[{"publication_status":"published","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2022-07-20T11:21:53Z","day":"20","ddc":["575"],"article_processing_charge":"No","_id":"11626","page":"248","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","file":[{"date_updated":"2022-07-25T09:08:47Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"11645","creator":"mgallei","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","file_size":9730864,"date_created":"2022-07-25T09:08:47Z","file_name":"Thesis_Gallei.pdf"},{"access_level":"closed","date_updated":"2022-07-25T09:39:58Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mgallei","file_id":"11646","relation":"source_file","file_name":"Thesis_Gallei_source.docx","file_size":19560720,"date_created":"2022-07-25T09:09:09Z","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb"},{"access_level":"closed","date_updated":"2022-07-25T09:39:58Z","content_type":"application/pdf","relation":"source_file","file_id":"11647","creator":"mgallei","file_name":"Thesis_Gallei_to_print.pdf","checksum":"3994f7f20058941b5bb8a16886b21e71","date_created":"2022-07-25T09:09:32Z","file_size":24542837,"description":"This is the print version of the thesis including the full appendix"},{"file_name":"Thesis_Gallei_Appendix.pdf","file_size":15435966,"date_created":"2022-07-25T11:48:45Z","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","access_level":"open_access","date_updated":"2022-07-25T11:48:45Z","content_type":"application/pdf","creator":"mgallei","relation":"main_file","file_id":"11650"}],"oa":1,"supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"full_name":"Shani, Eilon","last_name":"Shani","first_name":"Eilon"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"date_updated":"2026-06-18T19:02:05Z","year":"2022","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","related_material":{"record":[{"id":"8138","status":"public","relation":"part_of_dissertation"},{"id":"7142","relation":"part_of_dissertation","status":"public"},{"id":"10411","relation":"part_of_dissertation","status":"public"},{"id":"8931","relation":"part_of_dissertation","status":"public"},{"id":"7465","status":"public","relation":"part_of_dissertation"},{"id":"9287","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6260"}]},"author":[{"last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C"}],"oa_version":"Published Version","citation":{"ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","mla":"Gallei, Michelle C. <i>Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","apa":"Gallei, M. C. (2022). <i>Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>"},"abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"month":"07","doi":"10.15479/at:ista:11626","corr_author":"1","has_accepted_license":"1","file_date_updated":"2022-07-25T11:48:45Z","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"}],"ec_funded":1,"date_published":"2022-07-20T00:00:00Z","language":[{"iso":"eng"}]},{"project":[{"name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"}],"file_date_updated":"2022-07-25T07:38:49Z","has_accepted_license":"1","corr_author":"1","volume":20,"date_published":"2022-06-21T00:00:00Z","article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","month":"06","doi":"10.1371/journal.pbio.3001684","author":[{"first_name":"Lina","last_name":"Zhao","full_name":"Zhao, Lina"},{"last_name":"Fenk","first_name":"Lorenz A.","full_name":"Fenk, Lorenz A."},{"first_name":"Lars","last_name":"Nilsson","full_name":"Nilsson, Lars"},{"first_name":"Niko Paresh","last_name":"Amin-Wetzel","full_name":"Amin-Wetzel, Niko Paresh","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425"},{"first_name":"Nelson","last_name":"Ramirez","full_name":"Ramirez, Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono"},{"full_name":"Chen, Changchun","first_name":"Changchun","last_name":"Chen"}],"oa_version":"Published Version","abstract":[{"text":"The ability to detect and respond to acute oxygen (O2) shortages is indispensable to aerobic life. The molecular mechanisms and circuits underlying this capacity are poorly understood. Here, we characterize the behavioral responses of feeding Caenorhabditis elegans to approximately 1% O2. Acute hypoxia triggers a bout of turning maneuvers followed by a persistent switch to rapid forward movement as animals seek to avoid and escape hypoxia. While the behavioral responses to 1% O2 closely resemble those evoked by 21% O2, they have distinct molecular and circuit underpinnings. Disrupting phosphodiesterases (PDEs), specific G proteins, or BBSome function inhibits escape from 1% O2 due to increased cGMP signaling. A primary source of cGMP is GCY-28, the ortholog of the atrial natriuretic peptide (ANP) receptor. cGMP activates the protein kinase G EGL-4 and enhances neuroendocrine secretion to inhibit acute responses to 1% O2. Triggering a rise in cGMP optogenetically in multiple neurons, including AIA interneurons, rapidly and reversibly inhibits escape from 1% O2. Ca2+ imaging reveals that a 7% to 1% O2 stimulus evokes a Ca2+ decrease in several neurons. Defects in mitochondrial complex I (MCI) and mitochondrial complex I (MCIII), which lead to persistently high reactive oxygen species (ROS), abrogate acute hypoxia responses. In particular, repressing the expression of isp-1, which encodes the iron sulfur protein of MCIII, inhibits escape from 1% O2 without affecting responses to 21% O2. Both genetic and pharmacological up-regulation of mitochondrial ROS increase cGMP levels, which contribute to the reduced hypoxia responses. Our results implicate ROS and precise regulation of intracellular cGMP in the modulation of acute responses to hypoxia by C. elegans.","lang":"eng"}],"article_number":"e3001684","citation":{"short":"L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono, C. Chen, PLoS Biology 20 (2022).","mla":"Zhao, Lina, et al. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>, vol. 20, no. 6, e3001684, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>.","ieee":"L. Zhao <i>et al.</i>, “ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans,” <i>PLoS Biology</i>, vol. 20, no. 6. Public Library of Science, 2022.","ista":"Zhao L, Fenk LA, Nilsson L, Amin-Wetzel NP, Ramirez N, de Bono M, Chen C. 2022. