[{"external_id":{"arxiv":["1901.03790"],"isi":["000891796100007"]},"publication_status":"published","date_created":"2022-07-24T22:01:42Z","month":"12","issue":"12","scopus_import":"1","_id":"11639","citation":{"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>","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>","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.","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>.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786."},"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"}],"type":"journal_article","quality_controlled":"1","corr_author":"1","publisher":"IEEE","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1901.03790"}],"volume":68,"department":[{"_id":"MaMo"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","title":"List decoding random Euclidean codes and Infinite constellations","author":[{"last_name":"Zhang","full_name":"Zhang, Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","first_name":"Yihan"},{"first_name":"Shashank","last_name":"Vatedka","full_name":"Vatedka, Shashank"}],"page":"7753-7786","date_updated":"2024-10-09T21:02:55Z","article_type":"original","year":"2022","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].","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"oa":1,"doi":"10.1109/TIT.2022.3189542","day":"01","date_published":"2022-12-01T00:00:00Z","intvolume":"        68","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"publication":"IEEE Transactions on Information Theory","arxiv":1},{"pmid":1,"type":"journal_article","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."}],"citation":{"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>","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.","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>","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>.","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.","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>.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955."},"quality_controlled":"1","volume":22,"department":[{"_id":"NiBa"}],"publisher":"Wiley","corr_author":"1","publication_status":"published","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"date_created":"2022-07-24T22:01:43Z","external_id":{"isi":["000825873600001"],"pmid":["35765749"]},"_id":"11640","month":"11","scopus_import":"1","issue":"8","doi":"10.1111/1755-0998.13676","day":"01","oa":1,"file":[{"relation":"main_file","checksum":"3102e203e77b884bffffdbe8e548da88","content_type":"application/pdf","file_id":"12477","date_updated":"2023-02-02T08:11:23Z","access_level":"open_access","date_created":"2023-02-02T08:11:23Z","success":1,"file_name":"2022_MolecularEcologyRes_Szep.pdf","file_size":6431779,"creator":"dernst"}],"intvolume":"        22","date_published":"2022-11-01T00:00:00Z","ec_funded":1,"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.","article_type":"original","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"year":"2022","publication":"Molecular Ecology Resources","isi":1,"project":[{"name":"Rate of Adaptation in Changing Environment","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172","call_identifier":"H2020"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa_version":"Published Version","author":[{"first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko","last_name":"Szep"},{"full_name":"Trubenova, Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora"},{"full_name":"Csilléry, Katalin","last_name":"Csilléry","first_name":"Katalin"}],"title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","date_updated":"2025-06-11T14:01:43Z","page":"2941-2955","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2023-02-02T08:11:23Z","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"oa":1,"file":[{"access_level":"open_access","creator":"dernst","file_size":7812696,"date_created":"2023-02-03T08:34:48Z","success":1,"file_name":"2022_Microscopy_Gerle.pdf","content_type":"application/pdf","checksum":"23b51c163636bf9313f7f0818312e67e","relation":"main_file","date_updated":"2023-02-03T08:34:48Z","file_id":"12498"}],"day":"01","doi":"10.1093/jmicro/dfac037","date_published":"2022-10-01T00:00:00Z","intvolume":"        71","article_type":"original","publication_identifier":{"issn":["2050-5698"],"eissn":["2050-5701"]},"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.","year":"2022","isi":1,"publication":"Microscopy","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"oa_version":"Published Version","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","author":[{"last_name":"Gerle","full_name":"Gerle, Christoph","first_name":"Christoph"},{"first_name":"Jun-ichi","last_name":"Kishikawa","full_name":"Kishikawa, Jun-ichi"},{"full_name":"Yamaguchi, Tomoko","last_name":"Yamaguchi","first_name":"Tomoko"},{"first_name":"Atsuko","last_name":"Nakanishi","full_name":"Nakanishi, Atsuko"},{"full_name":"Çoruh, Mehmet Orkun","last_name":"Çoruh","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","orcid":"0000-0002-3219-2022","first_name":"Mehmet Orkun"},{"full_name":"Makino, Fumiaki","last_name":"Makino","first_name":"Fumiaki"},{"full_name":"Miyata, Tomoko","last_name":"Miyata","first_name":"Tomoko"},{"full_name":"Kawamoto, Akihiro","last_name":"Kawamoto","first_name":"Akihiro"},{"first_name":"Ken","full_name":"Yokoyama, Ken","last_name":"Yokoyama"},{"full_name":"Namba, Keiichi","last_name":"Namba","first_name":"Keiichi"},{"first_name":"Genji","last_name":"Kurisu","full_name":"Kurisu, Genji"},{"last_name":"Kato","full_name":"Kato, Takayuki","first_name":"Takayuki"}],"date_updated":"2023-08-03T12:13:37Z","page":"249-261","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2023-02-03T08:34:48Z","citation":{"chicago":"Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>.","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.","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>.","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>","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.","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>","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."