[{"publication_status":"published","oa_version":"Preprint","fulldoi":"https://doi.org/10.1103/PhysRevA.105.063329","oa":1,"article_processing_charge":"No","title":"Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations","_id":"11592","department":[{"_id":"MiLe"}],"date_created":"2022-07-17T22:01:55Z","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"volume":105,"article_number":"063329","abstract":[{"lang":"eng","text":"We compare recent experimental results [Science 375, 528 (2022)] of the superfluid unitary Fermi gas near the critical temperature with a thermodynamic model based on the elementary excitations of the system. We find good agreement between experimental data and our theory for several quantities such as first sound, second sound, and superfluid fraction. We also show that mode mixing between first and second sound occurs. Finally, we characterize the response amplitude to a density perturbation: Close to the critical temperature both first and second sound can be excited through a density perturbation, whereas at lower temperatures only the first sound mode exhibits a significant response."}],"arxiv":1,"date_updated":"2023-08-03T12:00:11Z","intvolume":"       105","year":"2022","language":[{"iso":"eng"}],"publisher":"American Physical Society","type":"journal_article","day":"30","article_type":"original","doi":"10.1103/PhysRevA.105.063329","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publication":"Physical Review A","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2206.03924"}],"issue":"6","status":"public","isi":1,"month":"06","author":[{"last_name":"Bighin","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"},{"last_name":"Cappellaro","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","first_name":"Alberto"},{"last_name":"Salasnich","full_name":"Salasnich, L.","first_name":"L."}],"citation":{"chicago":"Bighin, Giacomo, Alberto Cappellaro, and L. Salasnich. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>.","short":"G. Bighin, A. Cappellaro, L. Salasnich, Physical Review A 105 (2022).","ista":"Bighin G, Cappellaro A, Salasnich L. 2022. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. Physical Review A. 105(6), 063329.","apa":"Bighin, G., Cappellaro, A., &#38; Salasnich, L. (2022). Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>","mla":"Bighin, Giacomo, et al. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>, vol. 105, no. 6, 063329, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>.","ama":"Bighin G, Cappellaro A, Salasnich L. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>","ieee":"G. Bighin, A. Cappellaro, and L. Salasnich, “Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022."},"scopus_import":"1","external_id":{"isi":["000829758500010"],"arxiv":["2206.03924"]},"acknowledgement":"The authors gratefully acknowledge stimulating discussions with T. Enss, and thank an anonymous referee for suggestions and remarks that allowed us to improve the original manuscript. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster).","date_published":"2022-06-30T00:00:00Z"},{"citation":{"apa":"Fulek, R., &#38; Kynčl, J. (2022). The Z2-Genus of Kuratowski minors. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00412-w\">https://doi.org/10.1007/s00454-022-00412-w</a>","ista":"Fulek R, Kynčl J. 2022. The Z2-Genus of Kuratowski minors. Discrete and Computational Geometry. 68, 425–447.","short":"R. Fulek, J. Kynčl, Discrete and Computational Geometry 68 (2022) 425–447.","mla":"Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” <i>Discrete and Computational Geometry</i>, vol. 68, Springer Nature, 2022, pp. 425–47, doi:<a href=\"https://doi.org/10.1007/s00454-022-00412-w\">10.1007/s00454-022-00412-w</a>.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-022-00412-w\">https://doi.org/10.1007/s00454-022-00412-w</a>.","ieee":"R. Fulek and J. Kynčl, “The Z2-Genus of Kuratowski minors,” <i>Discrete and Computational Geometry</i>, vol. 68. Springer Nature, pp. 425–447, 2022.","ama":"Fulek R, Kynčl J. The Z2-Genus of Kuratowski minors. <i>Discrete and Computational Geometry</i>. 2022;68:425-447. doi:<a href=\"https://doi.org/10.1007/s00454-022-00412-w\">10.1007/s00454-022-00412-w</a>"},"scopus_import":"1","external_id":{"isi":["000825014500001"],"arxiv":["1803.05085"]},"date_published":"2022-09-01T00:00:00Z","acknowledgement":"We thank Zdeněk Dvořák, Xavier Goaoc, and Pavel Paták for helpful discussions. We also thank Bojan Mohar, Paul Seymour, Gelasio Salazar, Jim Geelen, and John Maharry for information about their unpublished results related to Conjecture 3.1. Finally we thank the reviewers for corrections and suggestions for improving the presentation.\r\nSupported by Austrian Science Fund (FWF): M2281-N35. Supported by project 19-04113Y of the Czech Science Foundation (GAČR), by the Czech-French collaboration project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM), and by Charles University project UNCE/SCI/004.","article_type":"original","day":"01","doi":"10.1007/s00454-022-00412-w","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Discrete and Computational Geometry","related_material":{"record":[{"id":"186","relation":"earlier_version","status":"public"}]},"quality_controlled":"1","author":[{"first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"}],"month":"09","isi":1,"status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z2 -genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t×t grid or one of the following so-called t -Kuratowski graphs: K3,t, or t copies of K5 or K3,3 sharing at most two common vertices. We show that the Z2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its Z2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani–Tutte theorem on orientable surfaces. We also obtain an analogous result for Euler genus and Euler Z2-genus of graphs.","lang":"eng"}],"arxiv":1,"page":"425-447","volume":68,"date_updated":"2025-04-14T13:52:37Z","intvolume":"        68","type":"journal_article","publisher":"Springer Nature","language":[{"iso":"eng"}],"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","grant_number":"M02281"}],"year":"2022","fulldoi":"https://doi.org/10.1007/s00454-022-00412-w","oa_version":"Preprint","publication_status":"published","article_processing_charge":"No","oa":1,"department":[{"_id":"UlWa"}],"_id":"11593","title":"The Z2-Genus of Kuratowski minors","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"date_created":"2022-07-17T22:01:56Z"},{"date_created":"2022-07-20T11:21:53Z","publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","_id":"11626","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"degree_awarded":"PhD","oa":1,"article_processing_charge":"No","publication_status":"published","OA_place":"publisher","oa_version":"Published Version","fulldoi":"https://doi.org/10.15479/at:ista:11626","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"year":"2022","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","file":[{"date_created":"2022-07-25T09:08:47Z","file_size":9730864,"checksum":"bd7ac35403cf5b4b2607287d2a104b3a","content_type":"application/pdf","file_id":"11645","creator":"mgallei","file_name":"Thesis_Gallei.pdf","access_level":"open_access","relation":"main_file","date_updated":"2022-07-25T09:08:47Z"},{"date_created":"2022-07-25T09:09:09Z","file_size":19560720,"checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"11646","creator":"mgallei","access_level":"closed","file_name":"Thesis_Gallei_source.docx","date_updated":"2022-07-25T09:39:58Z","relation":"source_file"},{"date_created":"2022-07-25T09:09:32Z","file_size":24542837,"checksum":"3994f7f20058941b5bb8a16886b21e71","content_type":"application/pdf","file_id":"11647","creator":"mgallei","access_level":"closed","file_name":"Thesis_Gallei_to_print.pdf","description":"This is the print version of the thesis including the full appendix","date_updated":"2022-07-25T09:39:58Z","relation":"source_file"},{"creator":"mgallei","content_type":"application/pdf","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","file_id":"11650","file_name":"Thesis_Gallei_Appendix.pdf","access_level":"open_access","relation":"main_file","date_updated":"2022-07-25T11:48:45Z","file_size":15435966,"date_created":"2022-07-25T11:48:45Z"}],"date_updated":"2026-06-18T19:02:05Z","page":"248","abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"status":"public","ddc":["575"],"month":"07","author":[{"orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei"}],"related_material":{"record":[{"id":"8138","relation":"part_of_dissertation","status":"public"},{"id":"7142","relation":"part_of_dissertation","status":"public"},{"id":"10411","status":"public","relation":"part_of_dissertation"},{"id":"8931","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7465"},{"status":"public","relation":"part_of_dissertation","id":"9287"},{"id":"6260","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/at:ista:11626","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"last_name":"Shani","first_name":"Eilon","full_name":"Shani, Eilon"}],"day":"20","has_accepted_license":"1","file_date_updated":"2022-07-25T11:48:45Z","date_published":"2022-07-20T00:00:00Z","corr_author":"1","ec_funded":1,"citation":{"ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","apa":"Gallei, M. C. (2022). <i>Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","mla":"Gallei, Michelle C. <i>Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>.","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>."