[{"license":"https://creativecommons.org/licenses/by/4.0/","volume":71,"issue":"5","publication_identifier":{"eissn":["2050-5701"],"issn":["2050-5698"]},"type":"journal_article","language":[{"iso":"eng"}],"pmid":1,"_id":"11648","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"}],"publication":"Microscopy","author":[{"last_name":"Gerle","first_name":"Christoph","full_name":"Gerle, Christoph"},{"full_name":"Kishikawa, Jun-ichi","first_name":"Jun-ichi","last_name":"Kishikawa"},{"last_name":"Yamaguchi","full_name":"Yamaguchi, Tomoko","first_name":"Tomoko"},{"full_name":"Nakanishi, Atsuko","first_name":"Atsuko","last_name":"Nakanishi"},{"orcid":"0000-0002-3219-2022","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","first_name":"Mehmet Orkun"},{"last_name":"Makino","first_name":"Fumiaki","full_name":"Makino, Fumiaki"},{"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","full_name":"Kurisu, Genji","first_name":"Genji"},{"last_name":"Kato","first_name":"Takayuki","full_name":"Kato, Takayuki"}],"date_published":"2022-10-01T00:00:00Z","oa":1,"oa_version":"Published Version","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"publication_status":"published","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>.","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>","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.","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>","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.","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>.","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."},"quality_controlled":"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.","day":"01","date_created":"2022-07-25T10:04:58Z","date_updated":"2023-08-03T12:13:37Z","intvolume":"        71","isi":1,"status":"public","publisher":"Oxford University Press","ddc":["570"],"has_accepted_license":"1","scopus_import":"1","month":"10","file_date_updated":"2023-02-03T08:34:48Z","file":[{"access_level":"open_access","file_name":"2022_Microscopy_Gerle.pdf","relation":"main_file","file_id":"12498","date_created":"2023-02-03T08:34:48Z","date_updated":"2023-02-03T08:34:48Z","success":1,"content_type":"application/pdf","file_size":7812696,"checksum":"23b51c163636bf9313f7f0818312e67e","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","page":"249-261","external_id":{"pmid":["35861182"],"isi":["000837950900001"]},"doi":"10.1093/jmicro/dfac037","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","article_type":"original","department":[{"_id":"LeSa"}],"title":"Structures of multisubunit membrane complexes with the CRYO ARM 200"},{"ddc":["510"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ec_funded":1,"status":"public","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"name":"Mathematics, Computer Science","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"date_created":"2022-07-27T09:27:34Z","date_updated":"2026-04-07T12:58:48Z","day":"27","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","year":"2022","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":639266,"creator":"scultrer","checksum":"b2f511e8b1cae5f1892b0cdec341acac","date_updated":"2022-07-27T09:25:53Z","date_created":"2022-07-27T09:25:53Z","file_id":"11659","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"D-S-E.pdf"}],"file_date_updated":"2022-07-27T09:25:53Z","month":"07","has_accepted_license":"1","_id":"11658","language":[{"iso":"eng"}],"type":"journal_article","related_material":{"record":[{"id":"15380","relation":"later_version","status":"public"},{"relation":"dissertation_contains","status":"public","id":"15094"}]},"quality_controlled":"1","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","citation":{"ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.).","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","mla":"Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth in arrangements: Dehn–Sommerville–Euler relations with applications,” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings on Mathematics."},"publication_status":"draft","oa_version":"Submitted Version","oa":1,"date_published":"2022-07-27T00:00:00Z","author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","orcid":"0000-0002-5372-7890","last_name":"Biswas"},{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","orcid":"0000-0001-6249-0832"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"last_name":"Saghafian","first_name":"Morteza","full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"publication":"Leibniz International Proceedings on Mathematics","abstract":[{"text":"The depth of a cell in an arrangement of n (non-vertical) great-spheres in Sd is the number of great-spheres that pass above the cell. We prove Euler-type relations, which imply extensions of the classic Dehn–Sommerville relations for convex polytopes to sublevel sets of the depth function, and we use the relations to extend the expressions for the number of faces of neighborly polytopes to the number of cells of levels in neighborly arrangements.","lang":"eng"}]},{"ec_funded":1,"ddc":["510"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"25","date_created":"2022-07-27T09:31:15Z","date_updated":"2026-04-07T12:58:47Z","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","name":"Mathematics, Computer Science","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"status":"public","year":"2022","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"title":"A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs","has_accepted_license":"1","file_date_updated":"2022-07-27T09:30:30Z","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","file":[{"file_name":"window 1.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"11661","date_created":"2022-07-27T09:30:30Z","date_updated":"2022-07-27T09:30:30Z","checksum":"95903f9d1649e8e437a967b6f2f64730","creator":"scultrer","file_size":564836}],"type":"journal_article","language":[{"iso":"eng"}],"_id":"11660","related_material":{"record":[{"id":"15094","status":"public","relation":"dissertation_contains"}]},"oa_version":"Submitted Version","publication_status":"submitted","citation":{"ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. LIPIcs.","mla":"Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs,” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs (n.d.).","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>."