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. PLoS Biology. 20(6), e3001684.","chicago":"Zhao, Lina, Lorenz A. Fenk, Lars Nilsson, Niko Paresh Amin-Wetzel, Nelson Ramirez, Mario de Bono, and Changchun Chen. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>.","ama":"Zhao L, Fenk LA, Nilsson L, et al. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. 2022;20(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>","apa":"Zhao, L., Fenk, L. A., Nilsson, L., Amin-Wetzel, N. P., Ramirez, N., de Bono, M., &#38; Chen, C. (2022). ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>"},"publication_identifier":{"eissn":["1545-7885"]},"type":"journal_article","date_updated":"2025-04-15T07:32:21Z","year":"2022","title":"ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans","publisher":"Public Library of Science","department":[{"_id":"MaDe"}],"file":[{"access_level":"open_access","date_updated":"2022-07-25T07:38:49Z","content_type":"application/pdf","creator":"dernst","file_id":"11643","relation":"main_file","success":1,"file_name":"2022_PLoSBiology_Zhao.pdf","file_size":3721585,"date_created":"2022-07-25T07:38:49Z","checksum":"df4902f854ad76769d3203bfdc69f16c"}],"oa":1,"publication":"PLoS Biology","status":"public","ddc":["570"],"external_id":{"pmid":["35727855"],"isi":["000828679600001"]},"quality_controlled":"1","article_processing_charge":"No","_id":"11637","isi":1,"acknowledgement":" This work was funded by H2020 European Research Council (ERC Advanced grant, 269058 ACMO, https://erc.europa.eu/funding/advanced-grants) and Wellcome Trust UK (Wellcome Investigator Award, 209504/Z/17/Z, https://wellcome.org/grant-funding/people-and-projects/grants-awarded/molecular-mechanisms-neural-circuit-function-0) to M.d.B, and by H2020 European Research Council (ERC starting grant, 802653 OXYGEN SENSING, https://erc.europa.eu/funding/starting-grants) and Vetenskapsrådet (VR starting grant, 2018-02216, https://www.vr.se/english.html) to C.C. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"pmid":1,"day":"21","date_created":"2022-07-24T22:01:42Z","publication_status":"published","intvolume":"        20"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"issue":"2","pmid":1,"day":"24","date_created":"2022-07-24T22:01:42Z","publication_status":"published","intvolume":"         4","publisher":"American Physical Society","department":[{"_id":"GaTk"}],"file":[{"relation":"main_file","file_id":"11644","creator":"dernst","date_updated":"2022-07-25T07:47:23Z","content_type":"application/pdf","access_level":"open_access","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","file_size":1379683,"date_created":"2022-07-25T07:47:23Z","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","success":1}],"oa":1,"publication":"Physical Review Research","status":"public","ddc":["530"],"external_id":{"arxiv":["2106.02349"],"pmid":["37576946"]},"quality_controlled":"1","article_processing_charge":"No","_id":"11638","acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030).","author":[{"last_name":"Ngampruetikorn","first_name":"Vudtiwat","full_name":"Ngampruetikorn, Vudtiwat"},{"last_name":"Sachdeva","first_name":"Vedant","full_name":"Sachdeva, Vedant"},{"last_name":"Torrence","first_name":"Johanna","full_name":"Torrence, Johanna"},{"full_name":"Humplik, Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Humplik"},{"full_name":"Schwab, David J.","last_name":"Schwab","first_name":"David J."},{"last_name":"Palmer","first_name":"Stephanie E.","full_name":"Palmer, Stephanie E."}],"oa_version":"Published Version","abstract":[{"text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data.","lang":"eng"}],"article_number":"023240","citation":{"ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>.","ieee":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” <i>Physical Review Research</i>, vol. 4, no. 2. American Physical Society, 2022.","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., &#38; Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>","ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. 2022;4(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>"},"publication_identifier":{"issn":["2643-1564"]},"arxiv":1,"type":"journal_article","date_updated":"2025-03-06T14:09:21Z","year":"2022","title":"Inferring couplings in networks across order-disorder phase transitions","has_accepted_license":"1","file_date_updated":"2022-07-25T07:47:23Z","date_published":"2022-06-24T00:00:00Z","volume":4,"article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","month":"06","doi":"10.1103/PhysRevResearch.4.023240"},{"publication_status":"published","intvolume":"        68","issue":"12","date_created":"2022-07-24T22:01:42Z","day":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1901.03790","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"_id":"11639","article_processing_charge":"No","acknowledgement":"This work was done when Shashank Vatedka was at the Chinese University of Hong Kong, where he was supported in part by CUHK Direct Grants 4055039 and 4055077. He would like to acknowledge funding from a seed grant offered by IIT Hyderabad and the Start-up Research Grant (SRG/2020/000910) from the Science and Engineering Board, India. Yihan Zhang has received funding from the European Union’s Horizon 2020 research and innovation programme\r\nunder grant agreement No 682203-ERC-[Inf-Speed-Tradeoff].","external_id":{"arxiv":["1901.03790"],"isi":["000891796100007"]},"quality_controlled":"1","status":"public","publication":"IEEE Transactions on Information Theory","page":"7753-7786","department":[{"_id":"MaMo"}],"publisher":"IEEE","oa":1,"year":"2022","title":"List decoding random Euclidean codes and Infinite constellations","type":"journal_article","arxiv":1,"publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"date_updated":"2024-10-09T21:02:55Z","citation":{"mla":"Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12, IEEE, 2022, pp. 7753–86, doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>.","ieee":"Y. Zhang and S. Vatedka, “List decoding random Euclidean codes and Infinite constellations,” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12. IEEE, pp. 7753–7786, 2022.","chicago":"Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2022. <a href=\"https://doi.org/10.1109/TIT.2022.3189542\">https://doi.org/10.1109/TIT.2022.3189542</a>.","ista":"Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786.","apa":"Zhang, Y., &#38; Vatedka, S. (2022). List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2022.3189542\">https://doi.org/10.1109/TIT.2022.3189542</a>","ama":"Zhang Y, Vatedka S. List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. 