–1930.","ieee":"M. Glanc <i>et al.</i>, “AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells,” <i>Current Biology</i>, vol. 31, no. 9. Elsevier, pp. 1918–1930, 2021."},"isi":1,"day":"10"},{"oa":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","ddc":["530"],"abstract":[{"lang":"eng","text":"This .zip File contains the transport data for figures presented in the main text and supplementary material of \"Enhancement of Proximity Induced Superconductivity in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html)."}],"date_created":"2021-03-27T13:47:49Z","author":[{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","file":[{"access_level":"open_access","checksum":"635df3c08fc13c3dac008cd421aefbe4","creator":"gkatsaro","date_updated":"2021-03-27T13:46:17Z","file_name":"Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip","date_created":"2021-03-27T13:46:17Z","relation":"main_file","content_type":"application/x-zip-compressed","file_size":10616071,"file_id":"9292","success":1},{"checksum":"12b3ca69ae7509a346711baae0b02a75","creator":"dernst","access_level":"open_access","date_updated":"2021-04-01T07:52:56Z","file_name":"README.txt","date_created":"2021-04-01T07:52:56Z","relation":"main_file","content_type":"text/plain","file_size":470,"success":1,"file_id":"9302"}],"date_updated":"2024-02-21T12:37:14Z","department":[{"_id":"GeKa"}],"day":"29","_id":"9291","year":"2021","citation":{"mla":"Katsaros, Georgios. <i>Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9291\">10.15479/AT:ISTA:9291</a>.","ama":"Katsaros G. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9291\">10.15479/AT:ISTA:9291</a>","apa":"Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9291\">https://doi.org/10.15479/AT:ISTA:9291</a>","chicago":"Katsaros, Georgios. “Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9291\">https://doi.org/10.15479/AT:ISTA:9291</a>.","ista":"Katsaros G. 2021. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9291\">10.15479/AT:ISTA:9291</a>.","ieee":"G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium.” Institute of Science and Technology Austria, 2021.","short":"G. Katsaros, (2021)."},"doi":"10.15479/AT:ISTA:9291","month":"03","title":"Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2021-03-29T00:00:00Z","status":"public","article_processing_charge":"No","file_date_updated":"2021-04-01T07:52:56Z"},{"quality_controlled":"1","publication_status":"published","type":"journal_article","corr_author":"1","department":[{"_id":"KrCh"}],"related_material":{"record":[{"id":"35","status":"public","relation":"earlier_version"}]},"publisher":"Elsevier","publication":"Artificial Intelligence","day":"16","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.07031","open_access":"1"}],"citation":{"apa":"Chatterjee, K., Dvořák, W., Henzinger, M., &#38; Svozil, A. (2021). Algorithms and conditional lower bounds for planning problems. <i>Artificial Intelligence</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.artint.2021.103499\">https://doi.org/10.1016/j.artint.2021.103499</a>","ama":"Chatterjee K, Dvořák W, Henzinger M, Svozil A. Algorithms and conditional lower bounds for planning problems. <i>Artificial Intelligence</i>. 2021;297(8). doi:<a href=\"https://doi.org/10.1016/j.artint.2021.103499\">10.1016/j.artint.2021.103499</a>","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” <i>Artificial Intelligence</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.artint.2021.103499\">https://doi.org/10.1016/j.artint.2021.103499</a>.","ista":"Chatterjee K, Dvořák W, Henzinger M, Svozil A. 2021. Algorithms and conditional lower bounds for planning problems. Artificial Intelligence. 297(8), 103499.","mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” <i>Artificial Intelligence</i>, vol. 297, no. 8, 103499, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.artint.2021.103499\">10.1016/j.artint.2021.103499</a>.","ieee":"K. Chatterjee, W. Dvořák, M. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” <i>Artificial Intelligence</i>, vol. 297, no. 8. Elsevier, 2021.","short":"K. Chatterjee, W. Dvořák, M. Henzinger, A. Svozil, Artificial Intelligence 297 (2021)."},"issue":"8","doi":"10.1016/j.artint.2021.103499","article_number":"103499","date_created":"2021-03-28T22:01:40Z","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Dvořák, Wolfgang","last_name":"Dvořák","first_name":"Wolfgang"},{"last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Svozil, Alexander","first_name":"Alexander","last_name":"Svozil"}],"date_updated":"2025-07-10T11:52:31Z","publication_identifier":{"issn":["0004-3702"]},"oa":1,"volume":297,"external_id":{"isi":["000657537500003"],"arxiv":["1804.07031"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","arxiv":1,"abstract":[{"lang":"eng","text":"We consider planning problems for graphs, Markov Decision Processes (MDPs), and games on graphs in an explicit state space. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems with k different target sets: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in a given sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds, based on the boolean matrix multiplication (BMM) conjecture and strong exponential time hypothesis (SETH), establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs, and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) problem-separation results showing that for MDPs the coverage problem is harder than the sequential target problem."}],"status":"public","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"year":"2021","_id":"9293","intvolume":"       297","month":"03","scopus_import":"1","title":"Algorithms and conditional lower bounds for planning problems","date_published":"2021-03-16T00:00:00Z"}]