}},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-06-21T00:00:00Z","file_date_updated":"2022-07-25T07:38:49Z","has_accepted_license":"1","acknowledgement":" This work was funded by H2020 European Research Council (ERC Advanced grant, 269058 ACMO, https://erc.europa.eu/funding/advanced-grants) and Wellcome Trust UK (Wellcome Investigator Award, 209504/Z/17/Z, https://wellcome.org/grant-funding/people-and-projects/grants-awarded/molecular-mechanisms-neural-circuit-function-0) to M.d.B, and by H2020 European Research Council (ERC starting grant, 802653 OXYGEN SENSING, https://erc.europa.eu/funding/starting-grants) and Vetenskapsrådet (VR starting grant, 2018-02216, https://www.vr.se/english.html) to C.C. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","corr_author":"1","external_id":{"isi":["000828679600001"],"pmid":["35727855"]},"scopus_import":"1","citation":{"mla":"Zhao, Lina, et al. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>, vol. 20, no. 6, e3001684, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>.","ista":"Zhao L, Fenk LA, Nilsson L, Amin-Wetzel NP, Ramirez N, de Bono M, Chen C. 2022. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. PLoS Biology. 20(6), e3001684.","short":"L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono, C. Chen, PLoS Biology 20 (2022).","apa":"Zhao, L., Fenk, L. A., Nilsson, L., Amin-Wetzel, N. P., Ramirez, N., de Bono, M., &#38; Chen, C. (2022). ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>","chicago":"Zhao, Lina, Lorenz A. Fenk, Lars Nilsson, Niko Paresh Amin-Wetzel, Nelson Ramirez, Mario de Bono, and Changchun Chen. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>.","ama":"Zhao L, Fenk LA, Nilsson L, et al. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. 2022;20(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>","ieee":"L. Zhao <i>et al.</i>, “ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans,” <i>PLoS Biology</i>, vol. 20, no. 6. Public Library of Science, 2022."},"status":"public","isi":1,"month":"06","ddc":["570"],"author":[{"last_name":"Zhao","first_name":"Lina","full_name":"Zhao, Lina"},{"last_name":"Fenk","first_name":"Lorenz A.","full_name":"Fenk, Lorenz A."},{"first_name":"Lars","full_name":"Nilsson, Lars","last_name":"Nilsson"},{"first_name":"Niko Paresh","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","full_name":"Amin-Wetzel, Niko Paresh","last_name":"Amin-Wetzel"},{"last_name":"Ramirez","first_name":"Nelson","full_name":"Ramirez, Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario","last_name":"De Bono"},{"first_name":"Changchun","full_name":"Chen, Changchun","last_name":"Chen"}],"issue":"6","publication":"PLoS Biology","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1371/journal.pbio.3001684","day":"21","article_type":"original","license":"https://creativecommons.org/licenses/by/4.0/","publisher":"Public Library of Science","type":"journal_article","project":[{"name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z"}],"year":"2022","language":[{"iso":"eng"}],"intvolume":"        20","date_updated":"2025-04-15T07:32:21Z","file":[{"access_level":"open_access","file_name":"2022_PLoSBiology_Zhao.pdf","relation":"main_file","date_updated":"2022-07-25T07:38:49Z","creator":"dernst","content_type":"application/pdf","checksum":"df4902f854ad76769d3203bfdc69f16c","file_id":"11643","file_size":3721585,"date_created":"2022-07-25T07:38:49Z","success":1}],"abstract":[{"lang":"eng","text":"The ability to detect and respond to acute oxygen (O2) shortages is indispensable to aerobic life. The molecular mechanisms and circuits underlying this capacity are poorly understood. Here, we characterize the behavioral responses of feeding Caenorhabditis elegans to approximately 1% O2. Acute hypoxia triggers a bout of turning maneuvers followed by a persistent switch to rapid forward movement as animals seek to avoid and escape hypoxia. While the behavioral responses to 1% O2 closely resemble those evoked by 21% O2, they have distinct molecular and circuit underpinnings. Disrupting phosphodiesterases (PDEs), specific G proteins, or BBSome function inhibits escape from 1% O2 due to increased cGMP signaling. A primary source of cGMP is GCY-28, the ortholog of the atrial natriuretic peptide (ANP) receptor. cGMP activates the protein kinase G EGL-4 and enhances neuroendocrine secretion to inhibit acute responses to 1% O2. Triggering a rise in cGMP optogenetically in multiple neurons, including AIA interneurons, rapidly and reversibly inhibits escape from 1% O2. Ca2+ imaging reveals that a 7% to 1% O2 stimulus evokes a Ca2+ decrease in several neurons. Defects in mitochondrial complex I (MCI) and mitochondrial complex I (MCIII), which lead to persistently high reactive oxygen species (ROS), abrogate acute hypoxia responses. In particular, repressing the expression of isp-1, which encodes the iron sulfur protein of MCIII, inhibits escape from 1% O2 without affecting responses to 21% O2. Both genetic and pharmacological up-regulation of mitochondrial ROS increase cGMP levels, which contribute to the reduced hypoxia responses. Our results implicate ROS and precise regulation of intracellular cGMP in the modulation of acute responses to hypoxia by C. elegans."}],"volume":20,"article_number":"e3001684","publication_identifier":{"eissn":["1545-7885"]},"date_created":"2022-07-24T22:01:42Z","department":[{"_id":"MaDe"}],"title":"ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans","_id":"11637","article_processing_charge":"No","oa":1,"oa_version":"Published Version","pmid":1,"fulldoi":"https://doi.org/10.1371/journal.pbio.3001684","publication_status":"published"},{"date_published":"2022-06-24T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","file_date_updated":"2022-07-25T07:47:23Z","acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030).","external_id":{"pmid":["37576946"],"arxiv":["2106.02349"]},"scopus_import":"1","citation":{"chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>.","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>.","apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., &#38; Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>","ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","ieee":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” <i>Physical Review Research</i>, vol. 4, no. 2. American Physical Society, 2022.","ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. 2022;4(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>"},"author":[{"first_name":"Vudtiwat","full_name":"Ngampruetikorn, Vudtiwat","last_name":"Ngampruetikorn"},{"last_name":"Sachdeva","full_name":"Sachdeva, Vedant","first_name":"Vedant"},{"full_name":"Torrence, Johanna","first_name":"Johanna","last_name":"Torrence"},{"last_name":"Humplik","first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","full_name":"Humplik, Jan"},{"last_name":"Schwab","first_name":"David J.","full_name":"Schwab, David J."},{"last_name":"Palmer","first_name":"Stephanie E.","full_name":"Palmer, Stephanie E."