2022;68(12):7753-7786. doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>"},"abstract":[{"text":"We study the list decodability of different ensembles of codes over the real alphabet under the assumption of an omniscient adversary. It is a well-known result that when the source and the adversary have power constraints P and N respectively, the list decoding capacity is equal to 1/2logP/N. Random spherical codes achieve constant list sizes, and the goal of the present paper is to obtain a better understanding of the smallest achievable list size as a function of the gap to capacity. We show a reduction from arbitrary codes to spherical codes, and derive a lower bound on the list size of typical random spherical codes. We also give an upper bound on the list size achievable using nested Construction-A lattices and infinite Construction-A lattices. We then define and study a class of infinite constellations that generalize Construction-A lattices and prove upper and lower bounds for the same. Other goodness properties such as packing goodness and AWGN goodness of infinite constellations are proved along the way. Finally, we consider random lattices sampled from the Haar distribution and show that if a certain conjecture that originates in analytic number theory is true, then the list size grows as a polynomial function of the gap-to-capacity.","lang":"eng"}],"author":[{"id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan","last_name":"Zhang","first_name":"Yihan","orcid":"0000-0002-6465-6258"},{"first_name":"Shashank","last_name":"Vatedka","full_name":"Vatedka, Shashank"}],"oa_version":"Preprint","doi":"10.1109/TIT.2022.3189542","month":"12","scopus_import":"1","article_type":"original","language":[{"iso":"eng"}],"corr_author":"1","date_published":"2022-12-01T00:00:00Z","volume":68},{"oa_version":"Published Version","author":[{"first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Katalin","last_name":"Csilléry","full_name":"Csilléry, Katalin"}],"citation":{"chicago":"Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>.","ista":"Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 22(8), 2941–2955.","mla":"Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>.","ieee":"E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size,” <i>Molecular Ecology Resources</i>, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","apa":"Szep, E., Trubenova, B., &#38; Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>","ama":"Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. 2022;22(8):2941-2955. doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>"},"abstract":[{"lang":"eng","text":"Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST, a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST. Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size."}],"date_updated":"2025-06-11T14:01:43Z","type":"journal_article","publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","year":"2022","ec_funded":1,"date_published":"2022-11-01T00:00:00Z","volume":22,"corr_author":"1","has_accepted_license":"1","file_date_updated":"2023-02-02T08:11:23Z","project":[{"call_identifier":"H2020","grant_number":"704172","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","name":"Rate of Adaptation in Changing Environment"}],"language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","doi":"10.1111/1755-0998.13676","month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","date_created":"2022-07-24T22:01:43Z","pmid":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"issue":"8","intvolume":"        22","publication_status":"published","oa":1,"file":[{"date_created":"2023-02-02T08:11:23Z","file_size":6431779,"checksum":"3102e203e77b884bffffdbe8e548da88","file_name":"2022_MolecularEcologyRes_Szep.pdf","success":1,"creator":"dernst","relation":"main_file","file_id":"12477","content_type":"application/pdf","date_updated":"2023-02-02T08:11:23Z","access_level":"open_access"}],"page":"2941-2955","department":[{"_id":"NiBa"}],"publisher":"Wiley","status":"public","publication":"Molecular Ecology Resources","quality_controlled":"1","external_id":{"isi":["000825873600001"],"pmid":["35765749"]},"ddc":["570"],"acknowledgement":"ES was supported by an IST studentship provided by IST Austria. BT was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project received further funding awarded to KC from the Swiss National Science Foundation (SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick Barton for many invaluable discussions and his comments on the thesis chapter and this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for providing us with the raw data from the LPX-Bern model for silver fir, and Willy Tinner for helpful insights about the demographic history of silver fir. We also thank the editor Alana Alexander for useful comments and advice on the manuscript. Open access funding provided by Eidgenossische Technische Hochschule Zurich.","isi":1,"article_processing_charge":"Yes (via OA deal)","_id":"11640"},{"ddc":["570"],"quality_controlled":"1","external_id":{"isi":["000837950900001"],"pmid":["35861182"]},"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.","_id":"11648","article_processing_charge":"No","isi":1,"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2023-02-03T08:34:48Z","creator":"dernst","relation":"main_file","file_id":"12498","success":1,"file_name":"2022_Microscopy_Gerle.pdf","date_created":"2023-02-03T08:34:48Z","file_size":7812696,"checksum":"23b51c163636bf9313f7f0818312e67e"}],"oa":1,"publisher":"Oxford University Press","department":[{"_id":"LeSa"}],"page":"249-261","publication":"Microscopy","status":"public","intvolume":"        