},"quality_controlled":"1","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35. ","abstract":[{"text":"We characterize critical points of 1-dimensional maps paired in persistent homology geometrically and this way get elementary proofs of theorems about the symmetry of persistence diagrams and the variation of such maps. In particular, we identify branching points and endpoints of networks as the sole source of asymmetry and relate the cycle basis in persistent homology with a version of the stable marriage problem. Our analysis provides the foundations of fast algorithms for maintaining collections of interrelated sorted lists together with their persistence diagrams. ","lang":"eng"}],"author":[{"orcid":"0000-0002-5372-7890","last_name":"Biswas","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita"},{"full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert"},{"first_name":"Morteza","full_name":"Saghafian, Morteza","last_name":"Saghafian"}],"publication":"LIPIcs","alternative_title":["LIPIcs"],"date_published":"2022-07-25T00:00:00Z","oa":1},{"acknowledgement":"We want to thank an anonymous referee who pointed out a mistake in our conference paper as well as suggesting a fix using an approach in References.","quality_controlled":"1","citation":{"chicago":"Henzinger, Monika, and Pan Peng. “Constant-Time Dynamic (Δ +1)-Coloring.” <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3501403\">https://doi.org/10.1145/3501403</a>.","ama":"Henzinger M, Peng P. Constant-time Dynamic (Δ +1)-Coloring. <i>ACM Transactions on Algorithms</i>. 2022;18(2). doi:<a href=\"https://doi.org/10.1145/3501403\">10.1145/3501403</a>","short":"M. Henzinger, P. Peng, ACM Transactions on Algorithms 18 (2022).","apa":"Henzinger, M., &#38; Peng, P. (2022). Constant-time Dynamic (Δ +1)-Coloring. <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3501403\">https://doi.org/10.1145/3501403</a>","mla":"Henzinger, Monika, and Pan Peng. “Constant-Time Dynamic (Δ +1)-Coloring.” <i>ACM Transactions on Algorithms</i>, vol. 18, no. 2, 16, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3501403\">10.1145/3501403</a>.","ieee":"M. Henzinger and P. Peng, “Constant-time Dynamic (Δ +1)-Coloring,” <i>ACM Transactions on Algorithms</i>, vol. 18, no. 2. Association for Computing Machinery, 2022.","ista":"Henzinger M, Peng P. 2022. Constant-time Dynamic (Δ +1)-Coloring. ACM Transactions on Algorithms. 18(2), 16."},"publication_status":"published","oa_version":"None","date_published":"2022-03-04T00:00:00Z","author":[{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"full_name":"Peng, Pan","first_name":"Pan","last_name":"Peng"}],"publication":"ACM Transactions on Algorithms","abstract":[{"text":"We give a fully dynamic (Las-Vegas style) algorithm with constant expected amortized time per update that maintains a proper (Δ +1)-vertex coloring of a graph with maximum degree at most Δ. This improves upon the previous O(log Δ)-time algorithm by Bhattacharya et al. (SODA 2018). Our algorithm uses an approach based on assigning random ranks to vertices and does not need to maintain a hierarchical graph decomposition. We show that our result does not only have optimal running time but is also optimal in the sense that already deciding whether a Δ-coloring exists in a dynamically changing graph with maximum degree at most Δ takes Ω (log n) time per operation.","lang":"eng"}],"_id":"11662","language":[{"iso":"eng"}],"type":"journal_article","issue":"2","publication_identifier":{"issn":["1549-6325"],"eissn":["1549-6333"]},"article_number":"16","extern":"1","volume":18,"title":"Constant-time Dynamic (Δ +1)-Coloring","article_type":"original","article_processing_charge":"No","doi":"10.1145/3501403","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","scopus_import":"1","publisher":"Association for Computing Machinery","status":"public","intvolume":"        18","date_created":"2022-07-27T10:58:53Z","date_updated":"2024-11-04T11:42:31Z","day":"04"},{"department":[{"_id":"NiBa"}],"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","article_processing_charge":"No","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"citation":{"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>.","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.","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>.","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>","short":"M. Turelli, N.H. Barton, (2022).","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>.","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>"},"keyword":["Biological sciences"],"doi":"10.25338/B81931","oa_version":"Published Version","year":"2022","oa":1,"date_published":"2022-01-06T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","corr_author":"1","month":"01","author":[{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"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"}],"publisher":"Dryad","_id":"11686","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25338/B81931"}],"ddc":["570"],"type":"research_data_reference","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10604"}]},"license":"https://creativecommons.org/publicdomain/zero/1.0/","date_updated":"2025-06-11T13:45:56Z","date_created":"2022-07-29T06:45:41Z","day":"06"},{"oa_version":"Published Version","year":"2022","doi":"10.5281/ZENODO.6542908","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","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":{"mla":"Parvizian, Mahsa, et al. <i>Data for “The Chemistry of Cu3N and Cu3PdN Nanocrystals.”</i> Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","ieee":"M. Parvizian <i>et al.</i>, “Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals.’” Zenodo, 2022.","ista":"Parvizian M, Duran Balsa A, Pokratath R, Kalha C, Lee S, Van den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","short":"M. Parvizian, A. Duran Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, (2022).","chicago":"Parvizian, Mahsa, Alejandra Duran Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “Data for ‘The Chemistry of Cu3N and Cu3PdN Nanocrystals.’” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6542908\">https://doi.org/10.5281/ZENODO.6542908</a>.","ama":"Parvizian M, Duran Balsa A, Pokratath R, et al. Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>","apa":"Parvizian, M., Duran Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van den Eynden, D., … De Roo, J. (2022). Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6542908\">https://doi.org/10.5281/ZENODO.6542908</a>"},"department":[{"_id":"MaIb"}],"title":"Data for \"The chemistry of Cu3N and Cu3PdN nanocrystals\"","abstract":[{"lang":"eng","text":"Data underlying the figures in the publication \"The chemistry of Cu3N and Cu3PdN nanocrystals\" "}],"month":"05","author":[{"first_name":"Mahsa","full_name":"Parvizian, Mahsa","last_name":"Parvizian"},{"full_name":"Duran Balsa, Alejandra","first_name":"Alejandra","last_name":"Duran Balsa"},{"last_name":"Pokratath","full_name":"Pokratath, Rohan","first_name":"Rohan"},{"full_name":"Kalha, Curran","first_name":"Curran","last_name":"Kalha"},{"last_name":"Lee","full_name":"Lee, Seungho","first_name":"Seungho"},{"first_name":"Dietger","full_name":"Van den Eynden, Dietger","last_name":"Van den Eynden"},{"last_name":"Ibáñez","orcid":"0000-0001-5013-2843","first_name":"Maria","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Regoutz","full_name":"Regoutz, Anna","first_name":"Anna"},{"last_name":"De Roo","first_name":"Jonathan","full_name":"De Roo, Jonathan"}],"date_published":"2022-05-12T00:00:00Z","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6542908"}],"_id":"11695","publisher":"Zenodo","ddc":["540"],"day":"12","date_updated":"2023-08-03T07:19:12Z","date_created":"2022-07-29T09:31:13Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11451"}]},"status":"public"},{"doi":"10.3934/nhm.2022023","external_id":{"arxiv":["2105.05677"],"isi":["000812422100001"]},"page":"687-717","year":"2022","title":"Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph","department":[{"_id":"JaMa"}],"article_type":"original","article_processing_charge":"No","scopus_import":"1","corr_author":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"10","ec_funded":1,"publisher":"American Institute of Mathematical Sciences","date_updated":"2025-04-14T07:27:47Z","date_created":"2022-07-31T22:01:46Z","day":"01","isi":1,"status":"public","intvolume":"        17","project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"oa_version":"Preprint","acknowledgement":"ME acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG), Grant SFB 1283/2 2021 – 317210226. DF and JM were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117). JM also acknowledges support by the Austrian Science Fund (FWF), Project SFB F65. The work of DM was partially supported by the Deutsche Forschungsgemeinschaft\r\n(DFG), Grant 397230547. This article is based upon work from COST Action\r\n18232 MAT-DYN-NET, supported by COST (European Cooperation in Science\r\nand Technology), www.cost.eu. We wish to thank Martin Burger and Jan-Frederik\r\nPietschmann for useful discussions. We are grateful to the anonymous referees for\r\ntheir careful reading and useful suggestions.","quality_controlled":"1","publication_status":"published","citation":{"short":"M. Erbar, D.L. Forkert, J. Maas, D. Mugnolo, Networks and Heterogeneous Media 17 (2022) 687–717.","chicago":"Erbar, Matthias, Dominik L Forkert, Jan Maas, and Delio Mugnolo. “Gradient Flow Formulation of Diffusion Equations in the Wasserstein Space over a Metric Graph.” <i>Networks and Heterogeneous Media</i>. American Institute of Mathematical Sciences, 2022. <a href=\"https://doi.org/10.3934/nhm.2022023\">https://doi.org/10.3934/nhm.2022023</a>.","ama":"Erbar M, Forkert DL, Maas J, Mugnolo D. Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. <i>Networks and Heterogeneous Media</i>. 2022;17(5):687-717. doi:<a href=\"https://doi.org/10.3934/nhm.2022023\">10.3934/nhm.2022023</a>","apa":"Erbar, M., Forkert, D. L., Maas, J., &#38; Mugnolo, D. (2022). Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. <i>Networks and Heterogeneous Media</i>. American Institute of Mathematical Sciences. <a href=\"https://doi.org/10.3934/nhm.2022023\">https://doi.org/10.3934/nhm.2022023</a>","ieee":"M. Erbar, D. L. Forkert, J. Maas, and D. Mugnolo, “Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph,” <i>Networks and Heterogeneous Media</i>, vol. 17, no. 5. American Institute of Mathematical Sciences, pp. 687–717, 2022.","mla":"Erbar, Matthias, et al. “Gradient Flow Formulation of Diffusion Equations in the Wasserstein Space over a Metric Graph.” <i>Networks and Heterogeneous Media</i>, vol. 17, no. 5, American Institute of Mathematical Sciences, 2022, pp. 687–717, doi:<a href=\"https://doi.org/10.3934/nhm.2022023\">10.3934/nhm.2022023</a>.","ista":"Erbar M, Forkert DL, Maas J, Mugnolo D. 2022. Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. Networks and Heterogeneous Media. 17(5), 687–717."},"abstract":[{"text":"This paper contains two contributions in the study of optimal transport on metric graphs. Firstly, we prove a Benamou–Brenier formula for the Wasserstein distance, which establishes the equivalence of static and dynamical optimal transport. Secondly, in the spirit of Jordan–Kinderlehrer–Otto, we show that McKean–Vlasov equations can be formulated as gradient flow of the free energy in the Wasserstein space of probability measures. The proofs of these results are based on careful regularisation arguments to circumvent some of the difficulties arising in metric graphs, namely, branching of geodesics and the failure of semi-convexity of entropy functionals in the Wasserstein space.","lang":"eng"}],"date_published":"2022-10-01T00:00:00Z","oa":1,"author":[{"full_name":"Erbar, Matthias","first_name":"Matthias","last_name":"Erbar"},{"full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","last_name":"Forkert"},{"orcid":"0000-0002-0845-1338","last_name":"Maas","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Mugnolo, Delio","first_name":"Delio","last_name":"Mugnolo"}],"publication":"Networks