[{"volume":12,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Hu, Yangjie","last_name":"Hu","first_name":"Yangjie"},{"full_name":"Omary, Moutasem","last_name":"Omary","first_name":"Moutasem"},{"last_name":"Hu","first_name":"Yun","full_name":"Hu, Yun"},{"last_name":"Doron","first_name":"Ohad","full_name":"Doron, Ohad"},{"full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","first_name":"Lukas"},{"first_name":"Qingguo","last_name":"Chen","full_name":"Chen, Qingguo"},{"first_name":"Or","last_name":"Megides","full_name":"Megides, Or"},{"last_name":"Chekli","first_name":"Ori","full_name":"Chekli, Ori"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhao, Yunde","last_name":"Zhao","first_name":"Yunde"},{"full_name":"Tsarfaty, Ilan","last_name":"Tsarfaty","first_name":"Ilan"},{"full_name":"Shani, Eilon","last_name":"Shani","first_name":"Eilon"}],"date_updated":"2023-08-07T14:17:55Z","publication":"Nature Communications","department":[{"_id":"JiFr"}],"intvolume":"        12","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-03-22T11:18:58Z","title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"acknowledgement":"This work was supported by grants from the Israel Science Foundation (2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.), the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships (to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF to I.T.).","article_type":"original","scopus_import":"1","doi":"10.1038/s41467-021-21802-3","file":[{"checksum":"e1022f3aee349853ded2b2b3e092362d","creator":"dernst","file_id":"9275","content_type":"application/pdf","date_updated":"2021-03-22T11:18:58Z","date_created":"2021-03-22T11:18:58Z","relation":"main_file","file_size":8602096,"success":1,"access_level":"open_access","file_name":"2021_NatureComm_Hu.pdf"}],"date_created":"2021-03-21T23:01:19Z","_id":"9254","abstract":[{"text":"Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms.","lang":"eng"}],"citation":{"short":"Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli, Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021).","chicago":"Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-21802-3\">https://doi.org/10.1038/s41467-021-21802-3</a>.","apa":"Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021). Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-21802-3\">https://doi.org/10.1038/s41467-021-21802-3</a>","mla":"Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” <i>Nature Communications</i>, vol. 12, 1657, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-21802-3\">10.1038/s41467-021-21802-3</a>.","ama":"Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-21802-3\">10.1038/s41467-021-21802-3</a>","ista":"Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 12, 1657.","ieee":"Y. Hu <i>et al.</i>, “Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021."},"article_number":"1657","year":"2021","type":"journal_article","external_id":{"isi":["000630419400048"],"pmid":["33712581"]},"date_published":"2021-03-12T00:00:00Z","pmid":1,"publisher":"Springer Nature","status":"public","isi":1,"month":"03","ddc":["580"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1"},{"article_type":"original","publication_identifier":{"eissn":["2056-6387"]},"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).","doi":"10.1038/s41534-021-00387-1","scopus_import":"1","file_date_updated":"2021-03-22T11:09:34Z","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"Semi-device-independent random number generation with flexible assumptions","abstract":[{"lang":"eng","text":"Our ability to trust that a random number is truly random is essential for fields as diverse as cryptography and fundamental tests of quantum mechanics. Existing solutions both come with drawbacks—device-independent quantum random number generators (QRNGs) are highly impractical and standard semi-device-independent QRNGs are limited to a specific physical implementation and level of trust. Here we propose a framework for semi-device-independent randomness certification, using a source of trusted vacuum in the form of a signal shutter. It employs a flexible set of assumptions and levels of trust, allowing it to be applied in a wide range of physical scenarios involving both quantum and classical entropy sources. We experimentally demonstrate our protocol with a photonic setup and generate secure random bits under three different assumptions with varying degrees of security and resulting data rates."}],"year":"2021","article_number":"50","citation":{"ista":"Pivoluska M, Plesch M, Farkas M, Ruzickova N, Flegel C, Valencia NH, Mccutcheon W, Malik M, Aguilar EA. 2021. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 7, 50.","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.","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>.","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>","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).","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>."},"_id":"9255","file":[{"content_type":"application/pdf","creator":"dernst","file_id":"9274","checksum":"26d3f2a2c8c8fa8c1002028326b45f64","file_name":"2021_NPJQuantumInformation_Pivoluska.pdf","success":1,"access_level":"open_access","date_updated":"2021-03-22T11:09:34Z","relation":"main_file","file_size":1360271,"date_created":"2021-03-22T11:09:34Z"}],"date_created":"2021-03-21T23:01:19Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Pivoluska, Matej","last_name":"Pivoluska","first_name":"Matej"},{"last_name":"Plesch","first_name":"Martin","full_name":"Plesch, Martin"},{"last_name":"Farkas","first_name":"Máté","full_name":"Farkas, Máté"},{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia","first_name":"Natalia","last_name":"Ruzickova"},{"full_name":"Flegel, Clara","last_name":"Flegel","first_name":"Clara"},{"first_name":"Natalia Herrera","last_name":"Valencia","full_name":"Valencia, Natalia Herrera"},{"first_name":"Will","last_name":"Mccutcheon","full_name":"Mccutcheon, Will"},{"full_name":"Malik, Mehul","last_name":"Malik","first_name":"Mehul"},{"last_name":"Aguilar","first_name":"Edgar A.","full_name":"Aguilar, Edgar A."}],"oa":1,"volume":7,"intvolume":"         7","publication":"npj Quantum Information","date_updated":"2023-08-07T14:17:26Z","department":[{"_id":"FyKo"}],"day":"15","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","publisher":"Springer Nature","date_published":"2021-03-15T00:00:00Z","external_id":{"isi":["000629173100001"]},"type":"journal_article","language":[{"iso":"eng"}],"ddc":["530"],"status":"public","month":"03","isi":1},{"language":[{"iso":"eng"}],"ddc":["510"],"month":"03","isi":1,"status":"public","publisher":"Springer Nature","date_published":"2021-03-09T00:00:00Z","external_id":{"isi":["000626837400001"]},"type":"journal_article","issue":"2","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"09","quality_controlled":"1","intvolume":"       111","department":[{"_id":"RoSe"}],"publication":"Letters in Mathematical Physics","date_updated":"2023-08-07T14:17:00Z","author":[{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","last_name":"Napiórkowski"},{"first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":111,"article_number":"31","year":"2021","citation":{"short":"M.M. Napiórkowski, R. Seiringer, Letters in Mathematical Physics 111 (2021).","chicago":"Napiórkowski, Marcin M, and Robert Seiringer. “Free Energy Asymptotics of the Quantum Heisenberg Spin Chain.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11005-021-01375-4\">https://doi.org/10.1007/s11005-021-01375-4</a>.","apa":"Napiórkowski, M. M., &#38; Seiringer, R. (2021). Free energy asymptotics of the quantum Heisenberg spin chain. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-021-01375-4\">https://doi.org/10.1007/s11005-021-01375-4</a>","mla":"Napiórkowski, Marcin M., and Robert Seiringer. “Free Energy Asymptotics of the Quantum Heisenberg Spin Chain.” <i>Letters in Mathematical Physics</i>, vol. 111, no. 2, 31, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11005-021-01375-4\">10.1007/s11005-021-01375-4</a>.","ieee":"M. M. Napiórkowski and R. Seiringer, “Free energy asymptotics of the quantum Heisenberg spin chain,” <i>Letters in Mathematical Physics</i>, vol. 111, no. 2. Springer Nature, 2021.","ista":"Napiórkowski MM, Seiringer R. 2021. Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. 111(2), 31.","ama":"Napiórkowski MM, Seiringer R. Free energy asymptotics of the quantum Heisenberg spin chain. <i>Letters in Mathematical Physics</i>. 2021;111(2). doi:<a href=\"https://doi.org/10.1007/s11005-021-01375-4\">10.1007/s11005-021-01375-4</a>"},"abstract":[{"text":"We consider the ferromagnetic quantum Heisenberg model in one dimension, for any spin S≥1/2. We give upper and lower bounds on the free energy, proving that at low temperature it is asymptotically equal to the one of an ideal Bose gas of magnons, as predicted by the spin-wave approximation. The trial state used in the upper bound yields an analogous estimate also in the case of two spatial dimensions, which is believed to be sharp at low temperature.","lang":"eng"}],"_id":"9256","date_created":"2021-03-21T23:01:19Z","file":[{"success":1,"access_level":"open_access","file_name":"2021_LettersMathPhysics_Napiorkowski.pdf","date_updated":"2021-03-22T11:01:09Z","date_created":"2021-03-22T11:01:09Z","file_size":397962,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"9273","checksum":"687fef1525789c0950de90468dd81604"}],"doi":"10.1007/s11005-021-01375-4","scopus_import":"1","article_type":"original","publication_identifier":{"eissn":["15730530"],"issn":["03779017"]},"acknowledgement":"The work of MN was supported by the National Science Centre (NCN) Project Nr. 2016/21/D/ST1/02430. The work of RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227).\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","title":"Free energy asymptotics of the quantum Heisenberg spin chain","publication_status":"published","file_date_updated":"2021-03-22T11:01:09Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)"},{"type":"journal_article","date_published":"2021-03-09T00:00:00Z","external_id":{"isi":["000627429100097"],"pmid":["33653960"]},"pmid":1,"publisher":"National Academy of Sciences","status":"public","isi":1,"month":"03","ddc":["530"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"09","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","issue":"10","volume":118,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter"},{"last_name":"King","first_name":"Ella M.","full_name":"King, Ella M."},{"last_name":"Schoenholz","first_name":"Samuel S.","full_name":"Schoenholz, Samuel S."},{"last_name":"Cubuk","first_name":"Ekin D.","full_name":"Cubuk, Ekin D."},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."}],"date_updated":"2023-08-07T14:19:34Z","publication":"Proceedings of the National Academy of Sciences","department":[{"_id":"CaGo"}],"intvolume":"       118","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-03-22T12:23:54Z","title":"Designing self-assembling kinetics with differentiable statistical physics models","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"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.","article_type":"original","scopus_import":"1","doi":"10.1073/pnas.2024083118","file":[{"date_created":"2021-03-22T12:23:54Z","file_size":1047954,"date_updated":"2021-03-22T12:23:54Z","relation":"main_file","access_level":"open_access","success":1,"file_name":"2021_PNAS_Goodrich.pdf","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","file_id":"9278","creator":"dernst","content_type":"application/pdf"}],"date_created":"2021-03-21T23:01:20Z","_id":"9257","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."}],"citation":{"mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>.","short":"C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>.","apa":"Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., &#38; Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>","ieee":"C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 10. National Academy of Sciences, 2021.","ista":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. 118(10), e2024083118.","ama":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(10). doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>"},"year":"2021","article_number":"e2024083118"},{"issue":"3","day":"01","page":"226-228","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","isi":1,"month":"03","pmid":1,"publisher":"Springer Nature","type":"journal_article","external_id":{"pmid":["33674797"],"isi":["000625600600007"]},"date_published":"2021-03-01T00:00:00Z","citation":{"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.","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.","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>","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>.","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.","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>.","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>"},"year":"2021","date_created":"2021-03-21T23:01:20Z","_id":"9258","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"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.","article_type":"letter_note","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41592-021-01087-6","open_access":"1"}],"doi":"10.1038/s41592-021-01087-6","article_processing_charge":"No","oa_version":"Published Version","title":"Pycro-Manager: Open-source software for customized and reproducible microscope control","publication_status":"published","intvolume":"        18","date_updated":"2023-08-07T14:19:08Z","publication":"Nature Methods","department":[{"_id":"JoDa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Henry","last_name":"Pinkard","full_name":"Pinkard, Henry"},{"last_name":"Stuurman","first_name":"Nico","full_name":"Stuurman, Nico"},{"full_name":"Ivanov, Ivan E.","first_name":"Ivan E.","last_name":"Ivanov"},{"full_name":"Anthony, Nicholas M.","last_name":"Anthony","first_name":"Nicholas M."},{"full_name":"Ouyang, Wei","last_name":"Ouyang","first_name":"Wei"},{"first_name":"Bin","last_name":"Li","full_name":"Li, Bin"},{"last_name":"Yang","first_name":"Bin","full_name":"Yang, Bin"},{"last_name":"Tsuchida","first_name":"Mark A.","full_name":"Tsuchida, Mark A."},{"last_name":"Chhun","first_name":"Bryant","full_name":"Chhun, Bryant"},{"first_name":"Grace","last_name":"Zhang","full_name":"Zhang, Grace"},{"last_name":"Mei","first_name":"Ryan","full_name":"Mei, Ryan"},{"last_name":"Anderson","first_name":"Michael","full_name":"Anderson, Michael"},{"last_name":"Shepherd","first_name":"Douglas P.","full_name":"Shepherd, Douglas P."},{"last_name":"Hunt-Isaak","first_name":"Ian","full_name":"Hunt-Isaak, Ian"},{"last_name":"Dunn","first_name":"Raymond L.","full_name":"Dunn, Raymond L."},{"first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke"},{"full_name":"Kato, Saul","last_name":"Kato","first_name":"Saul"},{"last_name":"Royer","first_name":"Loïc A.","full_name":"Royer, Loïc A."},{"full_name":"Thiagarajah, Jay R.","first_name":"Jay R.","last_name":"Thiagarajah"},{"full_name":"Eliceiri, Kevin W.","first_name":"Kevin W.","last_name":"Eliceiri"},{"full_name":"Lundberg, Emma","last_name":"Lundberg","first_name":"Emma"},{"full_name":"Mehta, Shalin B.","last_name":"Mehta","first_name":"Shalin B."},{"last_name":"Waller","first_name":"Laura","full_name":"Waller, Laura"}],"volume":18,"oa":1},{"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020"},{"grant_number":"Y 564-B12","call_identifier":"FWF","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","quality_controlled":"1","day":"25","status":"public","isi":1,"month":"02","ddc":["570"],"language":[{"iso":"eng"}],"type":"journal_article","external_id":{"pmid":["33717158"],"isi":["000627134400001"]},"date_published":"2021-02-25T00:00:00Z","pmid":1,"publisher":"Frontiers","date_created":"2021-03-21T23:01:20Z","file":[{"access_level":"open_access","success":1,"file_name":"2021_FrontiersImmumo_Vaahtomeri.pdf","date_updated":"2021-03-22T12:08:26Z","file_size":3740146,"date_created":"2021-03-22T12:08:26Z","relation":"main_file","content_type":"application/pdf","file_id":"9277","creator":"dernst","checksum":"663f5a48375e42afa4bfef58d42ec186"}],"_id":"9259","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."}],"citation":{"chicago":"Vaahtomeri, Kari, Christine Moussion, Robert Hauschild, and Michael K Sixt. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” <i>Frontiers in Immunology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fimmu.2021.630002\">https://doi.org/10.3389/fimmu.2021.630002</a>.","short":"K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology 12 (2021).","apa":"Vaahtomeri, K., Moussion, C., Hauschild, R., &#38; Sixt, M. K. (2021). Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. <i>Frontiers in Immunology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fimmu.2021.630002\">https://doi.org/10.3389/fimmu.2021.630002</a>","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>.","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>","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.","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."},"year":"2021","article_number":"630002","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-03-22T12:08:26Z","title":"Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium","publication_status":"published","acknowledgement":"This work was supported by Sigrid Juselius fellowship (KV), University of Helsinki 3-year research grant (KV), Academy of Finland Research fellow funding (315710, to KV), the European Research Council (ERC CoG 724373 to MS), and by the Austrian Science foundation (FWF) (Y564-B12 START award to MS).\r\nTaija Mäkinen is acknowledged for providing Prox1CreERT2 transgenic mice and Yu Yamaguchi for providing the conditional Ext1 mouse strain.","publication_identifier":{"eissn":["1664-3224"]},"article_type":"original","scopus_import":"1","doi":"10.3389/fimmu.2021.630002","ec_funded":1,"date_updated":"2023-08-07T14:18:26Z","publication":"Frontiers in Immunology","department":[{"_id":"MiSi"},{"_id":"Bio"}],"intvolume":"        12","volume":12,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Vaahtomeri, Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri","first_name":"Kari"},{"id":"3356F664-F248-11E8-B48F-1D18A9856A87","full_name":"Moussion, Christine","first_name":"Christine","last_name":"Moussion"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}]},{"publisher":"Springer Nature","external_id":{"isi":["000625573800002"]},"date_published":"2021-03-05T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["510"],"status":"public","month":"03","isi":1,"day":"05","page":"1071–1101","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"grant_number":"EP-P026710-2","name":"Between rational and integral points","_id":"26A8D266-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Browning","first_name":"Timothy D","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yamagishi, Shuntaro","first_name":"Shuntaro","last_name":"Yamagishi"}],"oa":1,"volume":299,"intvolume":"       299","publication":"Mathematische Zeitschrift","date_updated":"2023-08-07T14:20:00Z","department":[{"_id":"TiBr"}],"article_type":"original","acknowledgement":"While working on this paper the authors were both supported by EPSRC grant EP/P026710/1, and the second author received additional support from the NWO Veni Grant 016.Veni.192.047. Thanks are due to Marta Pieropan, Arne Smeets and Sho Tanimoto for useful conversations related to this topic, and to the anonymous referee for numerous helpful suggestions.","publication_identifier":{"issn":["0025-5874"],"eissn":["1432-1823"]},"doi":"10.1007/s00209-021-02695-w","scopus_import":"1","file_date_updated":"2021-03-22T12:41:26Z","article_processing_charge":"No","oa_version":"Published Version","title":"Arithmetic of higher-dimensional orbifolds and a mixed Waring problem","publication_status":"published","abstract":[{"text":"We study the density of rational points on a higher-dimensional orbifold (Pn−1,Δ) when Δ is a Q-divisor involving hyperplanes. This allows us to address a question of Tanimoto about whether the set of rational points on such an orbifold constitutes a thin set. Our approach relies on the Hardy–Littlewood circle method to first study an asymptotic version of Waring’s problem for mixed powers. In doing so we make crucial use of the recent resolution of the main conjecture in Vinogradov’s mean value theorem, due to Bourgain–Demeter–Guth and Wooley.","lang":"eng"}],"year":"2021","citation":{"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.","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>.","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.","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.","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>"},"_id":"9260","date_created":"2021-03-21T23:01:21Z","file":[{"content_type":"application/pdf","creator":"dernst","file_id":"9279","checksum":"8ed9f49568806894744096dbbca0ad7b","file_name":"2021_MathZeitschrift_Browning.pdf","access_level":"open_access","success":1,"file_size":492685,"date_updated":"2021-03-22T12:41:26Z","date_created":"2021-03-22T12:41:26Z","relation":"main_file"}]},{"_id":"9281","date_created":"2021-03-23T05:38:48Z","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"We comment on two formal proofs of Fermat's sum of two squares theorem, written using the Mathematical Components libraries of the Coq proof assistant. The first one follows Zagier's celebrated one-sentence proof; the second follows David Christopher's recent new proof relying on partition-theoretic arguments. Both formal proofs rely on a general property of involutions of finite sets, of independent interest. The proof technique consists for the most part of automating recurrent tasks (such as case distinctions and computations on natural numbers) via ad hoc tactics.","lang":"eng"}],"year":"2021","article_number":"2103.11389","citation":{"chicago":"Dubach, Guillaume, and Fabian Mühlböck. “Formal Verification of Zagier’s One-Sentence Proof.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2103.11389\">https://doi.org/10.48550/arXiv.2103.11389</a>.","apa":"Dubach, G., &#38; Mühlböck, F. (n.d.). Formal verification of Zagier’s one-sentence proof. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2103.11389\">https://doi.org/10.48550/arXiv.2103.11389</a>","short":"G. Dubach, F. Mühlböck, ArXiv (n.d.).","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>.","ista":"Dubach G, Mühlböck F. Formal verification of Zagier’s one-sentence proof. arXiv, 2103.11389.","ieee":"G. Dubach and F. Mühlböck, “Formal verification of Zagier’s one-sentence proof,” <i>arXiv</i>. .","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>"},"article_processing_charge":"No","oa_version":"Preprint","publication_status":"submitted","title":"Formal verification of Zagier's one-sentence proof","day":"21","main_file_link":[{"url":"https://arxiv.org/abs/2103.11389","open_access":"1"}],"doi":"10.48550/arXiv.2103.11389","status":"public","publication":"arXiv","ec_funded":1,"date_updated":"2023-05-03T10:26:45Z","month":"03","department":[{"_id":"LaEr"},{"_id":"ToHe"}],"arxiv":1,"language":[{"iso":"eng"}],"oa":1,"related_material":{"record":[{"id":"9946","relation":"other","status":"public"}]},"date_published":"2021-03-21T00:00:00Z","external_id":{"arxiv":["2103.11389"]},"type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-6892-8137","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","full_name":"Dubach, Guillaume","first_name":"Guillaume","last_name":"Dubach"},{"last_name":"Mühlböck","first_name":"Fabian","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425"}]},{"date_created":"2021-03-23T07:10:17Z","_id":"9282","abstract":[{"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.","lang":"eng"}],"citation":{"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>","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.","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>","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).","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>.","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>."