71","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"date_created":"2022-07-25T10:04:58Z","day":"01","issue":"5","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"scopus_import":"1","doi":"10.1093/jmicro/dfac037","month":"10","volume":71,"date_published":"2022-10-01T00:00:00Z","file_date_updated":"2023-02-03T08:34:48Z","has_accepted_license":"1","language":[{"iso":"eng"}],"article_type":"original","date_updated":"2023-08-03T12:13:37Z","publication_identifier":{"eissn":["2050-5701"],"issn":["2050-5698"]},"type":"journal_article","title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","year":"2022","oa_version":"Published Version","author":[{"full_name":"Gerle, Christoph","last_name":"Gerle","first_name":"Christoph"},{"last_name":"Kishikawa","first_name":"Jun-ichi","full_name":"Kishikawa, Jun-ichi"},{"last_name":"Yamaguchi","first_name":"Tomoko","full_name":"Yamaguchi, Tomoko"},{"first_name":"Atsuko","last_name":"Nakanishi","full_name":"Nakanishi, Atsuko"},{"orcid":"0000-0002-3219-2022","first_name":"Mehmet Orkun","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef"},{"first_name":"Fumiaki","last_name":"Makino","full_name":"Makino, Fumiaki"},{"first_name":"Tomoko","last_name":"Miyata","full_name":"Miyata, Tomoko"},{"full_name":"Kawamoto, Akihiro","last_name":"Kawamoto","first_name":"Akihiro"},{"last_name":"Yokoyama","first_name":"Ken","full_name":"Yokoyama, Ken"},{"last_name":"Namba","first_name":"Keiichi","full_name":"Namba, Keiichi"},{"last_name":"Kurisu","first_name":"Genji","full_name":"Kurisu, Genji"},{"first_name":"Takayuki","last_name":"Kato","full_name":"Kato, Takayuki"}],"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"}],"citation":{"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.","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.","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>.","mla":"Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>, vol. 71, no. 5, Oxford University Press, 2022, pp. 249–61, doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>.","ieee":"C. Gerle <i>et al.</i>, “Structures of multisubunit membrane complexes with the CRYO ARM 200,” <i>Microscopy</i>, vol. 71, no. 5. Oxford University Press, pp. 249–261, 2022.","ama":"Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. 2022;71(5):249-261. doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>","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>"}},{"oa_version":"Submitted Version","author":[{"last_name":"Biswas","orcid":"0000-0002-5372-7890","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita"},{"full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","last_name":"Cultrera di Montesano"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Saghafian","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza"}],"citation":{"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.","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.","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.","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.","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.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.)."},"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"}],"date_updated":"2026-04-07T12:58:48Z","type":"journal_article","title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","related_material":{"record":[{"status":"public","relation":"later_version","id":"15380"},{"status":"public","relation":"dissertation_contains","id":"15094"}]},"year":"2022","ec_funded":1,"date_published":"2022-07-27T00:00:00Z","corr_author":"1","has_accepted_license":"1","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"file_date_updated":"2022-07-27T09:25:53Z","language":[{"iso":"eng"}],"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-07-27T09:27:34Z","day":"27","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"draft","file":[{"file_id":"11659","relation":"main_file","creator":"scultrer","date_updated":"2022-07-27T09:25:53Z","content_type":"application/pdf","access_level":"open_access","checksum":"b2f511e8b1cae5f1892b0cdec341acac","date_created":"2022-07-27T09:25:53Z","file_size":639266,"file_name":"D-S-E.pdf"}],"oa":1,"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","publication":"Leibniz International Proceedings on Mathematics","quality_controlled":"1","ddc":["510"],"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.","_id":"11658","article_processing_charge":"No"},{"year":"2022","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15094"}]},"title":"A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs","type":"journal_article","date_updated":"2026-04-07T12:58:47Z","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"}],"citation":{"short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs (n.d.).","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.","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.","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.","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.","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>.","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."},"author":[{"first_name":"Ranita","orcid":"0000-0002-5372-7890","last_name":"Biswas","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","last_name":"Cultrera di Montesano"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza"}],"oa_version":"Submitted Version","month":"07","language":[{"iso":"eng"}],"has_accepted_license":"1","file_date_updated":"2022-07-27T09:30:30Z","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"name":"Mathematics, Computer Science","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","date_published":"2022-07-25T00:00:00Z","ec_funded":1,"publication_status":"submitted","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"25","date_created":"2022-07-27T09:31:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","_id":"11660","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. ","ddc":["510"],"quality_controlled":"1","publication":"LIPIcs","status":"public","alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"oa":1,"file":[{"file_name":"window 1.pdf","checksum":"95903f9d1649e8e437a967b6f2f64730","date_created":"2022-07-27T09:30:30Z","file_size":564836,"access_level":"open_access","date_updated":"2022-07-27T09:30:30Z","content_type":"application/pdf","file_id":"11661","relation":"main_file","creator":"scultrer"}]},{"article_number":"16","citation":{"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>","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>","short":"M. Henzinger, P. Peng, ACM Transactions on Algorithms 18 (2022).","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.","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>.","ista":"Henzinger M, Peng P. 2022. Constant-time Dynamic (Δ +1)-Coloring. ACM Transactions on Algorithms. 