}],"ddc":["530"],"month":"06","status":"public","issue":"2","publication":"Physical Review Research","quality_controlled":"1","doi":"10.1103/PhysRevResearch.4.023240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","day":"24","type":"journal_article","publisher":"American Physical Society","language":[{"iso":"eng"}],"year":"2022","intvolume":"         4","date_updated":"2025-03-06T14:09:21Z","file":[{"success":1,"file_size":1379683,"date_created":"2022-07-25T07:47:23Z","creator":"dernst","content_type":"application/pdf","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","file_id":"11644","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","access_level":"open_access","date_updated":"2022-07-25T07:47:23Z","relation":"main_file"}],"arxiv":1,"abstract":[{"lang":"eng","text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data."}],"article_number":"023240","volume":4,"publication_identifier":{"issn":["2643-1564"]},"date_created":"2022-07-24T22:01:42Z","department":[{"_id":"GaTk"}],"_id":"11638","title":"Inferring couplings in networks across order-disorder phase transitions","article_processing_charge":"No","oa":1,"fulldoi":"https://doi.org/10.1103/PhysRevResearch.4.023240","pmid":1,"oa_version":"Published Version","publication_status":"published"},{"citation":{"ieee":"Y. Zhang and S. Vatedka, “List decoding random Euclidean codes and Infinite constellations,” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12. IEEE, pp. 7753–7786, 2022.","ama":"Zhang Y, Vatedka S. List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. 2022;68(12):7753-7786. doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>","mla":"Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12, IEEE, 2022, pp. 7753–86, doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>.","apa":"Zhang, Y., &#38; Vatedka, S. (2022). List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2022.3189542\">https://doi.org/10.1109/TIT.2022.3189542</a>","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786.","ista":"Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.","chicago":"Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2022. <a href=\"https://doi.org/10.1109/TIT.2022.3189542\">https://doi.org/10.1109/TIT.2022.3189542</a>."},"scopus_import":"1","external_id":{"isi":["000891796100007"],"arxiv":["1901.03790"]},"corr_author":"1","acknowledgement":"This work was done when Shashank Vatedka was at the Chinese University of Hong Kong, where he was supported in part by CUHK Direct Grants 4055039 and 4055077. He would like to acknowledge funding from a seed grant offered by IIT Hyderabad and the Start-up Research Grant (SRG/2020/000910) from the Science and Engineering Board, India. Yihan Zhang has received funding from the European Union’s Horizon 2020 research and innovation programme\r\nunder grant agreement No 682203-ERC-[Inf-Speed-Tradeoff].","date_published":"2022-12-01T00:00:00Z","day":"01","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1109/TIT.2022.3189542","quality_controlled":"1","publication":"IEEE Transactions on Information Theory","issue":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1901.03790"}],"isi":1,"status":"public","month":"12","author":[{"last_name":"Zhang","full_name":"Zhang, Yihan","orcid":"0000-0002-6465-6258","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan"},{"first_name":"Shashank","full_name":"Vatedka, Shashank","last_name":"Vatedka"}],"volume":68,"page":"7753-7786","arxiv":1,"abstract":[{"text":"We study the list decodability of different ensembles of codes over the real alphabet under the assumption of an omniscient adversary. It is a well-known result that when the source and the adversary have power constraints P and N respectively, the list decoding capacity is equal to 1/2logP/N. Random spherical codes achieve constant list sizes, and the goal of the present paper is to obtain a better understanding of the smallest achievable list size as a function of the gap to capacity. We show a reduction from arbitrary codes to spherical codes, and derive a lower bound on the list size of typical random spherical codes. We also give an upper bound on the list size achievable using nested Construction-A lattices and infinite Construction-A lattices. We then define and study a class of infinite constellations that generalize Construction-A lattices and prove upper and lower bounds for the same. Other goodness properties such as packing goodness and AWGN goodness of infinite constellations are proved along the way. Finally, we consider random lattices sampled from the Haar distribution and show that if a certain conjecture that originates in analytic number theory is true, then the list size grows as a polynomial function of the gap-to-capacity.","lang":"eng"}],"date_updated":"2024-10-09T21:02:55Z","intvolume":"        68","year":"2022","language":[{"iso":"eng"}],"publisher":"IEEE","type":"journal_article","publication_status":"published","oa_version":"Preprint","fulldoi":"https://doi.org/10.1109/TIT.2022.3189542","oa":1,"article_processing_charge":"No","title":"List decoding random Euclidean codes and Infinite constellations","_id":"11639","department":[{"_id":"MaMo"}],"date_created":"2022-07-24T22:01:42Z","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]}},{"department":[{"_id":"NiBa"}],"title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","_id":"11640","publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"date_created":"2022-07-24T22:01:43Z","oa_version":"Published Version","fulldoi":"https://doi.org/10.1111/1755-0998.13676","pmid":1,"publication_status":"published","article_processing_charge":"Yes (via OA deal)","oa":1,"publisher":"Wiley","type":"journal_article","year":"2022","project":[{"name":"Rate of Adaptation in Changing Environment","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"704172"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST, a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST. Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size."}],"volume":22,"page":"2941-2955","intvolume":"        22","date_updated":"2025-06-11T14:01:43Z","file":[{"success":1,"file_size":6431779,"date_created":"2023-02-02T08:11:23Z","creator":"dernst","checksum":"3102e203e77b884bffffdbe8e548da88","content_type":"application/pdf","file_id":"12477","access_level":"open_access","file_name":"2022_MolecularEcologyRes_Szep.pdf","date_updated":"2023-02-02T08:11:23Z","relation":"main_file"}],"publication":"Molecular Ecology Resources","quality_controlled":"1","status":"public","isi":1,"ddc":["570"],"month":"11","author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko","first_name":"Eniko","last_name":"Szep"},{"last_name":"Trubenova","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"},{"first_name":"Katalin","full_name":"Csilléry, Katalin","last_name":"Csilléry"}],"issue":"8","day":"01","license":"https://creativecommons.org/licenses/by-nc/4.0/","article_type":"original","doi":"10.1111/1755-0998.13676","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","external_id":{"pmid":["35765749"],"isi":["000825873600001"]},"date_published":"2022-11-01T00:00:00Z","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file_date_updated":"2023-02-02T08:11:23Z","acknowledgement":"ES was supported by an IST studentship provided by IST Austria. BT was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project received further funding awarded to KC from the Swiss National Science Foundation (SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick Barton for many invaluable discussions and his comments on the thesis chapter and this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for providing us with the raw data from the LPX-Bern model for silver fir, and Willy Tinner for helpful insights about the demographic history of silver fir. We also thank the editor Alana Alexander for useful comments and advice on the manuscript. Open access funding provided by Eidgenossische Technische Hochschule Zurich.","has_accepted_license":"1","citation":{"mla":"Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>.","apa":"Szep, E., Trubenova, B., &#38; Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>","ista":"Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 22(8), 2941–2955.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","chicago":"Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>.","ama":"Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. 2022;22(8):2941-2955. doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>","ieee":"E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size,” <i>Molecular Ecology Resources</i>, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022."