},"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"}],"pmid":1,"type":"journal_article","quality_controlled":"1","volume":71,"department":[{"_id":"LeSa"}],"publisher":"Oxford University Press","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":"published","date_created":"2022-07-25T10:04:58Z","external_id":{"isi":["000837950900001"],"pmid":["35861182"]},"_id":"11648","month":"10","issue":"5","scopus_import":"1"},{"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Peng, Pan","last_name":"Peng","first_name":"Pan"}],"title":"Constant-time Dynamic (Δ +1)-Coloring","date_updated":"2024-11-04T11:42:31Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"ACM Transactions on Algorithms","article_number":"16","year":"2022","publication_identifier":{"issn":["1549-6325"],"eissn":["1549-6333"]},"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.","article_type":"original","day":"04","doi":"10.1145/3501403","intvolume":"        18","date_published":"2022-03-04T00:00:00Z","month":"03","scopus_import":"1","issue":"2","_id":"11662","publication_status":"published","date_created":"2022-07-27T10:58:53Z","publisher":"Association for Computing Machinery","volume":18,"type":"journal_article","abstract":[{"lang":"eng","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."}],"extern":"1","citation":{"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.","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>","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>","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>.","ista":"Henzinger M, Peng P. 2022. Constant-time Dynamic (Δ +1)-Coloring. ACM Transactions on Algorithms. 18(2), 16.","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>."},"quality_controlled":"1"},{"ddc":["570"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.25338/B81931"}],"corr_author":"1","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","license":"https://creativecommons.org/publicdomain/zero/1.0/","department":[{"_id":"NiBa"}],"acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","year":"2022","date_published":"2022-01-06T00:00:00Z","oa":1,"citation":{"short":"M. Turelli, N.H. Barton, (2022).","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>","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","ama":"Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>","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>.","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>."},"abstract":[{"lang":"eng","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."}],"type":"research_data_reference","day":"06","doi":"10.25338/B81931","article_processing_charge":"No","status":"public","month":"01","date_updated":"2025-06-11T13:45:56Z","_id":"11686","related_material":{"record":[{"status":"public","id":"10604","relation":"used_in_publication"}]},"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","author":[{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"},{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"keyword":["Biological sciences"],"oa_version":"Published Version","date_created":"2022-07-29T06:45:41Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"}},{"date_published":"2022-05-12T00:00:00Z","oa":1,"citation":{"chicago":"Parvizian, Mahsa, Alejandra Duran Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “Data for ‘The Chemistry of Cu3N and Cu3PdN Nanocrystals.’” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6542908\">https://doi.org/10.5281/ZENODO.6542908</a>.","ista":"Parvizian M, Duran Balsa A, Pokratath R, Kalha C, Lee S, Van den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","mla":"Parvizian, Mahsa, et al. <i>Data for “The Chemistry of Cu3N and Cu3PdN Nanocrystals.”</i> Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","apa":"Parvizian, M., Duran Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van den Eynden, D., … De Roo, J. (2022). Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6542908\">https://doi.org/10.5281/ZENODO.6542908</a>","ieee":"M. Parvizian <i>et al.</i>, “Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals.’” Zenodo, 2022.","ama":"Parvizian M, Duran Balsa A, Pokratath R, et al. Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>","short":"M. Parvizian, A. Duran Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, (2022)."},"abstract":[{"lang":"eng","text":"Data underlying the figures in the publication \"The chemistry of Cu3N and Cu3PdN nanocrystals\" "}],"day":"12","doi":"10.5281/ZENODO.6542908","type":"research_data_reference","year":"2022","department":[{"_id":"MaIb"}],"ddc":["540"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6542908"}],"publisher":"Zenodo","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_created":"2022-07-29T09:31:13Z","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"},"_id":"11695","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11451"}]},"date_updated":"2023-08-03T07:19:12Z","author":[{"full_name":"Parvizian, Mahsa","last_name":"Parvizian","first_name":"Mahsa"},{"full_name":"Duran Balsa, Alejandra","last_name":"Duran Balsa","first_name":"Alejandra"},{"full_name":"Pokratath, Rohan","last_name":"Pokratath","first_name":"Rohan"},{"last_name":"Kalha","full_name":"Kalha, Curran","first_name":"Curran"},{"first_name":"Seungho","full_name":"Lee, Seungho","last_name":"Lee"},{"full_name":"Van den Eynden, Dietger","last_name":"Van den Eynden","first_name":"Dietger"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"last_name":"Regoutz","full_name":"Regoutz, Anna","first_name":"Anna"},{"first_name":"Jonathan","full_name":"De Roo, Jonathan","last_name":"De Roo"}],"title":"Data for \"The chemistry of Cu3N and Cu3PdN nanocrystals\"","article_processing_charge":"No","month":"05","status":"public"},{"_id":"11700","scopus_import":"1","issue":"5","month":"10","date_created":"2022-07-31T22:01:46Z","publication_status":"published","external_id":{"isi":["000812422100001"],"arxiv":["2105.05677"]},"department":[{"_id":"JaMa"}],"volume":17,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.05677"}],"corr_author":"1","publisher":"American Institute of Mathematical Sciences","quality_controlled":"1","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."