18(2), 16.","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>."},"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"}],"oa_version":"None","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"first_name":"Pan","last_name":"Peng","full_name":"Peng, Pan"}],"title":"Constant-time Dynamic (Δ +1)-Coloring","year":"2022","date_updated":"2024-11-04T11:42:31Z","type":"journal_article","publication_identifier":{"eissn":["1549-6333"],"issn":["1549-6325"]},"language":[{"iso":"eng"}],"extern":"1","article_type":"original","volume":18,"date_published":"2022-03-04T00:00:00Z","doi":"10.1145/3501403","month":"03","scopus_import":"1","day":"04","date_created":"2022-07-27T10:58:53Z","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        18","publication_status":"published","status":"public","publication":"ACM Transactions on Algorithms","publisher":"Association for Computing Machinery","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.","_id":"11662","article_processing_charge":"No","quality_controlled":"1"},{"date_created":"2022-07-29T06:45:41Z","day":"06","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"}],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"short":"M. Turelli, N.H. Barton, (2022).","mla":"Turelli, Michael, and Nicholas H. Barton. <i>Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","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>.","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>.","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>","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>"},"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"main_file_link":[{"url":"https://doi.org/10.25338/B81931","open_access":"1"}],"related_material":{"record":[{"id":"10604","status":"public","relation":"used_in_publication"}]},"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","keyword":["Biological sciences"],"year":"2022","date_updated":"2025-06-11T13:45:56Z","type":"research_data_reference","status":"public","date_published":"2022-01-06T00:00:00Z","oa":1,"publisher":"Dryad","corr_author":"1","department":[{"_id":"NiBa"}],"acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"11686","month":"01","doi":"10.25338/B81931","article_processing_charge":"No","ddc":["570"]},{"publication_status":"published","intvolume":"        17","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.05677","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"5","date_created":"2022-07-31T22:01:46Z","day":"01","external_id":{"isi":["000812422100001"],"arxiv":["2105.05677"]},"quality_controlled":"1","isi":1,"_id":"11700","article_processing_charge":"No","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.","page":"687-717","department":[{"_id":"JaMa"}],"publisher":"American Institute of Mathematical Sciences","oa":1,"status":"public","publication":"Networks and Heterogeneous Media","type":"journal_article","arxiv":1,"publication_identifier":{"issn":["1556-1801"],"eissn":["1556-181X"]},"date_updated":"2025-04-14T07:27:47Z","year":"2022","title":"Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph","author":[{"last_name":"Erbar","first_name":"Matthias","full_name":"Erbar, Matthias"},{"last_name":"Forkert","first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","full_name":"Forkert, Dominik L"},{"orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mugnolo","first_name":"Delio","full_name":"Mugnolo, Delio"}],"oa_version":"Preprint","citation":{"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>","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>.","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.","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>."},"abstract":[{"lang":"eng","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."}],"scopus_import":"1","doi":"10.3934/nhm.2022023","month":"10","corr_author":"1","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"ec_funded":1,"volume":17,"date_published":"2022-10-01T00:00:00Z","article_type":"original","language":[{"iso":"eng"}]},{"acknowledgement":"The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","_id":"11701","article_processing_charge":"No","isi":1,"ddc":["510"],"quality_controlled":"1","external_id":{"isi":["000826695900001"],"arxiv":["2001.00512"]},"publication":"Nonlinearity","status":"public","oa":1,"file":[{"access_level":"open_access","date_updated":"2022-08-01T10:39:36Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"11715","success":1,"file_name":"2022_Nonlinearity_Agresti.pdf","file_size":2122096,"date_created":"2022-08-01T10:39:36Z","checksum":"997a4bff2dfbee3321d081328c2f1e1a"}],"publisher":"IOP Publishing","page":"4100-4210","department":[{"_id":"JuFi"}],"intvolume":"        35","publication_status":"published","day":"04","date_created":"2022-07-31T22:01:47Z","issue":"8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1088/1361-6544/abd613","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","volume":35,"date_published":"2022-08-04T00:00:00Z","file_date_updated":"2022-08-01T10:39:36Z","has_accepted_license":"1","title":"Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence","year":"2022","date_updated":"2023-08-03T12:25:08Z","publication_identifier":{"issn":["0951-7715"],"eissn":["1361-6544"]},"type":"journal_article","arxiv":1,"abstract":[{"lang":"eng","text":"In this paper we develop a new approach to nonlinear stochastic partial differential equations with Gaussian noise. Our aim is to provide an abstract framework which is applicable to a large class of SPDEs and includes many important cases of nonlinear parabolic problems which are of quasi- or semilinear type. This first part is on local existence and well-posedness. A second part in preparation is on blow-up criteria and regularization. Our theory is formulated in an Lp-setting, and because of this we can