and Heterogeneous Media","language":[{"iso":"eng"}],"type":"journal_article","issue":"5","publication_identifier":{"eissn":["1556-181X"],"issn":["1556-1801"]},"volume":17,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.05677"}],"_id":"11700","arxiv":1},{"publisher":"IOP Publishing","ddc":["510"],"day":"04","date_created":"2022-07-31T22:01:47Z","date_updated":"2023-08-03T12:25:08Z","intvolume":"        35","status":"public","isi":1,"year":"2022","page":"4100-4210","external_id":{"isi":["000826695900001"],"arxiv":["2001.00512"]},"doi":"10.1088/1361-6544/abd613","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png"},"article_type":"original","department":[{"_id":"JuFi"}],"title":"Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence","has_accepted_license":"1","scopus_import":"1","month":"08","file_date_updated":"2022-08-01T10:39:36Z","file":[{"file_id":"11715","date_updated":"2022-08-01T10:39:36Z","date_created":"2022-08-01T10:39:36Z","success":1,"content_type":"application/pdf","file_name":"2022_Nonlinearity_Agresti.pdf","access_level":"open_access","relation":"main_file","file_size":2122096,"checksum":"997a4bff2dfbee3321d081328c2f1e1a","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":35,"publication_identifier":{"eissn":["1361-6544"],"issn":["0951-7715"]},"issue":"8","language":[{"iso":"eng"}],"type":"journal_article","_id":"11701","license":"https://creativecommons.org/licenses/by/3.0/","arxiv":1,"oa_version":"Published Version","publication_status":"published","citation":{"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>","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>.","short":"A. Agresti, M. Veraar, Nonlinearity 35 (2022) 4100–4210.","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>","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>.","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.","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."},"acknowledgement":"The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","quality_controlled":"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."}],"publication":"Nonlinearity","author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio","first_name":"Antonio","orcid":"0000-0002-9573-2962","last_name":"Agresti"},{"last_name":"Veraar","first_name":"Mark","full_name":"Veraar, Mark"}],"oa":1,"date_published":"2022-08-04T00:00:00Z"},{"date_updated":"2025-05-14T11:01:10Z","date_created":"2022-07-31T22:01:47Z","day":"18","status":"public","intvolume":"       119","ddc":["570"],"publisher":"National Academy of Sciences","scopus_import":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","file":[{"checksum":"06c866196a8957f0c37b8a121771c885","creator":"dernst","file_size":848511,"file_name":"2022_PNAS_Barton.pdf","access_level":"open_access","relation":"main_file","success":1,"content_type":"application/pdf","file_id":"11716","date_updated":"2022-08-01T10:58:28Z","date_created":"2022-08-01T10:58:28Z"}],"file_date_updated":"2022-08-01T10:58:28Z","month":"07","external_id":{"pmid":["35858408"]},"doi":"10.1073/pnas.2122147119","year":"2022","article_type":"original","title":"The \"New Synthesis\"","department":[{"_id":"NiBa"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","pmid":1,"language":[{"iso":"eng"}],"type":"journal_article","article_number":"e2122147119","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"issue":"30","volume":119,"_id":"11702","abstract":[{"lang":"eng","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."}],"date_published":"2022-07-18T00:00:00Z","oa":1,"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","oa_version":"Published Version","acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","quality_controlled":"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>","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>.","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>","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>.","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.","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119."},"publication_status":"published"},{"ec_funded":1,"ddc":["570"],"publisher":"Public Library of Science","day":"06","date_created":"2022-07-31T22:01:48Z","date_updated":"2025-04-14T07:41:20Z","intvolume":"        18","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"isi":1,"status":"public","year":"2022","external_id":{"isi":["000886643100006"],"pmid":["35793353"]},"doi":"10.1371/journal.pgen.1010226","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","department":[{"_id":"BeVi"}],"title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","article_type":"original","scopus_import":"1","has_accepted_license":"1","month":"07","file_date_updated":"2022-08-01T07:49:25Z","corr_author":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":1620272,"creator":"dernst","checksum":"aa4c137f82635e700856c359dccfaa0a","relation":"main_file","access_level":"open_access","file_name":"2022_PLoSGenetics_Toups.pdf","date_updated":"2022-08-01T07:49:25Z","date_created":"2022-08-01T07:49:25Z","file_id":"11708","content_type":"application/pdf","success":1}],"publication_identifier":{"eissn":["1553-7404"]},"issue":"7","article_number":"e1010226","volume":18,"pmid":1,"type":"journal_article","language":[{"iso":"eng"}],"_id":"11703","oa_version":"Published Version","publication_status":"published","citation":{"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.","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>.","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.","short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022).","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>","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>.","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>"},"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.","quality_controlled":"1","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."