},"year":"2021","article_number":"035011","oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","title":"Complete mapping of magnetic anisotropy for prototype Ising van der Waals FePS3","publication_identifier":{"issn":["2053-1583"]},"article_type":"original","doi":"10.1088/2053-1583/abeed3","main_file_link":[{"url":"https://arxiv.org/abs/2103.09029","open_access":"1"}],"date_updated":"2021-12-01T10:36:56Z","publication":"2D Materials","department":[{"_id":"KiMo"}],"intvolume":"         8","arxiv":1,"volume":8,"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Nauman","first_name":"Muhammad","full_name":"Nauman, Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","orcid":"0000-0002-2111-4846"},{"first_name":"Do Hoon","last_name":"Kiem","full_name":"Kiem, Do Hoon"},{"full_name":"Lee, Sungmin","last_name":"Lee","first_name":"Sungmin"},{"last_name":"Son","first_name":"Suhan","full_name":"Son, Suhan"},{"last_name":"Park","first_name":"J-G","full_name":"Park, J-G"},{"full_name":"Kang, Woun","last_name":"Kang","first_name":"Woun"},{"last_name":"Han","first_name":"Myung Joon","full_name":"Han, Myung Joon"},{"full_name":"Jo, Youn Jung","last_name":"Jo","first_name":"Youn Jung"}],"issue":"3","quality_controlled":"1","day":"06","status":"public","month":"04","extern":"1","keyword":["Mechanical Engineering","General Materials Science","Mechanics of Materials","General Chemistry","Condensed Matter Physics"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2021-04-06T00:00:00Z","external_id":{"arxiv":["2103.09029"]},"publisher":"IOP Publishing"},{"keyword":["Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"03","isi":1,"publisher":"eLife Sciences Publications","external_id":{"isi":["000631050900001"]},"date_published":"2021-03-08T00:00:00Z","type":"journal_article","project":[{"name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","_id":"2517526A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"628377"},{"name":"CyberCircuits: Cybergenetic circuits to test composability of gene networks","_id":"268BFA92-B435-11E9-9278-68D0E5697425","grant_number":"I03901","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"08","quality_controlled":"1","intvolume":"        10","publication":"eLife","ec_funded":1,"date_updated":"2024-02-21T12:41:57Z","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","full_name":"Nagy-Staron, Anna A","first_name":"Anna A","last_name":"Nagy-Staron"},{"first_name":"Kathrin","last_name":"Tomasek","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin"},{"full_name":"Caruso Carter, Caroline","last_name":"Caruso Carter","first_name":"Caroline"},{"full_name":"Sonnleitner, Elisabeth","first_name":"Elisabeth","last_name":"Sonnleitner"},{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor"},{"full_name":"Paixão, Tiago","first_name":"Tiago","last_name":"Paixão"},{"last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8951","relation":"research_data","status":"public"}]},"oa":1,"volume":10,"abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs."}],"article_number":"e65993","year":"2021","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>.","short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).","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>.","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>","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.","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.","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>"},"_id":"9283","file":[{"file_name":"elife-65993-v2.pdf","access_level":"open_access","success":1,"date_created":"2021-03-23T10:12:58Z","date_updated":"2021-03-23T10:12:58Z","file_size":1390469,"relation":"main_file","file_id":"9284","creator":"bkavcic","content_type":"application/pdf","checksum":"3c2f44058c2dd45a5a1027f09d263f8e"}],"date_created":"2021-03-23T10:11:46Z","article_type":"original","publication_identifier":{"issn":["2050-084X"]},"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).","doi":"10.7554/elife.65993","file_date_updated":"2021-03-23T10:12:58Z","oa_version":"Published Version","article_processing_charge":"Yes","title":"Local genetic context shapes the function of a gene regulatory network","publication_status":"published"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"},{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"issue":"2","day":"01","page":"1122–1142","quality_controlled":"1","language":[{"iso":"eng"}],"ddc":["580"],"status":"public","month":"06","isi":1,"publisher":"Oxford University Press","pmid":1,"external_id":{"pmid":["33734402"],"isi":["000671555900031"]},"date_published":"2021-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. "}],"year":"2021","citation":{"ieee":"M. Narasimhan <i>et al.</i>, “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” <i>Plant Physiology</i>, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. 2021;186(2):1122–1142. doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>.","chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>.","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>","short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142."},"_id":"9287","file":[{"relation":"main_file","date_updated":"2021-11-11T15:07:51Z","date_created":"2021-11-11T15:07:51Z","file_size":2289127,"success":1,"access_level":"open_access","file_name":"2021_PlantPhysio_Narasimhan.pdf","checksum":"532bb9469d3b665907f06df8c383eade","content_type":"application/pdf","file_id":"10273","creator":"cziletti"}],"date_created":"2021-03-26T12:08:38Z","article_type":"original","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","doi":"10.1093/plphys/kiab134","file_date_updated":"2021-11-11T15:07:51Z","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","intvolume":"       186","publication":"Plant Physiology","date_updated":"2024-10-29T10:22:43Z","ec_funded":1,"department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha"},{"last_name":"Gallei","first_name":"Michelle C","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"first_name":"Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","first_name":"Inge","last_name":"Verstraeten"},{"orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li"},{"last_name":"Rodriguez Solovey","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","first_name":"Huibin","last_name":"Han"},{"first_name":"E","last_name":"Himschoot","full_name":"Himschoot, E"},{"first_name":"R","last_name":"Wang","full_name":"Wang, R"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"first_name":"J","last_name":"Sánchez-Simarro","full_name":"Sánchez-Simarro, J"},{"last_name":"Aniento","first_name":"F","full_name":"Aniento, F"},{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"oa":1,"related_material":{"link":[{"url":"10.1093/plphys/kiab380","relation":"erratum"}],"record":[{"status":"public","relation":"dissertation_contains","id":"11626"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"volume":186,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}]},{"intvolume":"       230","department":[{"_id":"JiFr"}],"date_updated":"2023-09-05T15:46:55Z","publication":"New Phytologist","author":[{"first_name":"I","last_name":"El Houari","full_name":"El Houari, I"},{"last_name":"Van Beirs","first_name":"C","full_name":"Van Beirs, C"},{"first_name":"HE","last_name":"Arents","full_name":"Arents, HE"},{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin"},{"full_name":"Chanoca, A","last_name":"Chanoca","first_name":"A"},{"full_name":"Opdenacker, D","last_name":"Opdenacker","first_name":"D"},{"full_name":"Pollier, J","first_name":"J","last_name":"Pollier"},{"first_name":"V","last_name":"Storme","full_name":"Storme, V"},{"first_name":"W","last_name":"Steenackers","full_name":"Steenackers, W"},{"last_name":"Quareshy","first_name":"M","full_name":"Quareshy, M"},{"first_name":"R","last_name":"Napier","full_name":"Napier, R"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"De Rybel, B","last_name":"De Rybel","first_name":"B"},{"full_name":"Boerjan, W","last_name":"Boerjan","first_name":"W"},{"full_name":"Vanholme, B","last_name":"Vanholme","first_name":"B"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":230,"oa":1,"citation":{"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>.","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>.","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.","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>","ista":"El Houari I, Van Beirs C, Arents H, Han H, Chanoca A, Opdenacker D, Pollier J, Storme V, Steenackers W, Quareshy M, Napier R, Beeckman T, Friml J, De Rybel B, Boerjan W, Vanholme B. 2021. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. 230(6), 2275–2291.","ieee":"I. El Houari <i>et al.</i>, “Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport,” <i>New Phytologist</i>, vol. 230, no. 6. Wiley, pp. 2275–2291, 2021."},"year":"2021","abstract":[{"lang":"eng","text":"• The phenylpropanoid pathway serves a central role in plant metabolism, providing numerous compounds involved in diverse physiological processes. Most carbon entering the pathway is incorporated into lignin. Although several phenylpropanoid pathway mutants show seedling growth arrest, the role for lignin in seedling growth and development is unexplored.\r\n• We use complementary pharmacological and genetic approaches to block CINNAMATE‐4‐HYDROXYLASE (C4H) functionality in Arabidopsis seedlings and a set of molecular and biochemical techniques to investigate the underlying phenotypes.\r\n• Blocking C4H resulted in reduced lateral rooting and increased adventitious rooting apically in the hypocotyl. These phenotypes coincided with an inhibition in auxin transport. The upstream accumulation in cis‐cinnamic acid was found to likely cause polar auxin transport inhibition. Conversely, a downstream depletion in lignin perturbed phloem‐mediated auxin transport. Restoring lignin deposition effectively reestablished phloem transport and, accordingly, auxin homeostasis.\r\n• Our results show that the accumulation of bioactive intermediates and depletion in lignin jointly cause the aberrant phenotypes upon blocking C4H, and demonstrate that proper deposition of lignin is essential for the establishment of auxin distribution in seedlings. Our data position the phenylpropanoid pathway and lignin in a new physiological framework, consolidating their importance in plant growth and development."}],"date_created":"2021-03-26T12:09:01Z","_id":"9288","scopus_import":"1","main_file_link":[{"url":"https://biblio.ugent.be/publication/8703799/file/8703800.pdf","open_access":"1"}],"doi":"10.1111/nph.17349","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"article_type":"original","publication_status":"published","title":"Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport","oa_version":"Published Version","article_processing_charge":"No","language":[{"iso":"eng"}],"isi":1,"month":"03","status":"public","pmid":1,"publisher":"Wiley","type":"journal_article","external_id":{"isi":["000639552400001"],"pmid":["33728703"]},"date_published":"2021-03-17T00:00:00Z","issue":"6","page":"2275-2291","day":"17","quality_controlled":"1"},{"department":[{"_id":"JiFr"}],"ec_funded":1,"date_updated":"2023-09-05T13:03:34Z","publication":"Current Biology","intvolume":"        31","acknowledged_ssus":[{"_id":"Bio"}],"volume":31,"oa":1,"author":[{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc"},{"full_name":"Van Gelderen, K","last_name":"Van Gelderen","first_name":"K"},{"first_name":"Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas"},{"last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285"},{"last_name":"Naramoto","first_name":"S","full_name":"Naramoto, S"},{"last_name":"Zhang","first_name":"Xixi","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"first_name":"David","last_name":"Domjan","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","orcid":"0000-0003-2267-106X","full_name":"Domjan, David"},{"full_name":"Vcelarova, L","last_name":"Vcelarova","first_name":"L"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild"},{"last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"de Koning, E","last_name":"de Koning","first_name":"E"},{"last_name":"van Dop","first_name":"M","full_name":"van Dop, M"},{"full_name":"Rademacher, E","first_name":"E","last_name":"Rademacher"},{"last_name":"Janson","first_name":"S","full_name":"Janson, S"},{"first_name":"X","last_name":"Wei","full_name":"Wei, X"},{"last_name":"Molnar","first_name":"Gergely","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Rybel","first_name":"B","full_name":"De Rybel, B"},{"full_name":"Offringa, R","last_name":"Offringa","first_name":"R"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2021-03-26T12:09:33Z","file":[{"checksum":"b1723040ecfd8c81194185472eb62546","creator":"dernst","file_id":"9303","content_type":"application/pdf","date_created":"2021-04-01T10:53:42Z","date_updated":"2021-04-01T10:53:42Z","file_size":4324371,"relation":"main_file","file_name":"2021_CurrentBiology_Glanc.pdf","success":1,"access_level":"open_access"}],"_id":"9290","citation":{"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>","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.","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.","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.","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>.","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>","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>."},"year":"2021","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."}],"title":"AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-04-01T10:53:42Z","doi":"10.1016/j.cub.2021.02.028","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"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.).","article_type":"original","isi":1,"month":"03","status":"public","ddc":["580"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2021-03-10T00:00:00Z","external_id":{"isi":["000653077800004"],"pmid":["33705718"]},"pmid":1,"publisher":"Elsevier","issue":"9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630"}],"quality_controlled":"1","page":"1918-1930","day":"10"},{"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-03-29T00:00:00Z","type":"research_data","oa":1,"ddc":["530"],"month":"03","department":[{"_id":"GeKa"}],"status":"public","date_updated":"2024-02-21T12:37:14Z","doi":"10.15479/AT:ISTA:9291","day":"29","title":"Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium","file_date_updated":"2021-04-01T07:52:56Z","oa_version":"Published Version","article_processing_charge":"No","year":"2021","citation":{"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>","ieee":"G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium.” Institute of Science and Technology Austria, 2021.","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>.","short":"G. Katsaros, (2021).","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>.","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>."},"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)."}],"_id":"9291","license":"https://creativecommons.org/publicdomain/zero/1.0/","file":[{"file_size":10616071,"date_updated":"2021-03-27T13:46:17Z","relation":"main_file","date_created":"2021-03-27T13:46:17Z","file_name":"Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip","success":1,"access_level":"open_access","checksum":"635df3c08fc13c3dac008cd421aefbe4","creator":"gkatsaro","file_id":"9292","content_type":"application/x-zip-compressed"},{"access_level":"open_access","success":1,"file_name":"README.txt","date_created":"2021-04-01T07:52:56Z","file_size":470,"date_updated":"2021-04-01T07:52:56Z","relation":"main_file","content_type":"text/plain","file_id":"9302","creator":"dernst","checksum":"12b3ca69ae7509a346711baae0b02a75"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"has_accepted_license":"1","date_created":"2021-03-27T13:47:49Z"},{"quality_controlled":"1","day":"16","issue":"8","type":"journal_article","date_published":"2021-03-16T00:00:00Z","external_id":{"arxiv":["1804.07031"],"isi":["000657537500003"]},"publisher":"Elsevier","isi":1,"month":"03","status":"public","language":[{"iso":"eng"}],"publication_status":"published","title":"Algorithms and conditional lower bounds for planning problems","article_processing_charge":"No","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07031"}],"doi":"10.1016/j.artint.2021.103499","publication_identifier":{"issn":["0004-3702"]},"article_type":"original","date_created":"2021-03-28T22:01:40Z","_id":"9293","citation":{"ama":"Chatterjee K, Dvořák W, Henzinger MH, 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>","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” <i>Artificial Intelligence</i>, vol. 297, no. 8. Elsevier, 2021.","ista":"Chatterjee K, Dvořák W, Henzinger MH, 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>.