deal with nonlinearities in a very efficient way. Applications to several concrete problems and their quasilinear variants are given. This includes Burgers' equation, the Allen–Cahn equation, the Cahn–Hilliard equation, reaction–diffusion equations, and the porous media equation. The interplay of the nonlinearities and the critical spaces of initial data leads to new results and insights for these SPDEs. The proofs are based on recent developments in maximal regularity theory for the linearized problem for deterministic and stochastic evolution equations. In particular, our theory can be seen as a stochastic version of the theory of critical spaces due to Prüss–Simonett–Wilke (2018). Sharp weighted time-regularity allow us to deal with rough initial values and obtain instantaneous regularization results. The abstract well-posedness results are obtained by a combination of several sophisticated splitting and truncation arguments."}],"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>","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>","short":"A. Agresti, M. Veraar, Nonlinearity 35 (2022) 4100–4210.","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.","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>.","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.","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>."},"oa_version":"Published Version","author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio","last_name":"Agresti","first_name":"Antonio","orcid":"0000-0002-9573-2962"},{"full_name":"Veraar, Mark","first_name":"Mark","last_name":"Veraar"}]},{"language":[{"iso":"eng"}],"article_type":"original","volume":119,"date_published":"2022-07-18T00:00:00Z","file_date_updated":"2022-08-01T10:58:28Z","has_accepted_license":"1","corr_author":"1","month":"07","doi":"10.1073/pnas.2122147119","scopus_import":"1","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."}],"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>","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>","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","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.","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>.","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119."},"article_number":"e2122147119","oa_version":"Published Version","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"title":"The \"New Synthesis\"","year":"2022","date_updated":"2025-05-14T11:01:10Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"type":"journal_article","publication":"Proceedings of the National Academy of Sciences of the United States of America","status":"public","file":[{"success":1,"file_size":848511,"date_created":"2022-08-01T10:58:28Z","checksum":"06c866196a8957f0c37b8a121771c885","file_name":"2022_PNAS_Barton.pdf","content_type":"application/pdf","date_updated":"2022-08-01T10:58:28Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"11716"}],"oa":1,"publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","_id":"11702","article_processing_charge":"No","ddc":["570"],"external_id":{"pmid":["35858408"]},"quality_controlled":"1","pmid":1,"date_created":"2022-07-31T22:01:47Z","day":"18","issue":"30","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       119","publication_status":"published"},{"date_updated":"2025-04-14T07:41:20Z","type":"journal_article","publication_identifier":{"eissn":["1553-7404"]},"title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","year":"2022","oa_version":"Published Version","author":[{"last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"first_name":"John R.","last_name":"Pannell","full_name":"Pannell, John R."}],"citation":{"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>","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>","short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (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>.","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.","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>.","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."},"article_number":"e1010226","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."}],"scopus_import":"1","doi":"10.1371/journal.pgen.1010226","month":"07","ec_funded":1,"volume":18,"date_published":"2022-07-06T00:00:00Z","corr_author":"1","file_date_updated":"2022-08-01T07:49:25Z","project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"article_type":"original","intvolume":"        18","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"06","date_created":"2022-07-31T22:01:48Z","pmid":1,"issue":"7","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","external_id":{"pmid":["35793353"],"isi":["000886643100006"]},"ddc":["570"],"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.","isi":1,"_id":"11703","article_processing_charge":"No","file":[{"file_name":"2022_PLoSGenetics_Toups.pdf","file_size":1620272,"date_created":"2022-08-01T07:49:25Z","checksum":"aa4c137f82635e700856c359dccfaa0a","success":1,"creator":"dernst","file_id":"11708","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-08-01T07:49:25Z"}],"oa":1,"department":[{"_id":"BeVi"}],"publisher":"Public Library of Science","status":"public","publication":"PLoS Genetics"},{"month":"07","doi":"10.1371/journal.pone.0269975","scopus_import":"1","article_type":"original","language":[{"iso":"eng"}],"corr_author":"1","has_accepted_license":"1","file_date_updated":"2022-08-01T08:02:38Z","date_published":"2022-07-18T00:00:00Z","volume":17,"year":"2022","title":"An autonomous compartmental model for accelerating epidemics","related_material":{"record":[{"relation":"research_data","status":"public","id":"11711"}]},"type":"journal_article","publication_identifier":{"eissn":["1932-6203"]},"date_updated":"2025-06-11T13:37:36Z","citation":{"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>","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>","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>.","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.","ista":"Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating epidemics. PLoS ONE. 17(7), e0269975.","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>.","short":"N.B. Budanur, B. Hof, PLoS ONE 17 (2022)."