},"ec_funded":1,"scopus_import":"1"},{"year":"2022","language":[{"iso":"eng"}],"publisher":"Oxford University Press","type":"journal_article","file":[{"file_name":"2022_Microscopy_Gerle.pdf","access_level":"open_access","relation":"main_file","date_updated":"2023-02-03T08:34:48Z","content_type":"application/pdf","checksum":"23b51c163636bf9313f7f0818312e67e","file_id":"12498","creator":"dernst","date_created":"2023-02-03T08:34:48Z","file_size":7812696,"success":1}],"intvolume":"        71","date_updated":"2023-08-03T12:13:37Z","volume":71,"page":"249-261","abstract":[{"text":"Progress in structural membrane biology has been significantly accelerated by the ongoing 'Resolution Revolution' in cryo electron microscopy (cryo-EM). In particular, structure determination by single particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella enterica.","lang":"eng"}],"date_created":"2022-07-25T10:04:58Z","publication_identifier":{"eissn":["2050-5701"],"issn":["2050-5698"]},"title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","_id":"11648","department":[{"_id":"LeSa"}],"oa":1,"article_processing_charge":"No","publication_status":"published","oa_version":"Published Version","pmid":1,"fulldoi":"https://doi.org/10.1093/jmicro/dfac037","has_accepted_license":"1","acknowledgement":"Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266 to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows (20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer project and also would like to thank Hideki Shigematsu for critical reading of the manuscript. And we are indebted to the two anonymous reviewers who helped us to improve our manuscript.","file_date_updated":"2023-02-03T08:34:48Z","date_published":"2022-10-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000837950900001"],"pmid":["35861182"]},"scopus_import":"1","citation":{"chicago":"Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>.","apa":"Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino, F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>","ista":"Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.","short":"C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino, T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy 71 (2022) 249–261.","mla":"Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>, vol. 71, no. 5, Oxford University Press, 2022, pp. 249–61, doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>.","ieee":"C. Gerle <i>et al.</i>, “Structures of multisubunit membrane complexes with the CRYO ARM 200,” <i>Microscopy</i>, vol. 71, no. 5. Oxford University Press, pp. 249–261, 2022.","ama":"Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. 2022;71(5):249-261. doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>"},"issue":"5","month":"10","ddc":["570"],"status":"public","isi":1,"author":[{"first_name":"Christoph","full_name":"Gerle, Christoph","last_name":"Gerle"},{"last_name":"Kishikawa","full_name":"Kishikawa, Jun-ichi","first_name":"Jun-ichi"},{"first_name":"Tomoko","full_name":"Yamaguchi, Tomoko","last_name":"Yamaguchi"},{"last_name":"Nakanishi","full_name":"Nakanishi, Atsuko","first_name":"Atsuko"},{"orcid":"0000-0002-3219-2022","full_name":"Çoruh, Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","first_name":"Mehmet Orkun","last_name":"Çoruh"},{"full_name":"Makino, Fumiaki","first_name":"Fumiaki","last_name":"Makino"},{"first_name":"Tomoko","full_name":"Miyata, Tomoko","last_name":"Miyata"},{"full_name":"Kawamoto, Akihiro","first_name":"Akihiro","last_name":"Kawamoto"},{"last_name":"Yokoyama","first_name":"Ken","full_name":"Yokoyama, Ken"},{"last_name":"Namba","full_name":"Namba, Keiichi","first_name":"Keiichi"},{"last_name":"Kurisu","first_name":"Genji","full_name":"Kurisu, Genji"},{"last_name":"Kato","first_name":"Takayuki","full_name":"Kato, Takayuki"}],"quality_controlled":"1","publication":"Microscopy","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1093/jmicro/dfac037","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"day":"01","article_type":"original"},{"oa_version":"Published Version","day":"06","fulldoi":"https://doi.org/10.25338/B81931","license":"https://creativecommons.org/publicdomain/zero/1.0/","keyword":["Biological sciences"],"article_processing_charge":"No","doi":"10.25338/B81931","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","_id":"11686","related_material":{"record":[{"id":"10604","status":"public","relation":"used_in_publication"}]},"ddc":["570"],"month":"01","status":"public","author":[{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"date_created":"2022-07-29T06:45:41Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25338/B81931"}],"abstract":[{"text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes.","lang":"eng"}],"citation":{"apa":"Turelli, M., &#38; Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>","ista":"Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control, Dryad, <a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","short":"M. Turelli, N.H. Barton, (2022).","mla":"Turelli, Michael, and Nicholas H. Barton. <i>Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","chicago":"Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>.","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","ama":"Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>"},"date_updated":"2025-06-11T13:45:56Z","corr_author":"1","publisher":"Dryad","type":"research_data_reference","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"date_published":"2022-01-06T00:00:00Z","year":"2022","acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815"},{"external_id":{"arxiv":["2001.00512"],"isi":["000826695900001"]},"file_date_updated":"2022-08-01T10:39:36Z","has_accepted_license":"1","acknowledgement":"The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"date_published":"2022-08-04T00:00:00Z","citation":{"mla":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.” <i>Nonlinearity</i>, vol. 35, no. 8, IOP Publishing, 2022, pp. 4100–210, doi:<a href=\"https://doi.org/10.1088/1361-6544/abd613\">10.1088/1361-6544/abd613</a>.","apa":"Agresti, A., &#38; Veraar, M. (2022). Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6544/abd613\">https://doi.org/10.1088/1361-6544/abd613</a>","ista":"Agresti A, Veraar M. 2022. Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence. Nonlinearity. 35(8), 4100–4210.","short":"A. Agresti, M. Veraar, Nonlinearity 35 (2022) 4100–4210.","chicago":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.” <i>Nonlinearity</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1361-6544/abd613\">https://doi.org/10.1088/1361-6544/abd613</a>.","ama":"Agresti A, Veraar M. Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence. <i>Nonlinearity</i>. 2022;35(8):4100-4210. doi:<a href=\"https://doi.org/10.1088/1361-6544/abd613\">10.1088/1361-6544/abd613</a>","ieee":"A. Agresti and M. Veraar, “Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence,” <i>Nonlinearity</i>, vol. 35, no. 8. IOP Publishing, pp. 4100–4210, 2022."},"scopus_import":"1","quality_controlled":"1","publication":"Nonlinearity","issue":"8","author":[{"orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","last_name":"Agresti"},{"last_name":"Veraar","first_name":"Mark","full_name":"Veraar, Mark"}],"status":"public","isi":1,"ddc":["510"],"month":"08","license":"https://creativecommons.org/licenses/by/3.0/","article_type":"original","day":"04","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1088/1361-6544/abd613","language":[{"iso":"eng"}],"year":"2022","type":"journal_article","publisher":"IOP Publishing","page":"4100-4210","volume":35,"arxiv":1,"abstract":[{"lang":"eng","text":"In this paper we develop a new approach to nonlinear stochastic partial differential equations with Gaussian noise. Our aim is to provide an abstract framework which is applicable to a large class of SPDEs and includes many important cases of nonlinear parabolic problems which are of quasi- or semilinear type. This first part is on local existence and well-posedness. A second part in preparation is on blow-up criteria and regularization. Our theory is formulated in an Lp-setting, and because of this we can deal with nonlinearities in a very efficient way. Applications to several concrete problems and their quasilinear variants are given. This includes Burgers' equation, the Allen–Cahn equation, the Cahn–Hilliard equation, reaction–diffusion equations, and the porous media equation. The interplay of the nonlinearities and the critical spaces of initial data leads to new results and insights for these SPDEs. The proofs are based on recent developments in maximal regularity theory for the linearized problem for deterministic and stochastic evolution equations. In particular, our theory can be seen as a stochastic version of the theory of critical spaces due to Prüss–Simonett–Wilke (2018). Sharp weighted time-regularity allow us to deal with rough initial values and obtain instantaneous regularization results. The abstract well-posedness results are obtained by a combination of several sophisticated splitting and truncation arguments."