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, Artificial Intelligence 297 (2021).","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H 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>.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., &#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>"},"article_number":"103499","year":"2021","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."}],"volume":297,"oa":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"35"}]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Dvořák","first_name":"Wolfgang","full_name":"Dvořák, Wolfgang"},{"last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"date_updated":"2023-09-26T10:41:42Z","publication":"Artificial Intelligence","arxiv":1,"intvolume":"       297"},{"intvolume":"        56","department":[{"_id":"MiSi"}],"date_updated":"2023-08-07T14:26:47Z","publication":"Developmental Cell","author":[{"orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":56,"oa":1,"citation":{"ama":"Gärtner FR, Sixt MK. Engaging the front wheels to drive through fibrous terrain. <i>Developmental Cell</i>. 2021;56(6):723-725. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.03.002\">10.1016/j.devcel.2021.03.002</a>","ista":"Gärtner FR, Sixt MK. 2021. Engaging the front wheels to drive through fibrous terrain. Developmental Cell. 56(6), 723–725.","ieee":"F. R. Gärtner and M. K. Sixt, “Engaging the front wheels to drive through fibrous terrain,” <i>Developmental Cell</i>, vol. 56, no. 6. Elsevier, pp. 723–725, 2021.","short":"F.R. Gärtner, M.K. Sixt, Developmental Cell 56 (2021) 723–725.","chicago":"Gärtner, Florian R, and Michael K Sixt. “Engaging the Front Wheels to Drive through Fibrous Terrain.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2021.03.002\">https://doi.org/10.1016/j.devcel.2021.03.002</a>.","apa":"Gärtner, F. R., &#38; Sixt, M. K. (2021). Engaging the front wheels to drive through fibrous terrain. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2021.03.002\">https://doi.org/10.1016/j.devcel.2021.03.002</a>","mla":"Gärtner, Florian R., and Michael K. Sixt. “Engaging the Front Wheels to Drive through Fibrous Terrain.” <i>Developmental Cell</i>, vol. 56, no. 6, Elsevier, 2021, pp. 723–25, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.03.002\">10.1016/j.devcel.2021.03.002</a>."},"year":"2021","abstract":[{"lang":"eng","text":"In this issue of Developmental Cell, Doyle and colleagues identify periodic anterior contraction as a characteristic feature of fibroblasts and mesenchymal cancer cells embedded in 3D collagen gels. This contractile mechanism generates a matrix prestrain required for crawling in fibrous 3D environments."}],"date_created":"2021-03-28T22:01:41Z","_id":"9294","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2021.03.002","open_access":"1"}],"doi":"10.1016/j.devcel.2021.03.002","publication_identifier":{"issn":["15345807"],"eissn":["18781551"]},"article_type":"original","publication_status":"published","title":"Engaging the front wheels to drive through fibrous terrain","article_processing_charge":"No","oa_version":"Published Version","language":[{"iso":"eng"}],"isi":1,"month":"03","status":"public","pmid":1,"publisher":"Elsevier","type":"journal_article","external_id":{"isi":["000631681200004"],"pmid":["33756118"]},"date_published":"2021-03-22T00:00:00Z","issue":"6","page":"723-725","day":"22","quality_controlled":"1"},{"arxiv":1,"intvolume":"        97","department":[{"_id":"UlWa"}],"ec_funded":1,"date_updated":"2023-08-07T14:26:15Z","publication":"Journal of Graph Theory","author":[{"first_name":"Alan M","last_name":"Arroyo Guevara","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","full_name":"Arroyo Guevara, Alan M"},{"first_name":"Dan","last_name":"Mcquillan","full_name":"Mcquillan, Dan"},{"full_name":"Richter, R. Bruce","last_name":"Richter","first_name":"R. Bruce"},{"full_name":"Salazar, Gelasio","first_name":"Gelasio","last_name":"Salazar"},{"full_name":"Sullivan, Matthew","first_name":"Matthew","last_name":"Sullivan"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":97,"oa":1,"citation":{"short":"A.M. Arroyo Guevara, D. Mcquillan, R.B. Richter, G. Salazar, M. Sullivan, Journal of Graph Theory 97 (2021) 426–440.","chicago":"Arroyo Guevara, Alan M, Dan Mcquillan, R. Bruce Richter, Gelasio Salazar, and Matthew Sullivan. “Drawings of Complete Graphs in the Projective Plane.” <i>Journal of Graph Theory</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/jgt.22665\">https://doi.org/10.1002/jgt.22665</a>.","apa":"Arroyo Guevara, A. M., Mcquillan, D., Richter, R. B., Salazar, G., &#38; Sullivan, M. (2021). Drawings of complete graphs in the projective plane. <i>Journal of Graph Theory</i>. Wiley. <a href=\"https://doi.org/10.1002/jgt.22665\">https://doi.org/10.1002/jgt.22665</a>","mla":"Arroyo Guevara, Alan M., et al. “Drawings of Complete Graphs in the Projective Plane.” <i>Journal of Graph Theory</i>, vol. 97, no. 3, Wiley, 2021, pp. 426–40, doi:<a href=\"https://doi.org/10.1002/jgt.22665\">10.1002/jgt.22665</a>.","ama":"Arroyo Guevara AM, Mcquillan D, Richter RB, Salazar G, Sullivan M. Drawings of complete graphs in the projective plane. <i>Journal of Graph Theory</i>. 2021;97(3):426-440. doi:<a href=\"https://doi.org/10.1002/jgt.22665\">10.1002/jgt.22665</a>","ieee":"A. M. Arroyo Guevara, D. Mcquillan, R. B. Richter, G. Salazar, and M. Sullivan, “Drawings of complete graphs in the projective plane,” <i>Journal of Graph Theory</i>, vol. 97, no. 3. Wiley, pp. 426–440, 2021.","ista":"Arroyo Guevara AM, Mcquillan D, Richter RB, Salazar G, Sullivan M. 2021. Drawings of complete graphs in the projective plane. Journal of Graph Theory. 97(3), 426–440."},"year":"2021","abstract":[{"text":"Hill's Conjecture states that the crossing number  cr(𝐾𝑛)  of the complete graph  𝐾𝑛  in the plane (equivalently, the sphere) is  14⌊𝑛2⌋⌊𝑛−12⌋⌊𝑛−22⌋⌊𝑛−32⌋=𝑛4/64+𝑂(𝑛3) . Moon proved that the expected number of crossings in a spherical drawing in which the points are randomly distributed and joined by geodesics is precisely  𝑛4/64+𝑂(𝑛3) , thus matching asymptotically the conjectured value of  cr(𝐾𝑛) . Let  cr𝑃(𝐺)  denote the crossing number of a graph  𝐺  in the projective plane. Recently, Elkies proved that the expected number of crossings in a naturally defined random projective plane drawing of  𝐾𝑛  is  (𝑛4/8𝜋2)+𝑂(𝑛3) . In analogy with the relation of Moon's result to Hill's conjecture, Elkies asked if  lim𝑛→∞ cr𝑃(𝐾𝑛)/𝑛4=1/8𝜋2 . We construct drawings of  𝐾𝑛  in the projective plane that disprove this.","lang":"eng"}],"date_created":"2021-03-28T22:01:41Z","_id":"9295","scopus_import":"1","doi":"10.1002/jgt.22665","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.02287"}],"acknowledgement":"We thank two reviewers for their corrections and suggestions on the original version of this\r\npaper. This project has received funding from NSERC Grant 50503-10940-500 and from the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement No 754411, IST, Klosterneuburg, Austria.","publication_identifier":{"issn":["0364-9024"],"eissn":["1097-0118"]},"article_type":"original","publication_status":"published","title":"Drawings of complete graphs in the projective plane","oa_version":"Preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"isi":1,"month":"03","status":"public","publisher":"Wiley","type":"journal_article","date_published":"2021-03-23T00:00:00Z","external_id":{"arxiv":["2002.02287"],"isi":["000631693200001"]},"issue":"3","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"page":"426-440","day":"23","quality_controlled":"1"},{"page":"221-233","day":"16","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"}],"publisher":"Springer Nature","external_id":{"arxiv":["2101.03928"]},"date_published":"2021-02-16T00:00:00Z","type":"conference","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"month":"02","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/2101.03928","open_access":"1"}],"doi":"10.1007/978-3-030-68211-8_18","scopus_import":"1","acknowledgement":"A.A. funded by the Marie Skłodowska-Curie grant agreement No. 754411. Z.M. partially funded by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. I.P., D.P., and B.V. partially supported by FWF within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. A.P. supported by a Schrödinger fellowship of the FWF: J-3847-N35. J.T. partially supported by ERC Start grant no. (279307: Graph Games), FWF grant no. P23499-N23 and S11407-N23 (RiSE).","publication_identifier":{"issn":["03029743"],"isbn":["9783030682101"],"eissn":["16113349"]},"publication_status":"published","title":"On compatible matchings","oa_version":"Preprint","article_processing_charge":"No","year":"2021","citation":{"ieee":"O. Aichholzer <i>et al.