},"article_number":"e0269975","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"}],"author":[{"last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"oa_version":"Published Version","isi":1,"article_processing_charge":"No","_id":"11704","quality_controlled":"1","external_id":{"pmid":["35849565"],"isi":["000911392100055"]},"ddc":["510"],"status":"public","publication":"PLoS ONE","department":[{"_id":"BjHo"}],"publisher":"Public Library of Science","oa":1,"file":[{"checksum":"1ddd9b91e6dec31ab0e7a8433ca2d452","file_size":1421256,"date_created":"2022-08-01T08:02:38Z","file_name":"2022_PLoSONE_Budanur.pdf","success":1,"relation":"main_file","file_id":"11712","creator":"dernst","date_updated":"2022-08-01T08:02:38Z","content_type":"application/pdf","access_level":"open_access"}],"publication_status":"published","intvolume":"        17","issue":"7","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2022-07-31T22:01:48Z","day":"18","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Springer Nature","series_title":"LNCS","page":"1-20","department":[{"_id":"DaAl"}],"oa":1,"publication":"International Colloquium on Structural Information and Communication Complexity","status":"public","quality_controlled":"1","external_id":{"isi":["000876977400001"],"arxiv":["2102.08703"]},"article_processing_charge":"No","_id":"11707","isi":1,"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.","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08703"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-07-31T22:01:49Z","day":"25","publication_status":"published","intvolume":"     13298","project":[{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020"}],"volume":13298,"date_published":"2022-06-25T00:00:00Z","ec_funded":1,"language":[{"iso":"eng"}],"scopus_import":"1","doi":"10.1007/978-3-031-09993-9_1","month":"06","author":[{"first_name":"Alkida","last_name":"Balliu","full_name":"Balliu, Alkida"},{"first_name":"Juho","last_name":"Hirvonen","full_name":"Hirvonen, Juho"},{"first_name":"Darya","last_name":"Melnyk","full_name":"Melnyk, Darya"},{"last_name":"Olivetti","first_name":"Dennis","full_name":"Olivetti, Dennis"},{"orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Suomela, Jukka","first_name":"Jukka","last_name":"Suomela"}],"editor":[{"full_name":"Parter, Merav","last_name":"Parter","first_name":"Merav"}],"oa_version":"Preprint","conference":{"name":"SIROCCO: Structural Information and Communication Complexity","start_date":"2022-06-27","location":"Paderborn, Germany","end_date":"2022-06-29"},"abstract":[{"text":"In this work we introduce the graph-theoretic notion of mendability: for each locally checkable graph problem we can define its mending radius, which captures the idea of how far one needs to modify a partial solution in order to “patch a hole.” We explore how mendability is connected to the existence of efficient algorithms, especially in distributed, parallel, and fault-tolerant settings. It is easy to see that O(1)-mendable problems are also solvable in O(log∗n) rounds in the LOCAL model of distributed computing. One of the surprises is that in paths and cycles, a converse also holds in the following sense: if a problem Π can be solved in O(log∗n), there is always a restriction Π′⊆Π that is still efficiently solvable but that is also O(1)-mendable. We also explore the structure of the landscape of mendability. For example, we show that in trees, the mending radius of any locally checkable problem is O(1), Θ(logn), or Θ(n), while in general graphs the structure is much more diverse.","lang":"eng"}],"citation":{"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>","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>","mla":"Balliu, Alkida, et al. “Local Mending.” <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, vol. 13298, Springer Nature, 2022, pp. 1–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>.","ieee":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, and J. Suomela, “Local mending,” in <i>International Colloquium on Structural Information and Communication Complexity</i>, Paderborn, Germany, 2022, vol. 13298, pp. 1–20.","chicago":"Balliu, Alkida, Juho Hirvonen, Darya Melnyk, Dennis Olivetti, Joel Rybicki, and Jukka Suomela. “Local Mending.” In <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, 13298:1–20. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>.","ista":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. 2022. Local mending. International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication ComplexityLNCS vol. 13298, 1–20.","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."},"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031099922"],"eissn":["1611-3349"]},"type":"conference","arxiv":1,"date_updated":"2025-04-14T07:50:55Z","year":"2022","title":"Local mending"},{"_id":"11711","doi":"10.5281/ZENODO.6802720","month":"07","article_processing_charge":"No","ddc":["000"],"status":"public","publisher":"Zenodo","has_accepted_license":"1","department":[{"_id":"BjHo"}],"corr_author":"1","date_published":"2022-07-06T00:00:00Z","oa":1,"year":"2022","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11704"}]},"title":"burakbudanur/autoacc-public","type":"research_data_reference","date_updated":"2025-06-11T13:37:36Z","abstract":[{"lang":"eng","text":"Codes and data for reproducing the results of N. B. Budanur and B. Hof \"An autonomous compartmental model for accelerating epidemics\""}],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"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>","ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">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>.","ista":"Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","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>.","short":"N.B. Budanur, (2022)."