}],"type":"journal_article","citation":{"mla":"Erbar, Matthias, et al. “Gradient Flow Formulation of Diffusion Equations in the Wasserstein Space over a Metric Graph.” <i>Networks and Heterogeneous Media</i>, vol. 17, no. 5, American Institute of Mathematical Sciences, 2022, pp. 687–717, doi:<a href=\"https://doi.org/10.3934/nhm.2022023\">10.3934/nhm.2022023</a>.","ista":"Erbar M, Forkert DL, Maas J, Mugnolo D. 2022. Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. Networks and Heterogeneous Media. 17(5), 687–717.","chicago":"Erbar, Matthias, Dominik L Forkert, Jan Maas, and Delio Mugnolo. “Gradient Flow Formulation of Diffusion Equations in the Wasserstein Space over a Metric Graph.” <i>Networks and Heterogeneous Media</i>. American Institute of Mathematical Sciences, 2022. <a href=\"https://doi.org/10.3934/nhm.2022023\">https://doi.org/10.3934/nhm.2022023</a>.","ama":"Erbar M, Forkert DL, Maas J, Mugnolo D. Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. <i>Networks and Heterogeneous Media</i>. 2022;17(5):687-717. doi:<a href=\"https://doi.org/10.3934/nhm.2022023\">10.3934/nhm.2022023</a>","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.","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."},"date_updated":"2025-04-14T07:27:47Z","page":"687-717","title":"Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph","author":[{"first_name":"Matthias","last_name":"Erbar","full_name":"Erbar, Matthias"},{"last_name":"Forkert","full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L"},{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"},{"full_name":"Mugnolo, Delio","last_name":"Mugnolo","first_name":"Delio"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","publication":"Networks and Heterogeneous Media","arxiv":1,"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"intvolume":"        17","date_published":"2022-10-01T00:00:00Z","day":"01","doi":"10.3934/nhm.2022023","oa":1,"ec_funded":1,"article_type":"original","publication_identifier":{"eissn":["1556-181X"],"issn":["1556-1801"]},"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.","year":"2022"},{"month":"08","scopus_import":"1","issue":"8","_id":"11701","external_id":{"arxiv":["2001.00512"],"isi":["000826695900001"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2022-07-31T22:01:47Z","publisher":"IOP Publishing","volume":35,"department":[{"_id":"JuFi"}],"citation":{"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.","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>","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>."},"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."}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2022-08-01T10:39:36Z","author":[{"first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","last_name":"Agresti","full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962"},{"last_name":"Veraar","full_name":"Veraar, Mark","first_name":"Mark"}],"title":"Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence","date_updated":"2023-08-03T12:25:08Z","page":"4100-4210","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/3.0/","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["510"],"isi":1,"arxiv":1,"publication":"Nonlinearity","article_type":"original","year":"2022","publication_identifier":{"eissn":["1361-6544"],"issn":["0951-7715"]},"acknowledgement":"The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","oa":1,"file":[{"date_created":"2022-08-01T10:39:36Z","success":1,"file_name":"2022_Nonlinearity_Agresti.pdf","file_size":2122096,"creator":"dernst","access_level":"open_access","file_id":"11715","date_updated":"2022-08-01T10:39:36Z","relation":"main_file","checksum":"997a4bff2dfbee3321d081328c2f1e1a","content_type":"application/pdf"}],"day":"04","doi":"10.1088/1361-6544/abd613","date_published":"2022-08-04T00:00:00Z","intvolume":"        35"},{"publisher":"National Academy of Sciences","corr_author":"1","volume":119,"department":[{"_id":"NiBa"}],"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."}],"pmid":1,"type":"journal_article","citation":{"short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119.","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>.","mla":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30, e2122147119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>.","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>","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."},"quality_controlled":"1","month":"07","issue":"30","scopus_import":"1","_id":"11702","external_id":{"pmid":["35858408"]},"publication_status":"published","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":"2022-07-31T22:01:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_number":"e2122147119","year":"2022","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_type":"original","acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","doi":"10.1073/pnas.2122147119","day":"18","file":[{"checksum":"06c866196a8957f0c37b8a121771c885","content_type":"application/pdf","relation":"main_file","date_updated":"2022-08-01T10:58:28Z","file_id":"11716","access_level":"open_access","file_name":"2022_PNAS_Barton.pdf","success":1,"date_created":"2022-08-01T10:58:28Z","creator":"dernst","file_size":848511}],"oa":1,"intvolume":"       119","date_published":"2022-07-18T00:00:00Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2022-08-01T10:58:28Z","article_processing_charge":"No","has_accepted_license":"1","title":"The \"New Synthesis\"","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"}],"date_updated":"2025-05-14T11:01:10Z","oa_version":"Published Version"},{"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>","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.","apa":"Toups, M. A., Vicoso, B., &#38; Pannell, J. R. (2022). Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>","mla":"Toups, Melissa A., et al. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>, vol. 18, no. 7, e1010226, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>.","chicago":"Toups, Melissa A, Beatriz Vicoso, and John R. Pannell. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>.","ista":"Toups MA, Vicoso B, Pannell JR. 2022. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. 18(7), e1010226.","short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022)."},"abstract":[{"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.","lang":"eng"}],"pmid":1,"type":"journal_article","quality_controlled":"1","volume":18,"department":[{"_id":"BeVi"}],"corr_author":"1","publisher":"Public Library of Science","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":"published","date_created":"2022-07-31T22:01:48Z","external_id":{"isi":["000886643100006"],"pmid":["35793353"]},"_id":"11703","month":"07","issue":"7","scopus_import":"1","oa":1,"file":[{"access_level":"open_access","date_created":"2022-08-01T07:49:25Z","success":1,"file_name":"2022_PLoSGenetics_Toups.pdf","creator":"dernst","file_size":1620272,"checksum":"aa4c137f82635e700856c359dccfaa0a","content_type":"application/pdf","relation":"main_file","date_updated":"2022-08-01T07:49:25Z","file_id":"11708"}],"day":"06","doi":"10.1371/journal.pgen.1010226","date_published":"2022-07-06T00:00:00Z","intvolume":"        18","article_number":"e1010226","article_type":"original","year":"2022","publication_identifier":{"eissn":["1553-7404"]},"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.","ec_funded":1,"isi":1,"publication":"PLoS Genetics","project":[{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"oa_version":"Published Version","title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","author":[{"first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","full_name":"Toups, Melissa A"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"full_name":"Pannell, John R.","last_name":"Pannell","first_name":"John R."}],"date_updated":"2025-04-14T07:41:20Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2022-08-01T07:49:25Z"},{"department":[{"_id":"BjHo"}],"volume":17,"corr_author":"1","publisher":"Public Library of Science","quality_controlled":"1","citation":{"chicago":"Budanur, Nazmi B, and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>.","ista":"Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating epidemics. PLoS ONE. 17(7), e0269975.","mla":"Budanur, Nazmi B., and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>, vol. 17, no. 7, e0269975, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>.","ama":"Budanur NB, Hof B. An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. 2022;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>","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>","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.","short":"N.B. Budanur, B. Hof, PLoS ONE 17 (2022)."},"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"}],"pmid":1,"type":"journal_article","_id":"11704","issue":"7","scopus_import":"1","month":"07","date_created":"2022-07-31T22:01:48Z","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":"published","external_id":{"pmid":["35849565"],"isi":["000911392100055"]},"isi":1,"publication":"PLoS ONE","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-07-18T00:00:00Z","intvolume":"        17","file":[{"file_id":"11712","date_updated":"2022-08-01T08:02:38Z","relation":"main_file","checksum":"1ddd9b91e6dec31ab0e7a8433ca2d452","content_type":"application/pdf","file_size":1421256,"creator":"dernst","file_name":"2022_PLoSONE_Budanur.pdf","date_created":"2022-08-01T08:02:38Z","success":1,"access_level":"open_access"}],"oa":1,"doi":"10.1371/journal.pone.0269975","day":"18","article_type":"original","publication_identifier":{"eissn":["1932-6203"]},"year":"2022","article_number":"e0269975","related_material":{"record":[{"status":"public","relation":"research_data","id":"11711"}]},"date_updated":"2025-06-11T13:37:36Z","title":"An autonomous compartmental model for accelerating epidemics","author":[{"orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2022-08-01T08:02:38Z","status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"intvolume":"        61","date_published":"2022-08-26T00:00:00Z","doi":"10.1002/anie.202207002","day":"26","file":[{"creator":"dernst","file_size":4072650,"file_name":"2022_AngewandteChemieInternat_Chang.pdf","success":1,"date_created":"2023-02-02T08:01:00Z","access_level":"open_access","date_updated":"2023-02-02T08:01:00Z","file_id":"12476","checksum":"ad601f2b9e26e46ab4785162be58b5ed","content_type":"application/pdf","relation":"main_file"}],"oa":1,"ec_funded":1,"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N). Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S. and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya.","year":"2022","article_type":"original","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"article_number":"e202207002","publication":"Angewandte Chemie - International Edition","isi":1,"ddc":["540"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"oa_version":"Published Version","date_updated":"2025-04-14T07:44:07Z","title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","author":[{"orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","full_name":"Chang, Cheng","first_name":"Cheng"},{"orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","full_name":"Liu, Yu","first_name":"Yu"},{"first_name":"Seungho","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Maria","full_name":"Spadaro, Maria","last_name":"Spadaro"},{"last_name":"Koskela","full_name":"Koskela, Kristopher M.","first_name":"Kristopher M."},{"first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns"},{"orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","full_name":"Costanzo, Tommaso","first_name":"Tommaso"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Brutchey, Richard L.","last_name":"Brutchey","first_name":"Richard L."},{"first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-02-02T08:01:00Z","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","abstract":[{"text":"The broad implementation of thermoelectricity requires high-performance and low-cost materials. One possibility is employing surfactant-free solution synthesis to produce nanopowders. We propose the strategy of functionalizing “naked” particles’ surface by inorganic molecules to control the nanostructure and, consequently, thermoelectric performance. In particular, we use bismuth thiolates to functionalize surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1) carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity reduction by small grain domains, grain boundaries and nanostructuration. Overall, the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed SnTe.","lang":"eng"}],"type":"journal_article","pmid":1,"citation":{"mla":"Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35, e202207002, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>.","chicago":"Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela, Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>.","ista":"Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 61(35), e202207002.","ama":"Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. 2022;61(35). doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>","apa":"Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T., … Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>","ieee":"C. Chang <i>et al.</i>, “Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35. Wiley, 2022.","short":"C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo, J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition 61 (2022)."},"department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"volume":61,"corr_author":"1","publisher":"Wiley","date_created":"2022-07-31T22:01:48Z","publication_status":"published","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":{"isi":["000828274200001"],"pmid":["38505739"]},"_id":"11705","issue":"35","scopus_import":"1","month":"08"},{"department":[{"_id":"DaAl"}],"volume":13298,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08703"}],"publisher":"Springer Nature","quality_controlled":"1","citation":{"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.","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.","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>.","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>.","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>","apa":"Balliu, A., Hirvonen, J., Melnyk, D., Olivetti, D., Rybicki, J., &#38; Suomela, J. (2022). Local mending. In M. Parter (Ed.), <i>International Colloquium on Structural Information and Communication Complexity</i> (Vol. 13298, pp. 1–20). Paderborn, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>","ieee":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, and J. Suomela, “Local mending,” in <i>International Colloquium on Structural Information and Communication Complexity</i>, Paderborn, Germany, 2022, vol. 13298, pp. 1–20."},"abstract":[{"lang":"eng","text":"In this work we introduce the graph-theoretic notion of mendability: for each locally checkable graph problem we can define its mending radius, which captures the idea of how far one needs to modify a partial solution in order to “patch a hole.” We explore how mendability is connected to the existence of efficient algorithms, especially in distributed, parallel, and fault-tolerant settings. It is easy to see that O(1)-mendable problems are also solvable in O(log∗n) rounds in the LOCAL model of distributed computing. One of the surprises is that in paths and cycles, a converse also holds in the following sense: if a problem Π can be solved in O(log∗n), there is always a restriction Π′⊆Π that is still efficiently solvable but that is also O(1)-mendable. We also explore the structure of the landscape of mendability. For example, we show that in trees, the mending radius of any locally checkable problem is O(1), Θ(logn), or Θ(n), while in general graphs the structure is much more diverse."