</i>, “On compatible matchings,” in <i>15th International Conference on Algorithms and Computation</i>, Yangon, Myanmar, 2021, vol. 12635, pp. 221–233.","ista":"Aichholzer O, Arroyo Guevara AM, Masárová Z, Parada I, Perz D, Pilz A, Tkadlec J, Vogtenhuber B. 2021. On compatible matchings. 15th International Conference on Algorithms and Computation. WALCOM: Algorithms and Computation, LNCS, vol. 12635, 221–233.","ama":"Aichholzer O, Arroyo Guevara AM, Masárová Z, et al. On compatible matchings. In: <i>15th International Conference on Algorithms and Computation</i>. Vol 12635. Springer Nature; 2021:221-233. doi:<a href=\"https://doi.org/10.1007/978-3-030-68211-8_18\">10.1007/978-3-030-68211-8_18</a>","mla":"Aichholzer, Oswin, et al. “On Compatible Matchings.” <i>15th International Conference on Algorithms and Computation</i>, vol. 12635, Springer Nature, 2021, pp. 221–33, doi:<a href=\"https://doi.org/10.1007/978-3-030-68211-8_18\">10.1007/978-3-030-68211-8_18</a>.","chicago":"Aichholzer, Oswin, Alan M Arroyo Guevara, Zuzana Masárová, Irene Parada, Daniel Perz, Alexander Pilz, Josef Tkadlec, and Birgit Vogtenhuber. “On Compatible Matchings.” In <i>15th International Conference on Algorithms and Computation</i>, 12635:221–33. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-68211-8_18\">https://doi.org/10.1007/978-3-030-68211-8_18</a>.","apa":"Aichholzer, O., Arroyo Guevara, A. M., Masárová, Z., Parada, I., Perz, D., Pilz, A., … Vogtenhuber, B. (2021). On compatible matchings. In <i>15th International Conference on Algorithms and Computation</i> (Vol. 12635, pp. 221–233). Yangon, Myanmar: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-68211-8_18\">https://doi.org/10.1007/978-3-030-68211-8_18</a>","short":"O. Aichholzer, A.M. Arroyo Guevara, Z. Masárová, I. Parada, D. Perz, A. Pilz, J. Tkadlec, B. Vogtenhuber, in:, 15th International Conference on Algorithms and Computation, Springer Nature, 2021, pp. 221–233."},"abstract":[{"lang":"eng","text":" matching is compatible to two or more labeled point sets of size n with labels   {1,…,n}  if its straight-line drawing on each of these point sets is crossing-free. We study the maximum number of edges in a matching compatible to two or more labeled point sets in general position in the plane. We show that for any two labeled convex sets of n points there exists a compatible matching with   ⌊2n−−√⌋  edges. More generally, for any   ℓ  labeled point sets we construct compatible matchings of size   Ω(n1/ℓ) . As a corresponding upper bound, we use probabilistic arguments to show that for any   ℓ  given sets of n points there exists a labeling of each set such that the largest compatible matching has   O(n2/(ℓ+1))  edges. Finally, we show that   Θ(logn)  copies of any set of n points are necessary and sufficient for the existence of a labeling such that any compatible matching consists only of a single edge."}],"conference":{"start_date":"2021-02-28","end_date":"2021-03-02","location":"Yangon, Myanmar","name":"WALCOM: Algorithms and Computation"},"_id":"9296","date_created":"2021-03-28T22:01:41Z","author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","last_name":"Arroyo Guevara"},{"orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","full_name":"Masárová, Zuzana","first_name":"Zuzana","last_name":"Masárová"},{"last_name":"Parada","first_name":"Irene","full_name":"Parada, Irene"},{"first_name":"Daniel","last_name":"Perz","full_name":"Perz, Daniel"},{"full_name":"Pilz, Alexander","first_name":"Alexander","last_name":"Pilz"},{"last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"last_name":"Vogtenhuber","first_name":"Birgit","full_name":"Vogtenhuber, Birgit"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","related_material":{"record":[{"id":"11938","relation":"later_version","status":"public"}]},"oa":1,"volume":12635,"arxiv":1,"intvolume":"     12635","department":[{"_id":"UlWa"},{"_id":"HeEd"},{"_id":"KrCh"}],"publication":"15th International Conference on Algorithms and Computation","ec_funded":1,"date_updated":"2023-02-21T16:33:44Z"},{"quality_controlled":"1","day":"17","isi":1,"month":"03","status":"public","language":[{"iso":"eng"}],"type":"journal_article","external_id":{"isi":["000629677500001"],"arxiv":["2008.08851"]},"date_published":"2021-03-17T00:00:00Z","publisher":"Cambridge University Press","date_created":"2021-03-28T22:01:42Z","_id":"9297","citation":{"mla":"Liu, T., et al. “Decay of Streaks and Rolls in Plane Couette-Poiseuille Flow.” <i>Journal of Fluid Mechanics</i>, vol. 915, A65, Cambridge University Press, 2021, doi:<a href=\"https://doi.org/10.1017/jfm.2021.89\">10.1017/jfm.2021.89</a>.","apa":"Liu, T., Semin, B., Klotz, L., Godoy-Diana, R., Wesfreid, J. E., &#38; Mullin, T. (2021). Decay of streaks and rolls in plane Couette-Poiseuille flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2021.89\">https://doi.org/10.1017/jfm.2021.89</a>","short":"T. Liu, B. Semin, L. Klotz, R. Godoy-Diana, J.E. Wesfreid, T. Mullin, Journal of Fluid Mechanics 915 (2021).","chicago":"Liu, T., B. Semin, Lukasz Klotz, R. Godoy-Diana, J. E. Wesfreid, and T. Mullin. “Decay of Streaks and Rolls in Plane Couette-Poiseuille Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/jfm.2021.89\">https://doi.org/10.1017/jfm.2021.89</a>.","ama":"Liu T, Semin B, Klotz L, Godoy-Diana R, Wesfreid JE, Mullin T. Decay of streaks and rolls in plane Couette-Poiseuille flow. <i>Journal of Fluid Mechanics</i>. 2021;915. doi:<a href=\"https://doi.org/10.1017/jfm.2021.89\">10.1017/jfm.2021.89</a>","ista":"Liu T, Semin B, Klotz L, Godoy-Diana R, Wesfreid JE, Mullin T. 2021. Decay of streaks and rolls in plane Couette-Poiseuille flow. Journal of Fluid Mechanics. 915, A65.","ieee":"T. Liu, B. Semin, L. Klotz, R. Godoy-Diana, J. E. Wesfreid, and T. Mullin, “Decay of streaks and rolls in plane Couette-Poiseuille flow,” <i>Journal of Fluid Mechanics</i>, vol. 915. Cambridge University Press, 2021."},"article_number":"A65","year":"2021","abstract":[{"lang":"eng","text":"We report the results of an experimental investigation into the decay of turbulence in plane Couette–Poiseuille flow using ‘quench’ experiments where the flow laminarises after a sudden reduction in Reynolds number Re. Specifically, we study the velocity field in the streamwise–spanwise plane. We show that the spanwise velocity containing rolls decays faster than the streamwise velocity, which displays elongated regions of higher or lower velocity called streaks. At final Reynolds numbers above 425, the decay of streaks displays two stages: first a slow decay when rolls are present and secondly a more rapid decay of streaks alone. The difference in behaviour results from the regeneration of streaks by rolls, called the lift-up effect. We define the turbulent fraction as the portion of the flow containing turbulence and this is estimated by thresholding the spanwise velocity component. It decreases linearly with time in the whole range of final Re. The corresponding decay slope increases linearly with final Re. The extrapolated value at which this decay slope vanishes is Reaz≈656±10, close to Reg≈670 at which turbulence is self-sustained. The decay of the energy computed from the spanwise velocity component is found to be exponential. The corresponding decay rate increases linearly with Re, with an extrapolated vanishing value at ReAz≈688±10. This value is also close to the value at which the turbulence is self-sustained, showing that valuable information on the transition can be obtained over a wide range of Re."