}],"author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","first_name":"Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pannell, John R.","first_name":"John R.","last_name":"Pannell"}],"publication":"PLoS Genetics","oa":1,"date_published":"2022-07-06T00:00:00Z"},{"related_material":{"record":[{"id":"11711","status":"public","relation":"research_data"}]},"_id":"11704","volume":17,"publication_identifier":{"eissn":["1932-6203"]},"article_number":"e0269975","issue":"7","type":"journal_article","language":[{"iso":"eng"}],"pmid":1,"publication":"PLoS ONE","author":[{"orcid":"0000-0003-0423-5010","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","first_name":"Nazmi B"},{"first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"oa":1,"date_published":"2022-07-18T00:00:00Z","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"}],"citation":{"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.","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>.","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).","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>.","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>","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>"},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","intvolume":"        17","isi":1,"status":"public","day":"18","date_created":"2022-07-31T22:01:48Z","date_updated":"2025-06-11T13:37:36Z","publisher":"Public Library of Science","ddc":["510"],"file_date_updated":"2022-08-01T08:02:38Z","month":"07","file":[{"file_size":1421256,"creator":"dernst","checksum":"1ddd9b91e6dec31ab0e7a8433ca2d452","relation":"main_file","access_level":"open_access","file_name":"2022_PLoSONE_Budanur.pdf","date_created":"2022-08-01T08:02:38Z","date_updated":"2022-08-01T08:02:38Z","file_id":"11712","content_type":"application/pdf","success":1}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","scopus_import":"1","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"An autonomous compartmental model for accelerating epidemics","department":[{"_id":"BjHo"}],"article_type":"original","year":"2022","external_id":{"pmid":["35849565"],"isi":["000911392100055"]},"doi":"10.1371/journal.pone.0269975"},{"abstract":[{"lang":"eng","text":"The broad implementation of thermoelectricity requires high-performance and low-cost materials. One possibility is employing surfactant-free solution synthesis to produce nanopowders. We propose the strategy of functionalizing “naked” particles’ surface by inorganic molecules to control the nanostructure and, consequently, thermoelectric performance. In particular, we use bismuth thiolates to functionalize surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1) carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity reduction by small grain domains, grain boundaries and nanostructuration. Overall, the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed SnTe."}],"publication":"Angewandte Chemie - International Edition","author":[{"orcid":"0000-0002-9515-4277","last_name":"Chang","full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng"},{"first_name":"Yu","full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","orcid":"0000-0001-7313-6740"},{"first_name":"Seungho","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","orcid":"0000-0002-6962-8598"},{"last_name":"Spadaro","first_name":"Maria","full_name":"Spadaro, Maria"},{"first_name":"Kristopher M.","full_name":"Koskela, Kristopher M.","last_name":"Koskela"},{"last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"orcid":"0000-0001-9732-3815","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","first_name":"Tommaso"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Brutchey, Richard L.","first_name":"Richard L.","last_name":"Brutchey"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"}],"oa":1,"date_published":"2022-08-26T00:00:00Z","oa_version":"Published Version","publication_status":"published","citation":{"chicago":"Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela, Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>.","short":"C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo, J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition 61 (2022).","ama":"Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. 2022;61(35). doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>","apa":"Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T., … Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>","mla":"Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35, e202207002, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>.","ieee":"C. Chang <i>et al.</i>, “Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35. Wiley, 2022.","ista":"Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 61(35), e202207002."},"quality_controlled":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N). Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S. and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya.","volume":61,"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"article_number":"e202207002","issue":"35","type":"journal_article","language":[{"iso":"eng"}],"pmid":1,"_id":"11705","has_accepted_license":"1","scopus_import":"1","file_date_updated":"2023-02-02T08:01:00Z","month":"08","file":[{"file_id":"12476","date_created":"2023-02-02T08:01:00Z","date_updated":"2023-02-02T08:01:00Z","success":1,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_AngewandteChemieInternat_Chang.pdf","relation":"main_file","file_size":4072650,"checksum":"ad601f2b9e26e46ab4785162be58b5ed","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","year":"2022","doi":"10.1002/anie.202207002","external_id":{"pmid":["38505739"],"isi":["000828274200001"]},"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","article_type":"original","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"day":"26","date_updated":"2025-04-14T07:44:07Z","date_created":"2022-07-31T22:01:48Z","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"intvolume":"        61","isi":1,"status":"public","ec_funded":1,"publisher":"Wiley","ddc":["540"]},{"day":"25","conference":{"location":"Paderborn, Germany","end_date":"2022-06-29","start_date":"2022-06-27","name":"SIROCCO: Structural Information and Communication Complexity"},"date_updated":"2025-04-14T07:50:55Z","date_created":"2022-07-31T22:01:49Z","project":[{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems","grant_number":"840605","call_identifier":"H2020"}],"intvolume":"     13298","isi":1,"status":"public","ec_funded":1,"publisher":"Springer Nature","scopus_import":"1","month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","page":"1-20","doi":"10.1007/978-3-031-09993-9_1","external_id":{"isi":["000876977400001"],"arxiv":["2102.08703"]},"article_processing_charge":"No","title":"Local mending","department":[{"_id":"DaAl"}],"arxiv":1,"volume":13298,"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031099922"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/2102.08703","open_access":"1"}],"_id":"11707","abstract":[{"lang":"eng","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."