}],"file":[{"creator":"dernst","checksum":"997a4bff2dfbee3321d081328c2f1e1a","content_type":"application/pdf","file_id":"11715","file_name":"2022_Nonlinearity_Agresti.pdf","access_level":"open_access","relation":"main_file","date_updated":"2022-08-01T10:39:36Z","success":1,"file_size":2122096,"date_created":"2022-08-01T10:39:36Z"}],"intvolume":"        35","date_updated":"2023-08-03T12:25:08Z","_id":"11701","title":"Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence","department":[{"_id":"JuFi"}],"date_created":"2022-07-31T22:01:47Z","publication_identifier":{"issn":["0951-7715"],"eissn":["1361-6544"]},"publication_status":"published","fulldoi":"https://doi.org/10.1088/1361-6544/abd613","oa_version":"Published Version","oa":1,"article_processing_charge":"No"},{"article_processing_charge":"No","oa":1,"oa_version":"Published Version","pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.2122147119","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"date_created":"2022-07-31T22:01:47Z","department":[{"_id":"NiBa"}],"title":"The \"New Synthesis\"","_id":"11702","date_updated":"2025-05-14T11:01:10Z","intvolume":"       119","file":[{"date_created":"2022-08-01T10:58:28Z","file_size":848511,"success":1,"access_level":"open_access","file_name":"2022_PNAS_Barton.pdf","date_updated":"2022-08-01T10:58:28Z","relation":"main_file","content_type":"application/pdf","checksum":"06c866196a8957f0c37b8a121771c885","file_id":"11716","creator":"dernst"}],"abstract":[{"text":"When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function.","lang":"eng"}],"volume":119,"article_number":"e2122147119","publisher":"National Academy of Sciences","type":"journal_article","year":"2022","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1073/pnas.2122147119","day":"18","article_type":"original","ddc":["570"],"status":"public","month":"07","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"issue":"30","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","scopus_import":"1","citation":{"ama":"Barton NH. The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(30). doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>","ieee":"N. H. Barton, “The ‘New Synthesis,’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30. National Academy of Sciences, 2022.","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>.","mla":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30, e2122147119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>.","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Barton, N. H. (2022). The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119."},"date_published":"2022-07-18T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","file_date_updated":"2022-08-01T10:58:28Z","has_accepted_license":"1","corr_author":"1","external_id":{"pmid":["35858408"]}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1371/journal.pgen.1010226","article_type":"original","day":"06","issue":"7","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"},{"first_name":"John R.","full_name":"Pannell, John R.","last_name":"Pannell"}],"isi":1,"month":"07","ddc":["570"],"status":"public","quality_controlled":"1","publication":"PLoS Genetics","scopus_import":"1","ec_funded":1,"citation":{"short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022).","ista":"Toups MA, Vicoso B, Pannell JR. 2022. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. 18(7), e1010226.","apa":"Toups, M. A., Vicoso, B., &#38; Pannell, J. R. (2022). Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>","mla":"Toups, Melissa A., et al. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>, vol. 18, no. 7, e1010226, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>.","chicago":"Toups, Melissa A, Beatriz Vicoso, and John R. Pannell. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>.","ama":"Toups MA, Vicoso B, Pannell JR. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. 2022;18(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>","ieee":"M. A. Toups, B. Vicoso, and J. R. Pannell, “Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis,” <i>PLoS Genetics</i>, vol. 18, no. 7. Public Library of Science, 2022."},"acknowledgement":"JRP was supported by the Swiss National Science Foundation (https://www.snf.ch/en), Sinergia grant 26073998. BV was supported by the European Research Council (https://erc.europa.eu/) under the European Union’s Horizon 2020 research and innovation program, grant number 715257. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\r\nPlants were grown in Lausanne by Aline Revel, and RNA extraction and library preparation were performed by Dessislava Savova Bianchi. All sequencing and the IsoSeq3 analysis were carried out by Center for Integrative Genomics at the University of Lausanne. All other computational analyses were performed on the server at IST Austria.","has_accepted_license":"1","file_date_updated":"2022-08-01T07:49:25Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-07-06T00:00:00Z","external_id":{"pmid":["35793353"],"isi":["000886643100006"]},"corr_author":"1","oa":1,"article_processing_charge":"No","publication_status":"published","pmid":1,"fulldoi":"https://doi.org/10.1371/journal.pgen.1010226","oa_version":"Published Version","date_created":"2022-07-31T22:01:48Z","publication_identifier":{"eissn":["1553-7404"]},"_id":"11703","title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","department":[{"_id":"BeVi"}],"file":[{"date_created":"2022-08-01T07:49:25Z","file_size":1620272,"success":1,"access_level":"open_access","file_name":"2022_PLoSGenetics_Toups.pdf","date_updated":"2022-08-01T07:49:25Z","relation":"main_file","checksum":"aa4c137f82635e700856c359dccfaa0a","content_type":"application/pdf","file_id":"11708","creator":"dernst"}],"date_updated":"2025-04-14T07:41:20Z","intvolume":"        18","article_number":"e1010226","volume":18,"abstract":[{"lang":"eng","text":"Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism."}],"language":[{"iso":"eng"}],"year":"2022","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"type":"journal_article","publisher":"Public Library of Science"},{"language":[{"iso":"eng"}],"year":"2022","type":"journal_article","publisher":"Public Library of Science","file":[{"creator":"dernst","file_id":"11712","content_type":"application/pdf","checksum":"1ddd9b91e6dec31ab0e7a8433ca2d452","date_updated":"2022-08-01T08:02:38Z","relation":"main_file","access_level":"open_access","file_name":"2022_PLoSONE_Budanur.pdf","success":1,"file_size":1421256,"date_created":"2022-08-01T08:02:38Z"}],"intvolume":"        17","date_updated":"2025-06-11T13:37:36Z","article_number":"e0269975","volume":17,"abstract":[{"text":"In Fall 2020, several European countries reported rapid increases in COVID-19 cases along with growing estimates of the effective reproduction rates. Such an acceleration in epidemic spread is usually attributed to time-dependent effects, e.g. human travel, seasonal behavioral changes, mutations of the pathogen etc. In this case however the acceleration occurred when counter measures such as testing and contact tracing exceeded their capacity limit. Considering Austria as an example, here we show that this dynamics can be captured by a time-independent, i.e. autonomous, compartmental model that incorporates these capacity limits. In this model, the epidemic acceleration coincides with the exhaustion of mitigation efforts, resulting in an increasing fraction of undetected cases that drive the effective reproduction rate progressively higher. We demonstrate