}],"type":"conference","_id":"11707","scopus_import":"1","month":"06","date_created":"2022-07-31T22:01:49Z","publication_status":"published","external_id":{"isi":["000876977400001"],"arxiv":["2102.08703"]},"conference":{"end_date":"2022-06-29","location":"Paderborn, Germany","name":"SIROCCO: Structural Information and Communication Complexity","start_date":"2022-06-27"},"isi":1,"publication":"International Colloquium on Structural Information and Communication Complexity","arxiv":1,"series_title":"LNCS","project":[{"call_identifier":"H2020","grant_number":"840605","name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-06-25T00:00:00Z","intvolume":"     13298","oa":1,"day":"25","doi":"10.1007/978-3-031-09993-9_1","year":"2022","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.","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031099922"],"issn":["0302-9743"]},"ec_funded":1,"date_updated":"2025-04-14T07:50:55Z","page":"1-20","title":"Local mending","author":[{"first_name":"Alkida","last_name":"Balliu","full_name":"Balliu, Alkida"},{"first_name":"Juho","last_name":"Hirvonen","full_name":"Hirvonen, Juho"},{"full_name":"Melnyk, Darya","last_name":"Melnyk","first_name":"Darya"},{"full_name":"Olivetti, Dennis","last_name":"Olivetti","first_name":"Dennis"},{"first_name":"Joel","full_name":"Rybicki, Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646"},{"first_name":"Jukka","full_name":"Suomela, Jukka","last_name":"Suomela"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","editor":[{"last_name":"Parter","full_name":"Parter, Merav","first_name":"Merav"}]},{"article_processing_charge":"No","has_accepted_license":"1","month":"07","status":"public","date_updated":"2025-06-11T13:37:36Z","_id":"11711","related_material":{"record":[{"status":"public","id":"11704","relation":"used_in_publication"}]},"author":[{"first_name":"Nazmi B","last_name":"Budanur","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010"}],"title":"burakbudanur/autoacc-public","date_created":"2022-08-01T08:06:33Z","oa_version":"Published Version","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6802720"}],"ddc":["000"],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Zenodo","corr_author":"1","department":[{"_id":"BjHo"}],"year":"2022","date_published":"2022-07-06T00:00:00Z","day":"06","doi":"10.5281/ZENODO.6802720","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\""}],"type":"research_data_reference","citation":{"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>.","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>.","ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>","apa":"Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","short":"N.B. Budanur, (2022)."},"oa":1},{"file_date_updated":"2022-08-01T09:24:42Z","article_processing_charge":"No","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://doi.org/10.1186/s13104-022-06152-7","relation":"erratum"}]},"date_updated":"2025-04-14T09:24:53Z","title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","author":[{"first_name":"Nela","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martina","full_name":"Sauert, Martina","last_name":"Sauert"},{"first_name":"Tanino G.","last_name":"Albanese","full_name":"Albanese, Tanino G."},{"first_name":"Isabella","last_name":"Moll","full_name":"Moll, Isabella"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"oa_version":"Published Version","ddc":["570"],"project":[{"name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","_id":"26956E74-B435-11E9-9278-68D0E5697425","grant_number":"V00738","call_identifier":"FWF"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"BMC Research Notes","publication_identifier":{"issn":["1756-0500"]},"article_type":"letter_note","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.","year":"2022","article_number":"173","intvolume":"        15","date_published":"2022-05-13T00:00:00Z","doi":"10.1186/s13104-022-06061-9","day":"13","file":[{"date_updated":"2022-08-01T09:24:42Z","file_id":"11714","checksum":"008156e5340e9789f0f6d82bde4d347a","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_size":1545310,"file_name":"2022_BMCResearchNotes_Nikolic.pdf","date_created":"2022-08-01T09:24:42Z","success":1,"access_level":"open_access"}],"oa":1,"scopus_import":"1","month":"05","_id":"11713","external_id":{"pmid":["35562780"]},"date_created":"2022-08-01T09:04:27Z","publication_status":"published","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"},"corr_author":"1","publisher":"Springer Nature","department":[{"_id":"CaGu"}],"volume":15,"quality_controlled":"1","type":"journal_article","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"}],"pmid":1,"citation":{"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>","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.","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.","mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>.","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022)."}},{"corr_author":"1","publisher":"Elsevier","volume":408,"department":[{"_id":"VaKa"}],"type":"journal_article","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."}],"citation":{"chicago":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>.","ista":"Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics. 408(Part A), 108591.","mla":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>, vol. 408, no. Part A, 108591, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>.","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>","ieee":"K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” <i>Advances in Mathematics</i>, vol. 408, no. Part A. Elsevier, 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>","short":"K. Drach, D. Schleicher, Advances in Mathematics 408 (2022)."},"quality_controlled":"1","month":"10","issue":"Part A","scopus_import":"1","_id":"11717","external_id":{"isi":["000860924200005"]},"publication_status":"published","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":"2022-08-01T17:08:16Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707","call_identifier":"H2020"}],"ddc":["510"],"publication":"Advances in Mathematics","isi":1,"article_number":"108591","ec_funded":1,"publication_identifier":{"issn":["0001-8708"]},"year":"2022","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).","article_type":"original","day":"29","doi":"10.1016/j.aim.2022.108591","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","file_id":"12474","date_updated":"2023-02-02T07:39:09Z","access_level":"open_access","file_size":2164036,"creator":"dernst","date_created":"2023-02-02T07:39:09Z","success":1,"file_name":"2022_AdvancesMathematics_Drach.pdf"}],"oa":1,"intvolume":"       