}],"editor":[{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"publication":"International Colloquium on Structural Information and Communication Complexity","author":[{"last_name":"Balliu","full_name":"Balliu, Alkida","first_name":"Alkida"},{"full_name":"Hirvonen, Juho","first_name":"Juho","last_name":"Hirvonen"},{"first_name":"Darya","full_name":"Melnyk, Darya","last_name":"Melnyk"},{"first_name":"Dennis","full_name":"Olivetti, Dennis","last_name":"Olivetti"},{"orcid":"0000-0002-6432-6646","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","first_name":"Joel"},{"first_name":"Jukka","full_name":"Suomela, Jukka","last_name":"Suomela"}],"date_published":"2022-06-25T00:00:00Z","oa":1,"oa_version":"Preprint","series_title":"LNCS","citation":{"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>","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>.","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.","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>","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.","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>.","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."},"publication_status":"published","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.","quality_controlled":"1"},{"ddc":["000"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6802720"}],"_id":"11711","publisher":"Zenodo","type":"research_data_reference","related_material":{"record":[{"id":"11704","relation":"used_in_publication","status":"public"}]},"status":"public","day":"06","date_updated":"2025-06-11T13:37:36Z","date_created":"2022-08-01T08:06:33Z","citation":{"ista":"Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6802720\">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>.","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","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>","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>.","short":"N.B. Budanur, (2022).","ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>"},"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"article_processing_charge":"No","department":[{"_id":"BjHo"}],"title":"burakbudanur/autoacc-public","oa_version":"Published Version","year":"2022","doi":"10.5281/ZENODO.6802720","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur"}],"month":"07","corr_author":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2022-07-06T00:00:00Z","oa":1,"has_accepted_license":"1","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\""}]},{"intvolume":"        15","project":[{"_id":"26956E74-B435-11E9-9278-68D0E5697425","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","grant_number":"V00738","call_identifier":"FWF"}],"status":"public","day":"13","date_created":"2022-08-01T09:04:27Z","date_updated":"2025-04-14T09:24:53Z","ddc":["570"],"publisher":"Springer Nature","month":"05","file_date_updated":"2022-08-01T09:24:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","file":[{"file_size":1545310,"creator":"dernst","checksum":"008156e5340e9789f0f6d82bde4d347a","date_created":"2022-08-01T09:24:42Z","date_updated":"2022-08-01T09:24:42Z","file_id":"11714","content_type":"application/pdf","success":1,"relation":"main_file","access_level":"open_access","file_name":"2022_BMCResearchNotes_Nikolic.pdf"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","department":[{"_id":"CaGu"}],"article_type":"letter_note","year":"2022","external_id":{"pmid":["35562780"]},"doi":"10.1186/s13104-022-06061-9","related_material":{"link":[{"url":"https://doi.org/10.1186/s13104-022-06152-7","relation":"erratum"}]},"_id":"11713","article_number":"173","publication_identifier":{"issn":["1756-0500"]},"volume":15,"pmid":1,"language":[{"iso":"eng"}],"type":"journal_article","author":[{"first_name":"Nela","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","orcid":"0000-0001-9068-6090"},{"last_name":"Sauert","first_name":"Martina","full_name":"Sauert, Martina"},{"last_name":"Albanese","first_name":"Tanino G.","full_name":"Albanese, Tanino G."},{"full_name":"Moll, Isabella","first_name":"Isabella","last_name":"Moll"}],"publication":"BMC Research Notes","date_published":"2022-05-13T00:00:00Z","oa":1,"abstract":[{"lang":"eng","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."}],"publication_status":"published","citation":{"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.","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>.","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.","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>","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","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>.","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>"},"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.","quality_controlled":"1","oa_version":"Published Version","keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"]},{"keyword":["General Mathematics"],"oa_version":"Published Version","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).","quality_controlled":"1","publication_status":"published","citation":{"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>","short":"K. Drach, D. Schleicher, Advances in Mathematics 408 (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>","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>.","ista":"Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics. 408(Part A), 108591.","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>.","ieee":"K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” <i>Advances in Mathematics</i>, vol. 408, no. Part A. Elsevier, 2022."