that standard models which does not include this effect necessarily result in a systematic underestimation of the effective reproduction rate.","lang":"eng"}],"date_created":"2022-07-31T22:01:48Z","publication_identifier":{"eissn":["1932-6203"]},"_id":"11704","title":"An autonomous compartmental model for accelerating epidemics","department":[{"_id":"BjHo"}],"oa":1,"article_processing_charge":"No","publication_status":"published","pmid":1,"fulldoi":"https://doi.org/10.1371/journal.pone.0269975","oa_version":"Published Version","file_date_updated":"2022-08-01T08:02:38Z","has_accepted_license":"1","date_published":"2022-07-18T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["35849565"],"isi":["000911392100055"]},"corr_author":"1","scopus_import":"1","citation":{"chicago":"Budanur, Nazmi B, and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>.","ista":"Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating epidemics. PLoS ONE. 17(7), e0269975.","short":"N.B. Budanur, B. Hof, PLoS ONE 17 (2022).","apa":"Budanur, N. B., &#38; Hof, B. (2022). An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>","mla":"Budanur, Nazmi B., and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>, vol. 17, no. 7, e0269975, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>.","ama":"Budanur NB, Hof B. An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. 2022;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>","ieee":"N. B. Budanur and B. Hof, “An autonomous compartmental model for accelerating epidemics,” <i>PLoS ONE</i>, vol. 17, no. 7. Public Library of Science, 2022."},"issue":"7","author":[{"last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"ddc":["510"],"isi":1,"month":"07","status":"public","related_material":{"record":[{"relation":"research_data","status":"public","id":"11711"}]},"quality_controlled":"1","publication":"PLoS ONE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1371/journal.pone.0269975","article_type":"original","day":"18"},{"language":[{"iso":"eng"}],"year":"2022","project":[{"grant_number":"840605","name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"type":"conference","publisher":"Springer Nature","page":"1-20","volume":13298,"arxiv":1,"abstract":[{"text":"In this work we introduce the graph-theoretic notion of mendability: for each locally checkable graph problem we can define its mending radius, which captures the idea of how far one needs to modify a partial solution in order to “patch a hole.” We explore how mendability is connected to the existence of efficient algorithms, especially in distributed, parallel, and fault-tolerant settings. It is easy to see that O(1)-mendable problems are also solvable in O(log∗n) rounds in the LOCAL model of distributed computing. One of the surprises is that in paths and cycles, a converse also holds in the following sense: if a problem Π can be solved in O(log∗n), there is always a restriction Π′⊆Π that is still efficiently solvable but that is also O(1)-mendable. We also explore the structure of the landscape of mendability. For example, we show that in trees, the mending radius of any locally checkable problem is O(1), Θ(logn), or Θ(n), while in general graphs the structure is much more diverse.","lang":"eng"}],"conference":{"name":"SIROCCO: Structural Information and Communication Complexity","end_date":"2022-06-29","start_date":"2022-06-27","location":"Paderborn, Germany"},"date_updated":"2025-04-14T07:50:55Z","intvolume":"     13298","_id":"11707","title":"Local mending","department":[{"_id":"DaAl"}],"date_created":"2022-07-31T22:01:49Z","publication_identifier":{"isbn":["9783031099922"],"issn":["0302-9743"],"eissn":["1611-3349"]},"publication_status":"published","fulldoi":"https://doi.org/10.1007/978-3-031-09993-9_1","oa_version":"Preprint","oa":1,"editor":[{"last_name":"Parter","full_name":"Parter, Merav","first_name":"Merav"}],"article_processing_charge":"No","external_id":{"isi":["000876977400001"],"arxiv":["2102.08703"]},"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 840605. This work was supported in part by the Academy of Finland, Grants 314888 and 333837. The authors would also like to thank David Harris, Neven Villani, and the anonymous reviewers for their very helpful comments and feedback on previous versions of this work.","date_published":"2022-06-25T00:00:00Z","citation":{"chicago":"Balliu, Alkida, Juho Hirvonen, Darya Melnyk, Dennis Olivetti, Joel Rybicki, and Jukka Suomela. “Local Mending.” In <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, 13298:1–20. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>.","ista":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. 2022. Local mending. International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication ComplexityLNCS vol. 13298, 1–20.","apa":"Balliu, A., Hirvonen, J., Melnyk, D., Olivetti, D., Rybicki, J., &#38; Suomela, J. (2022). Local mending. In M. Parter (Ed.), <i>International Colloquium on Structural Information and Communication Complexity</i> (Vol. 13298, pp. 1–20). Paderborn, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>","short":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, J. Suomela, in:, M. Parter (Ed.), International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2022, pp. 1–20.","mla":"Balliu, Alkida, et al. “Local Mending.” <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, vol. 13298, Springer Nature, 2022, pp. 1–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>.","ieee":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, and J. Suomela, “Local mending,” in <i>International Colloquium on Structural Information and Communication Complexity</i>, Paderborn, Germany, 2022, vol. 13298, pp. 1–20.","ama":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. Local mending. In: Parter M, ed. <i>International Colloquium on Structural Information and Communication Complexity</i>. Vol 13298. LNCS. Springer Nature; 2022:1-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>"},"scopus_import":"1","ec_funded":1,"quality_controlled":"1","publication":"International Colloquium on Structural Information and Communication Complexity","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08703"}],"series_title":"LNCS","author":[{"full_name":"Balliu, Alkida","first_name":"Alkida","last_name":"Balliu"},{"full_name":"Hirvonen, Juho","first_name":"Juho","last_name":"Hirvonen"},{"full_name":"Melnyk, Darya","first_name":"Darya","last_name":"Melnyk"},{"last_name":"Olivetti","first_name":"Dennis","full_name":"Olivetti, Dennis"},{"first_name":"Joel","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki"},{"first_name":"Jukka","full_name":"Suomela, Jukka","last_name":"Suomela"}],"month":"06","isi":1,"status":"public","day":"25","doi":"10.1007/978-3-031-09993-9_1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_published":"2022-07-06T00:00:00Z","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"type":"research_data_reference","publisher":"Zenodo","has_accepted_license":"1","year":"2022","corr_author":"1","date_updated":"2025-06-11T13:37:36Z","abstract":[{"lang":"eng","text":"Codes and data for reproducing the results of N. B. Budanur and B. Hof \"An autonomous compartmental model for accelerating epidemics\""}],"citation":{"ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","chicago":"Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>.","mla":"Budanur, Nazmi B. <i>Burakbudanur/Autoacc-Public</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","apa":"Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>","short":"N.B. Budanur, (2022).","ista":"Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>."