408","date_published":"2022-10-29T00:00:00Z","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2023-02-02T07:39:09Z","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","author":[{"orcid":"0000-0002-9156-8616","full_name":"Drach, Kostiantyn","last_name":"Drach","id":"fe8209e2-906f-11eb-847d-950f8fc09115","first_name":"Kostiantyn"},{"first_name":"Dierk","full_name":"Schleicher, Dierk","last_name":"Schleicher"}],"title":"Rigidity of Newton dynamics","date_updated":"2025-04-14T07:53:45Z","keyword":["General Mathematics"],"oa_version":"Published Version"},{"keyword":["Multidisciplinary"],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2022-08-08T07:42:09Z","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-05-14T11:01:00Z","title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","author":[{"orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"},{"first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen"},{"first_name":"Saqer S.","last_name":"Alotaibi","full_name":"Alotaibi, Saqer S."},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"first_name":"Maciek","full_name":"Adamowski, Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"year":"2022","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_type":"original","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).”","article_number":"e2121058119","date_published":"2022-07-25T00:00:00Z","intvolume":"       119","file":[{"file_size":2506262,"creator":"dernst","date_created":"2022-08-08T07:42:09Z","success":1,"file_name":"2022_PNAS_Li.pdf","access_level":"open_access","file_id":"11747","date_updated":"2022-08-08T07:42:09Z","relation":"main_file","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","content_type":"application/pdf"}],"oa":1,"day":"25","doi":"10.1073/pnas.2121058119","ddc":["580"],"project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","external_id":{"isi":["000881496900002"],"pmid":["35878023"]},"date_created":"2022-08-04T20:06:49Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_status":"published","scopus_import":"1","issue":"31","month":"07","_id":"11723","quality_controlled":"1","citation":{"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).","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.","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.","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"}],"pmid":1,"type":"journal_article","corr_author":"1","publisher":"National Academy of Sciences","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"volume":119},{"department":[{"_id":"MaRo"}],"volume":119,"corr_author":"1","publisher":"National Academy of Sciences","quality_controlled":"1","abstract":[{"text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP. We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies.","lang":"eng"}],"pmid":1,"type":"journal_article","citation":{"apa":"Orliac, E. J., Trejo Banos, D., Ojavee, S. E., Läll, K., Mägi, R., Visscher, P. M., &#38; Robinson, M. R. (2022). Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>","ieee":"E. J. Orliac <i>et al.</i>, “Improving GWAS discovery and genomic prediction accuracy in biobank data,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","ama":"Orliac EJ, Trejo Banos D, Ojavee SE, et al. Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>","chicago":"Orliac, Etienne J., Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik Mägi, Peter M. Visscher, and Matthew Richard Robinson. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>.","ista":"Orliac EJ, Trejo Banos D, Ojavee SE, Läll K, Mägi R, Visscher PM, Robinson MR. 2022. Improving GWAS discovery and genomic prediction accuracy in biobank data. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121279119.","mla":"Orliac, Etienne J., et al. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121279119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>.","short":"E.J. Orliac, D. Trejo Banos, S.E. Ojavee, K. Läll, R. Mägi, P.M. Visscher, M.R. Robinson, Proceedings of the National Academy of Sciences of the United States of America 119 (2022)."},"_id":"11733","issue":"31","scopus_import":"1","month":"07","date_created":"2022-08-07T22:01:56Z","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000881496900003"],"pmid":["35905320"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       119","date_published":"2022-07-29T00:00:00Z","day":"29","doi":"10.1073/pnas.2121279119","oa":1,"file":[{"access_level":"open_access","file_name":"2022_PNAS_Orliac.pdf","date_created":"2022-08-08T07:31:19Z","success":1,"file_size":1001164,"creator":"dernst","relation":"main_file","checksum":"b5d2024e19fbad6f85a5e384e44d0f3b","content_type":"application/pdf","file_id":"11745","date_updated":"2022-08-08T07:31:19Z"}],"article_type":"original","publication_identifier":{"eissn":["1091-6490"]},"year":"2022","acknowledgement":"This project was funded by Swiss National Science Foundation Eccellenza Grant PCEGP3-181181(toM.R.R.) and by core funding from the Institute of Science and Technology Austria. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). K.L. and R.M. were supported by the Estonian Research Council Grant PRG687. Estonian Biobank computations were performed in the High-Performance Computing Centre, University of Tartu.","article_number":"e2121279119","related_material":{"record":[{"status":"public","id":"13064","relation":"research_data"}]},"date_updated":"2025-06-12T06:22:37Z","author":[{"full_name":"Orliac, Etienne J.","last_name":"Orliac","first_name":"Etienne J."},{"first_name":"Daniel","full_name":"Trejo Banos, Daniel","last_name":"Trejo Banos"},{"last_name":"Ojavee","full_name":"Ojavee, Sven E.","first_name":"Sven E."