},"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"}],"date_published":"2022-10-29T00:00:00Z","oa":1,"author":[{"orcid":"0000-0002-9156-8616","last_name":"Drach","id":"fe8209e2-906f-11eb-847d-950f8fc09115","full_name":"Drach, Kostiantyn","first_name":"Kostiantyn"},{"first_name":"Dierk","full_name":"Schleicher, Dierk","last_name":"Schleicher"}],"publication":"Advances in Mathematics","language":[{"iso":"eng"}],"type":"journal_article","article_number":"108591","issue":"Part A","publication_identifier":{"issn":["0001-8708"]},"volume":408,"_id":"11717","doi":"10.1016/j.aim.2022.108591","external_id":{"isi":["000860924200005"]},"year":"2022","title":"Rigidity of Newton dynamics","article_type":"original","department":[{"_id":"VaKa"}],"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","corr_author":"1","file":[{"file_size":2164036,"creator":"dernst","checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","date_created":"2023-02-02T07:39:09Z","date_updated":"2023-02-02T07:39:09Z","file_id":"12474","content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2022_AdvancesMathematics_Drach.pdf","access_level":"open_access"}],"file_date_updated":"2023-02-02T07:39:09Z","month":"10","ec_funded":1,"ddc":["510"],"publisher":"Elsevier","date_updated":"2025-04-14T07:53:45Z","date_created":"2022-08-01T17:08:16Z","day":"29","status":"public","isi":1,"intvolume":"       408","project":[{"call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}]},{"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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)"},"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","article_type":"original","year":"2022","external_id":{"isi":["000881496900002"],"pmid":["35878023"]},"doi":"10.1073/pnas.2121058119","month":"07","file_date_updated":"2022-08-08T07:42:09Z","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"success":1,"content_type":"application/pdf","file_id":"11747","date_created":"2022-08-08T07:42:09Z","date_updated":"2022-08-08T07:42:09Z","access_level":"open_access","file_name":"2022_PNAS_Li.pdf","relation":"main_file","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","creator":"dernst","file_size":2506262}],"scopus_import":"1","has_accepted_license":"1","ddc":["580"],"publisher":"National Academy of Sciences","intvolume":"       119","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"},{"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"}],"status":"public","isi":1,"day":"25","date_created":"2022-08-04T20:06:49Z","date_updated":"2025-05-14T11:01:00Z","citation":{"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.","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.","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>","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>.","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>"},"publication_status":"published","quality_controlled":"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).”","oa_version":"Published Version","keyword":["Multidisciplinary"],"author":[{"last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang"},{"last_name":"Alotaibi","first_name":"Saqer S.","full_name":"Alotaibi, Saqer S."},{"full_name":"Pěnčík, Aleš","first_name":"Aleš","last_name":"Pěnčík"},{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2022-07-25T00:00:00Z","oa":1,"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."}],"_id":"11723","article_number":"e2121058119","issue":"31","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"volume":119,"pmid":1,"type":"journal_article","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"_id":"11732","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"article_number":"5","volume":189,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19540"},{"status":"public","relation":"dissertation_contains","id":"18135"}]},"acknowledgement":"We are grateful to Robert Seiringer for helpful discussions and many valuable comments\r\non an earlier version of the manuscript. J.H. acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond’ No. 101020331. Open access funding provided by Institute of Science and Technology (IST Austria)","quality_controlled":"1","publication_status":"published","citation":{"ista":"Henheik SJ, Lauritsen AB. 2022. The BCS energy gap at high density. Journal of Statistical Physics. 189, 5.","ieee":"S. J. Henheik and A. B. Lauritsen, “The BCS energy gap at high density,” <i>Journal of Statistical Physics</i>, vol. 189. Springer Nature, 2022.","mla":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>, vol. 189, 5, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>.","apa":"Henheik, S. J., &#38; Lauritsen, A. B. (2022). The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>","ama":"Henheik SJ, Lauritsen AB. The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. 2022;189. doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>","chicago":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>.","short":"S.J. Henheik, A.B. Lauritsen, Journal of Statistical Physics 189 (2022)."},"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"oa_version":"Published Version","oa":1,"date_published":"2022-07-29T00:00:00Z","author":[{"first_name":"Sven Joscha","full_name":"Henheik, Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","last_name":"Henheik","orcid":"0000-0003-1106-327X"},{"orcid":"0000-0003-4476-2288","last_name":"Lauritsen","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard"}],"publication":"Journal of Statistical Physics","abstract":[{"lang":"eng","text":"We study the BCS energy gap Ξ in the high–density limit and derive an asymptotic formula, which strongly depends on the strength of the interaction potential V on the Fermi surface. In combination with the recent result by one of us (Math. Phys. Anal. Geom. 25, 3, 2022) on the critical temperature Tc at high densities, we prove the universality of the ratio of the energy gap and the critical temperature."