},"author":[{"last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"}],"status":"public","ddc":["000"],"month":"07","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.6802720","open_access":"1"}],"date_created":"2022-08-01T08:06:33Z","department":[{"_id":"BjHo"}],"_id":"11711","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11704"}]},"title":"burakbudanur/autoacc-public","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5281/ZENODO.6802720","oa":1,"fulldoi":"https://doi.org/10.5281/ZENODO.6802720","day":"06","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"year":"2022","project":[{"name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","_id":"26956E74-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"V00738"}],"type":"journal_article","publisher":"Springer Nature","article_number":"173","volume":15,"abstract":[{"text":"Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes.","lang":"eng"}],"file":[{"creator":"dernst","checksum":"008156e5340e9789f0f6d82bde4d347a","content_type":"application/pdf","file_id":"11714","access_level":"open_access","file_name":"2022_BMCResearchNotes_Nikolic.pdf","relation":"main_file","date_updated":"2022-08-01T09:24:42Z","success":1,"file_size":1545310,"date_created":"2022-08-01T09:24:42Z"}],"intvolume":"        15","date_updated":"2025-04-14T09:24:53Z","_id":"11713","title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","department":[{"_id":"CaGu"}],"date_created":"2022-08-01T09:04:27Z","publication_identifier":{"issn":["1756-0500"]},"publication_status":"published","fulldoi":"https://doi.org/10.1186/s13104-022-06061-9","pmid":1,"oa_version":"Published Version","oa":1,"article_processing_charge":"No","external_id":{"pmid":["35562780"]},"corr_author":"1","acknowledgement":"We acknowledge the Max Perutz Labs FACS Facility together with Thomas Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207), to IM. Open access funding provided by the Austrian Science Fund.","has_accepted_license":"1","file_date_updated":"2022-08-01T09:24:42Z","date_published":"2022-05-13T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"chicago":"Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>.","mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>.","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","ista":"Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. BMC Research Notes. 15, 173.","apa":"Nikolic, N., Sauert, M., Albanese, T. G., &#38; Moll, I. (2022). Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>","ieee":"N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli,” <i>BMC Research Notes</i>, vol. 15. Springer Nature, 2022.","ama":"Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. 2022;15. doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>"},"scopus_import":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13104-022-06152-7"}]},"quality_controlled":"1","publication":"BMC Research Notes","author":[{"last_name":"Nikolic","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090"},{"full_name":"Sauert, Martina","first_name":"Martina","last_name":"Sauert"},{"first_name":"Tanino G.","full_name":"Albanese, Tanino G.","last_name":"Albanese"},{"last_name":"Moll","full_name":"Moll, Isabella","first_name":"Isabella"}],"status":"public","month":"05","ddc":["570"],"article_type":"letter_note","day":"13","doi":"10.1186/s13104-022-06061-9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"]},{"corr_author":"1","external_id":{"isi":["000860924200005"]},"date_published":"2022-10-29T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledgement":"We are grateful to a number of colleagues for helpful and inspiring discussions during the time when we worked on this project, in particular Dima Dudko, Misha Hlushchanka, John Hubbard, Misha Lyubich, Oleg Kozlovski, and Sebastian van Strien. Finally, we would like to thank our dynamics research group for numerous helpful and enjoyable discussions: Konstantin Bogdanov, Roman Chernov, Russell Lodge, Steffen Maaß, David Pfrang, Bernhard Reinke, Sergey Shemyakov, and Maik Sowinski. We gratefully acknowledge support by the Advanced Grant “HOLOGRAM” (#695 621) of the European Research Council (ERC), as well as hospitality of Cornell University in the spring of 2018 while much of this work was prepared. The first-named author also acknowledges the support of the ERC Advanced Grant “SPERIG” (#885 707).","file_date_updated":"2023-02-02T07:39:09Z","has_accepted_license":"1","citation":{"ieee":"K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” <i>Advances in Mathematics</i>, vol. 408, no. Part A. Elsevier, 2022.","ama":"Drach K, Schleicher D. Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. 2022;408(Part A). doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>","ista":"Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics. 408(Part A), 108591.","short":"K. Drach, D. Schleicher, Advances in Mathematics 408 (2022).","apa":"Drach, K., &#38; Schleicher, D. (2022). Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>","mla":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>, vol. 408, no. Part A, 108591, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>.","chicago":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>."},"ec_funded":1,"scopus_import":"1","publication":"Advances in Mathematics","quality_controlled":"1","author":[{"last_name":"Drach","first_name":"Kostiantyn","orcid":"0000-0002-9156-8616","full_name":"Drach, Kostiantyn","id":"fe8209e2-906f-11eb-847d-950f8fc09115"},{"last_name":"Schleicher","full_name":"Schleicher, Dierk","first_name":"Dierk"}],"isi":1,"status":"public","ddc":["510"],"month":"10","issue":"Part A","article_type":"original","day":"29","keyword":["General Mathematics"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.aim.2022.108591","type":"journal_article","publisher":"Elsevier","language":[{"iso":"eng"}],"year":"2022","project":[{"grant_number":"885707","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020"}],"abstract":[{"text":"We study rigidity of rational maps that come from Newton's root finding method for polynomials of arbitrary degrees. We establish dynamical rigidity of these maps: each point in the Julia set of a Newton map is either rigid (i.e. its orbit can be distinguished in combinatorial terms from all other orbits), or the orbit of this point eventually lands in the filled-in Julia set of a polynomial-like restriction of the original map. As a corollary, we show that the Julia sets of Newton maps in many non-trivial cases are locally connected; in particular, every cubic Newton map without Siegel points has locally connected Julia set.\r\nIn the parameter space of Newton maps of arbitrary degree we obtain the following rigidity result: any two combinatorially equivalent Newton maps are quasiconformally conjugate in a neighborhood of their Julia sets provided that they either non-renormalizable, or they are both renormalizable “in the same way”.\r\nOur main tool is a generalized renormalization concept called “complex box mappings” for which we extend a dynamical rigidity result by Kozlovski and van Strien so as to include irrationally indifferent and renormalizable situations.","lang":"eng"}],"article_number":"108591","volume":408,"intvolume":"       408","date_updated":"2025-04-14T07:53:45Z","file":[{"relation":"main_file","date_updated":"2023-02-02T07:39:09Z","file_name":"2022_AdvancesMathematics_Drach.pdf","access_level":"open_access","creator":"dernst","file_id":"12474","checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","content_type":"application/pdf","file_size":2164036,"date_created":"2023-02-02T07:39:09Z","success":1}],"department":[{"_id":"VaKa"}],"_id":"11717","title":"Rigidity of Newton dynamics","publication_identifier":{"issn":["0001-8708"]},"date_created":"2022-08-01T17:08:16Z","fulldoi":"https://doi.org/10.1016/j.aim.2022.108591","oa_version":"Published Version","publication_status":"published","article_processing_charge":"Yes (via OA deal)","oa":1},{"citation":{"ieee":"L. Li <i>et al.</i>, “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>","mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121058119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &#38; Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121058119.","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>."