},"day":"06","date_created":"2022-08-01T08:06:33Z","author":[{"first_name":"Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.6802720","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version"},{"intvolume":"        15","publication_status":"published","keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-08-01T09:04:27Z","day":"13","pmid":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["35562780"]},"quality_controlled":"1","ddc":["570"],"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.","_id":"11713","article_processing_charge":"No","file":[{"checksum":"008156e5340e9789f0f6d82bde4d347a","date_created":"2022-08-01T09:24:42Z","file_size":1545310,"file_name":"2022_BMCResearchNotes_Nikolic.pdf","success":1,"relation":"main_file","file_id":"11714","creator":"dernst","date_updated":"2022-08-01T09:24:42Z","content_type":"application/pdf","access_level":"open_access"}],"oa":1,"department":[{"_id":"CaGu"}],"publisher":"Springer Nature","status":"public","publication":"BMC Research Notes","date_updated":"2025-04-14T09:24:53Z","type":"journal_article","publication_identifier":{"issn":["1756-0500"]},"title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13104-022-06152-7"}]},"year":"2022","oa_version":"Published Version","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090"},{"full_name":"Sauert, Martina","first_name":"Martina","last_name":"Sauert"},{"full_name":"Albanese, Tanino G.","first_name":"Tanino G.","last_name":"Albanese"},{"full_name":"Moll, Isabella","last_name":"Moll","first_name":"Isabella"}],"article_number":"173","citation":{"short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","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>.","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>.","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>","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>"},"abstract":[{"text":"Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes.","lang":"eng"}],"scopus_import":"1","doi":"10.1186/s13104-022-06061-9","month":"05","volume":15,"date_published":"2022-05-13T00:00:00Z","corr_author":"1","has_accepted_license":"1","project":[{"call_identifier":"FWF","_id":"26956E74-B435-11E9-9278-68D0E5697425","grant_number":"V00738","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms"}],"file_date_updated":"2022-08-01T09:24:42Z","language":[{"iso":"eng"}],"article_type":"letter_note"},{"status":"public","publication":"Advances in Mathematics","file":[{"success":1,"date_created":"2023-02-02T07:39:09Z","file_size":2164036,"checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","file_name":"2022_AdvancesMathematics_Drach.pdf","content_type":"application/pdf","date_updated":"2023-02-02T07:39:09Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"12474"}],"oa":1,"department":[{"_id":"VaKa"}],"publisher":"Elsevier","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).","isi":1,"_id":"11717","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000860924200005"]},"quality_controlled":"1","ddc":["510"],"date_created":"2022-08-01T17:08:16Z","day":"29","issue":"Part A","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       408","keyword":["General Mathematics"],"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","ec_funded":1,"date_published":"2022-10-29T00:00:00Z","volume":408,"corr_author":"1","file_date_updated":"2023-02-02T07:39:09Z","has_accepted_license":"1","project":[{"name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020"}],"month":"10","doi":"10.1016/j.aim.2022.108591","scopus_import":"1","article_number":"108591","citation":{"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.","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.","short":"K. Drach, D. Schleicher, Advances in Mathematics 408 (2022).","apa":"Drach, K., &#38; Schleicher, D. (2022). Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>","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>"},"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","author":[{"id":"fe8209e2-906f-11eb-847d-950f8fc09115","full_name":"Drach, Kostiantyn","last_name":"Drach","orcid":"0000-0002-9156-8616","first_name":"Kostiantyn"},{"full_name":"Schleicher, Dierk","last_name":"Schleicher","first_name":"Dierk"}],"title":"Rigidity of Newton dynamics","year":"2022","date_updated":"2025-04-14T07:53:45Z","type":"journal_article","publication_identifier":{"issn":["0001-8708"]}},{"oa_version":"Published Version","author":[{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li"},{"first_name":"Huihuang","last_name":"Chen","full_name":"Chen, Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f"},{"last_name":"Alotaibi","first_name":"Saqer S.","full_name":"Alotaibi, Saqer S."},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","first_name":"Maciek"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_number":"e2121058119","citation":{"ieee":"L. Li <i>et al.</i>, “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","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>.","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>.","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121058119.","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","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>","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>"},"abstract":[{"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.","lang":"eng"}],"date_updated":"2025-05-14T11:01:00Z","type":"journal_article","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","year":"2022","volume":119,"date_published":"2022-07-25T00:00:00Z","corr_author":"1","file_date_updated":"2022-08-08T07:42:09Z","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","month":"07","doi":"10.1073/pnas.2121058119","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"25","date_created":"2022-08-04T20:06:49Z","pmid":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"issue":"31","intvolume":"       119","publication_status":"published","keyword":["Multidisciplinary"],"file":[{"file_name":"2022_PNAS_Li.pdf","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","file_size":2506262,"date_created":"2022-08-08T07:42:09Z","success":1,"relation":"main_file","file_id":"11747","creator":"dernst","access_level":"open_access","date_updated":"2022-08-08T07:42:09Z","content_type":"application/pdf"}],"oa":1,"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publisher":"National Academy of Sciences","status":"public","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","external_id":{"isi":["000881496900002"],"pmid":["35878023"]},"ddc":["580"],"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).”","isi":1,"_id":"11723","article_processing_charge":"No"}]