}],"ddc":["530"],"publisher":"Springer Nature","ec_funded":1,"isi":1,"status":"public","intvolume":"       189","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"date_updated":"2026-04-07T13:01:40Z","date_created":"2022-08-05T11:36:56Z","day":"29","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"title":"The BCS energy gap at high density","article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s10955-022-02965-9","external_id":{"isi":["000833007200002"]},"year":"2022","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","corr_author":"1","file":[{"success":1,"content_type":"application/pdf","file_id":"11746","date_created":"2022-08-08T07:36:34Z","date_updated":"2022-08-08T07:36:34Z","file_name":"2022_JourStatisticalPhysics_Henheik.pdf","access_level":"open_access","relation":"main_file","checksum":"b398c4dbf65f71d417981d6e366427e9","creator":"dernst","file_size":419563}],"month":"07","file_date_updated":"2022-08-08T07:36:34Z","scopus_import":"1","has_accepted_license":"1"},{"ddc":["570"],"publisher":"National Academy of Sciences","isi":1,"status":"public","intvolume":"       119","date_created":"2022-08-07T22:01:56Z","date_updated":"2025-06-12T06:22:37Z","day":"29","article_type":"original","title":"Improving GWAS discovery and genomic prediction accuracy in biobank data","department":[{"_id":"MaRo"}],"article_processing_charge":"No","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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)"},"doi":"10.1073/pnas.2121279119","external_id":{"isi":["000881496900003"],"pmid":["35905320"]},"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","file":[{"file_size":1001164,"checksum":"b5d2024e19fbad6f85a5e384e44d0f3b","creator":"dernst","file_id":"11745","date_updated":"2022-08-08T07:31:19Z","date_created":"2022-08-08T07:31:19Z","success":1,"content_type":"application/pdf","file_name":"2022_PNAS_Orliac.pdf","access_level":"open_access","relation":"main_file"}],"file_date_updated":"2022-08-08T07:31:19Z","month":"07","scopus_import":"1","has_accepted_license":"1","_id":"11733","pmid":1,"language":[{"iso":"eng"}],"type":"journal_article","publication_identifier":{"eissn":["1091-6490"]},"article_number":"e2121279119","issue":"31","volume":119,"related_material":{"record":[{"id":"13064","status":"public","relation":"research_data"}]},"quality_controlled":"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.","publication_status":"published","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>","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>.","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).","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>","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.","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>.","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."},"oa_version":"Published Version","date_published":"2022-07-29T00:00:00Z","oa":1,"author":[{"first_name":"Etienne J.","full_name":"Orliac, Etienne J.","last_name":"Orliac"},{"last_name":"Trejo Banos","first_name":"Daniel","full_name":"Trejo Banos, Daniel"},{"last_name":"Ojavee","full_name":"Ojavee, Sven E.","first_name":"Sven E."},{"full_name":"Läll, Kristi","first_name":"Kristi","last_name":"Läll"},{"full_name":"Mägi, Reedik","first_name":"Reedik","last_name":"Mägi"},{"last_name":"Visscher","full_name":"Visscher, Peter M.","first_name":"Peter M."},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","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."}]},{"_id":"11734","pmid":1,"type":"journal_article","language":[{"iso":"eng"}],"article_number":"e2122460119","publication_identifier":{"eissn":["1091-6490"]},"issue":"31","volume":119,"oa":1,"date_published":"2022-07-25T00:00:00Z","author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","first_name":"Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia"},{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina","first_name":"Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"last_name":"Bouguyon","first_name":"Eleonore","full_name":"Bouguyon, Eleonore"},{"full_name":"Domanegg, Kevin","id":"a24c7829-16e8-11ed-8527-c4d36ffb7539","first_name":"Kevin","orcid":"0000-0002-1215-4264","last_name":"Domanegg"},{"last_name":"Krapp","first_name":"Anne","full_name":"Krapp, Anne"},{"last_name":"Nacry","first_name":"Philip","full_name":"Nacry, Philip"},{"last_name":"Gojon","full_name":"Gojon, Alain","first_name":"Alain"},{"last_name":"Lacombe","first_name":"Benoit","full_name":"Lacombe, Benoit"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","abstract":[{"lang":"eng","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."}],"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).","quality_controlled":"1","publication_status":"published","citation":{"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>.","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.","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>","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).","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>.","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>"},"oa_version":"Published Version","status":"public","isi":1,"intvolume":"       119","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"}],"date_created":"2022-08-07T22:01:57Z","date_updated":"2025-05-14T11:00:29Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"day":"25","ddc":["570"],"publisher":"National Academy of Sciences","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_name":"2022_PNAS_Abualia.pdf","access_level":"open_access","date_updated":"2022-08-08T07:09:58Z","date_created":"2022-08-08T07:09:58Z","file_id":"11744","content_type":"application/pdf","success":1,"file_size":3092330,"creator":"dernst","checksum":"6e97dedc281247fc3fe238a209f14af0"}],"file_date_updated":"2022-08-08T07:09:58Z","month":"07","scopus_import":"1","has_accepted_license":"1","article_type":"original","department":[{"_id":"EvBe"}],"title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","article_processing_charge":"No","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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)"},"external_id":{"pmid":["35878040"],"isi":["000881496900007"]},"doi":"10.1073/pnas.2122460119","year":"2022"}]