}],"publication_status":"published","title":"Decay of streaks and rolls in plane Couette-Poiseuille flow","oa_version":"Preprint","article_processing_charge":"No","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.08851"}],"doi":"10.1017/jfm.2021.89","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"acknowledgement":"We gratefully acknowledge Joran Rolland, Yohann Duguet, Romain Monchaux, S´ebastien Gom´e, Laurette Tuckerman, Dwight Barkley, Olivier Dauchot and Sabine Bottin for fruitful discussions. We thank Xavier Benoit-Gonin, Amaury Fourgeaud, Thierry Darnige, Olivier Brouard and Justine Laurent for technical help. This work has benefited from the ANR TransFlow, and by starting grants obtained by B.S. from CNRS (INSIS) and ESPCI. T.M. was\r\nsupported by a Joliot visiting professorship grant from ESPCI.","article_type":"original","department":[{"_id":"BjHo"}],"date_updated":"2023-08-07T14:30:11Z","publication":"Journal of Fluid Mechanics","arxiv":1,"intvolume":"       915","volume":915,"oa":1,"author":[{"full_name":"Liu, T.","first_name":"T.","last_name":"Liu"},{"full_name":"Semin, B.","first_name":"B.","last_name":"Semin"},{"first_name":"Lukasz","last_name":"Klotz","orcid":"0000-0003-1740-7635","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","full_name":"Klotz, Lukasz"},{"first_name":"R.","last_name":"Godoy-Diana","full_name":"Godoy-Diana, R."},{"full_name":"Wesfreid, J. E.","last_name":"Wesfreid","first_name":"J. E."},{"first_name":"T.","last_name":"Mullin","full_name":"Mullin, T."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"abstract":[{"text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. ","lang":"eng"}],"citation":{"ama":"Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). <i>Autophagy</i>. 2021;17(1):1-382. doi:<a href=\"https://doi.org/10.1080/15548627.2020.1797280\">10.1080/15548627.2020.1797280</a>","ieee":"D. J. Klionsky <i>et al.</i>, “Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition),” <i>Autophagy</i>, vol. 17, no. 1. Taylor &#38; Francis, pp. 1–382, 2021.","ista":"Klionsky DJ et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 17(1), 1–382.","apa":"Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., … Tong, C. K. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>","short":"D.J. Klionsky, A.K. Abdel-Aziz, S. Abdelfatah, M. Abdellatif, A. Abdoli, S. Abel, H. Abeliovich, M.H. Abildgaard, Y.P. Abudu, A. Acevedo-Arozena, I.E. Adamopoulos, K. Adeli, T.E. Adolph, A. Adornetto, E. Aflaki, G. Agam, A. Agarwal, B.B. Aggarwal, M. Agnello, P. Agostinis, J.N. Agrewala, A. Agrotis, P.V. Aguilar, S.T. Ahmad, Z.M. Ahmed, U. Ahumada-Castro, S. Aits, S. Aizawa, Y. Akkoc, T. Akoumianaki, H.A. Akpinar, A.M. Al-Abd, L. Al-Akra, A. Al-Gharaibeh, M.A. Alaoui-Jamali, S. Alberti, E. Alcocer-Gómez, C. Alessandri, M. Ali, M.A. Alim Al-Bari, S. Aliwaini, J. Alizadeh, E. Almacellas, A. Almasan, A. Alonso, G.D. Alonso, N. Altan-Bonnet, D.C. Altieri, É.M.C. Álvarez, S. Alves, C. Alves Da Costa, M.M. Alzaharna, M. Amadio, C. Amantini, C. Amaral, S. Ambrosio, A.O. Amer, V. Ammanathan, Z. An, S.U. Andersen, S.A. Andrabi, M. Andrade-Silva, A.M. Andres, S. Angelini, D. Ann, U.C. Anozie, M.Y. Ansari, P. Antas, A. Antebi, Z. Antón, T. Anwar, L. Apetoh, N. Apostolova, T. Araki, Y. Araki, K. Arasaki, W.L. Araújo, J. Araya, C. Arden, M.A. Arévalo, S. Arguelles, E. Arias, J. Arikkath, H. Arimoto, A.R. Ariosa, D. Armstrong-James, L. Arnauné-Pelloquin, A. Aroca, D.S. Arroyo, I. Arsov, R. Artero, D.M.L. Asaro, M. Aschner, M. Ashrafizadeh, O. Ashur-Fabian, A.G. Atanasov, A.K. Au, P. Auberger, H.W. Auner, L. Aurelian, R. Autelli, L. Avagliano, Y. Ávalos, S. Aveic, C.A. Aveleira, T. Avin-Wittenberg, Y. Aydin, S. Ayton, S. Ayyadevara, M. Azzopardi, M. Baba, J.M. Backer, S.K. Backues, D.H. Bae, O.N. Bae, S.H. Bae, E.H. Baehrecke, A. Baek, S.H. Baek, S.H. Baek, G. Bagetta, A. Bagniewska-Zadworna, H. Bai, J. Bai, X. Bai, Y. Bai, N. Bairagi, S. Baksi, T. Balbi, C.T. Baldari, W. Balduini, A. Ballabio, M. Ballester, S. Balazadeh, R. Balzan, R. Bandopadhyay, S. Banerjee, S. Banerjee, Á. Bánréti, Y. Bao, M.S. Baptista, A. Baracca, C. Barbati, A. Bargiela, D. Barilà, P.G. Barlow, S.J. Barmada, E. Barreiro, G.E. Barreto, J. Bartek, B. Bartel, A. Bartolome, G.R. Barve, S.H. Basagoudanavar, D.C. Bassham, R.C. Bast, A. Basu, H. Batoko, I. Batten, E.E. Baulieu, B.L. Baumgarner, J. Bayry, R. Beale, I. Beau, F. Beaumatin, L.R.G. Bechara, G.R. Beck, M.F. Beers, J. Begun, C. Behrends, G.M.N. Behrens, R. Bei, E. Bejarano, S. Bel, C. Behl, A. Belaid, N. Belgareh-Touzé, C. Bellarosa, F. Belleudi, M. Belló Pérez, R. Bello-Morales, J.S.D.O. Beltran, S. Beltran, D.M. Benbrook, M. Bendorius, B.A. Benitez, I. Benito-Cuesta, J. Bensalem, M.W. Berchtold, S. Berezowska, D. Bergamaschi, M. Bergami, A. Bergmann, L. Berliocchi, C. Berlioz-Torrent, A. Bernard, L. Berthoux, C.G. Besirli, S. Besteiro, V.M. Betin, R. Beyaert, J.S. Bezbradica, K. Bhaskar, I. Bhatia-Kissova, R. Bhattacharya, S. Bhattacharya, S. Bhattacharyya, M.S. Bhuiyan, S.K. Bhutia, L. Bi, X. Bi, T.J. Biden, K. Bijian, V.A. Billes, N. Binart, C. Bincoletto, A.B. Birgisdottir, G. 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Taylor &#38; Francis, 2021. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>.","mla":"Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” <i>Autophagy</i>, vol. 17, no. 1, Taylor &#38; Francis, 2021, pp. 1–382, doi:<a href=\"https://doi.org/10.1080/15548627.2020.1797280\">10.1080/15548627.2020.1797280</a>."},"year":"2021","date_created":"2021-03-28T22:01:44Z","_id":"9298","publication_identifier":{"eissn":["1554-8635"],"issn":["1554-8627"]},"acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support.","article_type":"review","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1080/15548627.2020.1797280","open_access":"1"}],"doi":"10.1080/15548627.2020.1797280","oa_version":"Published Version","article_processing_charge":"No","title":"Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)","publication_status":"published","intvolume":"        17","date_updated":"2023-10-16T09:43:56Z","publication":"Autophagy","department":[{"_id":"JiFr"},{"_id":"CaHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Daniel J.","last_name":"Klionsky","full_name":"Klionsky, Daniel J."},{"first_name":"Amal Kamal","last_name":"Abdel-Aziz","full_name":"Abdel-Aziz, Amal Kamal"},{"full_name":"Abdelfatah, Sara","first_name":"Sara","last_name":"Abdelfatah"},{"last_name":"Abdellatif","first_name":"Mahmoud","full_name":"Abdellatif, Mahmoud"},{"first_name":"Asghar","last_name":"Abdoli","full_name":"Abdoli, Asghar"},{"full_name":"Abel, Steffen","first_name":"Steffen","last_name":"Abel"},{"full_name":"Abeliovich, Hagai","first_name":"Hagai","last_name":"Abeliovich"},{"full_name":"Abildgaard, Marie H.","first_name":"Marie H.","last_name":"Abildgaard"},{"first_name":"Yakubu Princely","last_name":"Abudu","full_name":"Abudu, Yakubu Princely"},{"last_name":"Acevedo-Arozena","first_name":"Abraham","full_name":"Acevedo-Arozena, Abraham"},{"first_name":"Iannis E.","last_name":"Adamopoulos","full_name":"Adamopoulos, Iannis E."},{"full_name":"Adeli, Khosrow","first_name":"Khosrow","last_name":"Adeli"},{"last_name":"Adolph","first_name":"Timon E.","full_name":"Adolph, Timon E."},{"last_name":"Adornetto","first_name":"Annagrazia","full_name":"Adornetto, Annagrazia"},{"full_name":"Aflaki, Elma","first_name":"Elma","last_name":"Aflaki"},{"full_name":"Agam, Galila","first_name":"Galila","last_name":"Agam"},{"first_name":"Anupam","last_name":"Agarwal","full_name":"Agarwal, Anupam"},{"full_name":"Aggarwal, Bharat B.","last_name":"Aggarwal","first_name":"Bharat B."},{"last_name":"Agnello","first_name":"Maria","full_name":"Agnello, Maria"},{"full_name":"Agostinis, Patrizia","last_name":"Agostinis","first_name":"Patrizia"},{"full_name":"Agrewala, Javed N.","last_name":"Agrewala","first_name":"Javed N."},{"last_name":"Agrotis","first_name":"Alexander","full_name":"Agrotis, Alexander"},{"last_name":"Aguilar","first_name":"Patricia V.","full_name":"Aguilar, Patricia V."},{"full_name":"Ahmad, S. 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