},"scopus_import":"1","external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"corr_author":"1","acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”","file_date_updated":"2022-08-08T07:42:09Z","has_accepted_license":"1","date_published":"2022-07-25T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"day":"25","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1073/pnas.2121058119","keyword":["Multidisciplinary"],"quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"31","ddc":["580"],"isi":1,"status":"public","month":"07","author":[{"first_name":"Lanxin","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen"},{"full_name":"Alotaibi, Saqer S.","first_name":"Saqer S.","last_name":"Alotaibi"},{"first_name":"Aleš","full_name":"Pěnčík, Aleš","last_name":"Pěnčík"},{"first_name":"Maciek","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"volume":119,"article_number":"e2121058119","abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}],"file":[{"success":1,"date_created":"2022-08-08T07:42:09Z","file_size":2506262,"checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","content_type":"application/pdf","file_id":"11747","creator":"dernst","file_name":"2022_PNAS_Li.pdf","access_level":"open_access","relation":"main_file","date_updated":"2022-08-08T07:42:09Z"}],"date_updated":"2025-05-14T11:01:00Z","intvolume":"       119","year":"2022","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","type":"journal_article","publication_status":"published","oa_version":"Published Version","pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.2121058119","oa":1,"article_processing_charge":"No","title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","_id":"11723","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"date_created":"2022-08-04T20:06:49Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]}},{"related_material":{"record":[{"status":"public","relation":"research_data","id":"13064"}]},"quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"31","ddc":["570"],"status":"public","month":"07","isi":1,"author":[{"full_name":"Orliac, Etienne J.","first_name":"Etienne J.","last_name":"Orliac"},{"last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel","first_name":"Daniel"},{"full_name":"Ojavee, Sven E.","first_name":"Sven E.","last_name":"Ojavee"},{"last_name":"Läll","first_name":"Kristi","full_name":"Läll, Kristi"},{"first_name":"Reedik","full_name":"Mägi, Reedik","last_name":"Mägi"},{"last_name":"Visscher","first_name":"Peter M.","full_name":"Visscher, Peter M."},{"last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard"}],"day":"29","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1073/pnas.2121279119","external_id":{"isi":["000881496900003"],"pmid":["35905320"]},"corr_author":"1","has_accepted_license":"1","acknowledgement":"This project was funded by Swiss National Science Foundation Eccellenza Grant PCEGP3-181181(toM.R.R.) and by core funding from the Institute of Science and Technology Austria. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). K.L. and R.M. were supported by the Estonian Research Council Grant PRG687. Estonian Biobank computations were performed in the High-Performance Computing Centre, University of Tartu.","file_date_updated":"2022-08-08T07:31:19Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"date_published":"2022-07-29T00:00:00Z","citation":{"apa":"Orliac, E. J., Trejo Banos, D., Ojavee, S. E., Läll, K., Mägi, R., Visscher, P. M., &#38; Robinson, M. R. (2022). Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>","ista":"Orliac EJ, Trejo Banos D, Ojavee SE, Läll K, Mägi R, Visscher PM, Robinson MR. 2022. Improving GWAS discovery and genomic prediction accuracy in biobank data. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121279119.","short":"E.J. Orliac, D. Trejo Banos, S.E. Ojavee, K. Läll, R. Mägi, P.M. Visscher, M.R. Robinson, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Orliac, Etienne J., et al. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121279119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>.","chicago":"Orliac, Etienne J., Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik Mägi, Peter M. Visscher, and Matthew Richard Robinson. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>.","ama":"Orliac EJ, Trejo Banos D, Ojavee SE, et al. Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>","ieee":"E. J. Orliac <i>et al.</i>, “Improving GWAS discovery and genomic prediction accuracy in biobank data,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022."},"scopus_import":"1","title":"Improving GWAS discovery and genomic prediction accuracy in biobank data","_id":"11733","department":[{"_id":"MaRo"}],"date_created":"2022-08-07T22:01:56Z","publication_identifier":{"eissn":["1091-6490"]},"publication_status":"published","oa_version":"Published Version","pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.2121279119","oa":1,"article_processing_charge":"No","year":"2022","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","type":"journal_article","volume":119,"article_number":"e2121279119","abstract":[{"lang":"eng","text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP. We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies."}],"file":[{"success":1,"date_created":"2022-08-08T07:31:19Z","file_size":1001164,"file_id":"11745","checksum":"b5d2024e19fbad6f85a5e384e44d0f3b","content_type":"application/pdf","creator":"dernst","relation":"main_file","date_updated":"2022-08-08T07:31:19Z","access_level":"open_access","file_name":"2022_PNAS_Orliac.pdf"}],"intvolume":"       119","date_updated":"2025-06-12T06:22:37Z"},{"department":[{"_id":"EvBe"}],"_id":"11734","title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","publication_identifier":{"eissn":["1091-6490"]},"date_created":"2022-08-07T22:01:57Z","pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.2122460119","oa_version":"Published Version","publication_status":"published","article_processing_charge":"No","oa":1,"type":"journal_article","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"year":"2022","project":[{"grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"abstract":[{"text":"Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.","lang":"eng"}],"article_number":"e2122460119","volume":119,"intvolume":"       119","date_updated":"2025-05-14T11:00:29Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file":[{"access_level":"open_access","file_name":"2022_PNAS_Abualia.pdf","relation":"main_file","date_updated":"2022-08-08T07:09:58Z","creator":"dernst","content_type":"application/pdf","checksum":"6e97dedc281247fc3fe238a209f14af0","file_id":"11744","file_size":3092330,"date_created":"2022-08-08T07:09:58Z","success":1}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","author":[{"full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","last_name":"Abualia"},{"last_name":"Ötvös","first_name":"Krisztina","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"last_name":"Bouguyon","first_name":"Eleonore","full_name":"Bouguyon, Eleonore"},{"last_name":"Domanegg","first_name":"Kevin","id":"a24c7829-16e8-11ed-8527-c4d36ffb7539","full_name":"Domanegg, Kevin","orcid":"0000-0002-1215-4264"},{"first_name":"Anne","full_name":"Krapp, Anne","last_name":"Krapp"},{"last_name":"Nacry","first_name":"Philip","full_name":"Nacry, Philip"},{"last_name":"Gojon","first_name":"Alain","full_name":"Gojon, Alain"},{"full_name":"Lacombe, Benoit","first_name":"Benoit","last_name":"Lacombe"},{"first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}],"status":"public","ddc":["570"],"month":"07","isi":1,"issue":"31","article_type":"original","day":"25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1073/pnas.2122460119","corr_author":"1","external_id":{"isi":["000881496900007"],"pmid":["35878040"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"date_published":"2022-07-25T00:00:00Z","has_accepted_license":"1","acknowledgement":"We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari, Marc¸al Gallem\u0003ı, Kaori Tabata, Andrej Hurn\u0003y, and Sascha Waidmann for sharing materials; and Marina Borges Osorio for critical reading of the manuscript. Work in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science Facilities of the Institute of Science\r\nand Technology Austria. We give sincere thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses. This work was funded by the Czech Science Foundation (Project No. 19-00973S).","file_date_updated":"2022-08-08T07:09:58Z","citation":{"ieee":"R. Abualia <i>et al.</i>, “Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","ama":"Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>","short":"R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry, A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., … Benková, E. (2022). Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>","ista":"Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2122460119.","mla":"Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2122460119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>.","chicago":"Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>."},"scopus_import":"1"}]