},{"full_name":"Läll, Kristi","last_name":"Läll","first_name":"Kristi"},{"first_name":"Reedik","full_name":"Mägi, Reedik","last_name":"Mägi"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"}],"title":"Improving GWAS discovery and genomic prediction accuracy in biobank data","file_date_updated":"2022-08-08T07:31:19Z","has_accepted_license":"1","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"pmid":1,"abstract":[{"text":"Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.","lang":"eng"}],"type":"journal_article","citation":{"short":"R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry, A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., … Benková, E. (2022). Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>","ieee":"R. Abualia <i>et al.</i>, “Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","ama":"Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>","mla":"Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2122460119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>.","ista":"Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2122460119.","chicago":"Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>."},"quality_controlled":"1","volume":119,"department":[{"_id":"EvBe"}],"publisher":"National Academy of Sciences","corr_author":"1","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"date_created":"2022-08-07T22:01:57Z","external_id":{"isi":["000881496900007"],"pmid":["35878040"]},"_id":"11734","month":"07","issue":"31","scopus_import":"1","doi":"10.1073/pnas.2122460119","day":"25","file":[{"file_id":"11744","date_updated":"2022-08-08T07:09:58Z","relation":"main_file","content_type":"application/pdf","checksum":"6e97dedc281247fc3fe238a209f14af0","date_created":"2022-08-08T07:09:58Z","success":1,"file_name":"2022_PNAS_Abualia.pdf","file_size":3092330,"creator":"dernst","access_level":"open_access"}],"oa":1,"intvolume":"       119","date_published":"2022-07-25T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_number":"e2122460119","acknowledgement":"We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari, Marc¸al Gallem\u0003ı, Kaori Tabata, Andrej Hurn\u0003y, and Sascha Waidmann for sharing materials; and Marina Borges Osorio for critical reading of the manuscript. Work in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science Facilities of the Institute of Science\r\nand Technology Austria. We give sincere thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses. This work was funded by the Czech Science Foundation (Project No. 19-00973S).","article_type":"original","publication_identifier":{"eissn":["1091-6490"]},"year":"2022","publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"project":[{"call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa_version":"Published Version","author":[{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","full_name":"Abualia, Rashed","first_name":"Rashed"},{"first_name":"Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina","last_name":"Ötvös"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Bouguyon, Eleonore","last_name":"Bouguyon","first_name":"Eleonore"},{"first_name":"Kevin","last_name":"Domanegg","full_name":"Domanegg, Kevin","id":"a24c7829-16e8-11ed-8527-c4d36ffb7539","orcid":"0000-0002-1215-4264"},{"first_name":"Anne","full_name":"Krapp, Anne","last_name":"Krapp"},{"full_name":"Nacry, Philip","last_name":"Nacry","first_name":"Philip"},{"first_name":"Alain","last_name":"Gojon","full_name":"Gojon, Alain"},{"full_name":"Lacombe, Benoit","last_name":"Lacombe","first_name":"Benoit"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","date_updated":"2025-05-14T11:00:29Z","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2022-08-08T07:09:58Z","has_accepted_license":"1","article_processing_charge":"No"},{"citation":{"short":"R. Chen, Z. Wang, P. Song, B. Bickel, ACM Transactions on Graphics 41 (2022).","apa":"Chen, R., Wang, Z., Song, P., &#38; Bickel, B. (2022). Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>","ieee":"R. Chen, Z. Wang, P. Song, and B. Bickel, “Computational design of high-level interlocking puzzles,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","ama":"Chen R, Wang Z, Song P, Bickel B. Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>","mla":"Chen, Rulin, et al. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 150, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>.","chicago":"Chen, Rulin, Ziqi Wang, Peng Song, and Bernd Bickel. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>.","ista":"Chen R, Wang Z, Song P, Bickel B. 2022. Computational design of high-level interlocking puzzles. ACM Transactions on Graphics. 41(4), 150."},"type":"journal_article","abstract":[{"text":"Interlocking puzzles are intriguing geometric games where the puzzle pieces are held together based on their geometric arrangement, preventing the puzzle from falling apart. High-level-of-difficulty, or simply high-level, interlocking puzzles are a subclass of interlocking puzzles that require multiple moves to take out the first subassembly from the puzzle. Solving a high-level interlocking puzzle is a challenging task since one has to explore many different configurations of the puzzle pieces until reaching a configuration where the first subassembly can be taken out. Designing a high-level interlocking puzzle with a user-specified level of difficulty is even harder since the puzzle pieces have to be interlocking in all the configurations before the first subassembly is taken out.\r\n\r\nIn this paper, we present a computational approach to design high-level interlocking puzzles. The core idea is to represent all possible configurations of an interlocking puzzle as well as transitions among these configurations using a rooted, undirected graph called a disassembly graph and leverage this graph to find a disassembly plan that requires a minimal number of moves to take out the first subassembly from the puzzle. At the design stage, our algorithm iteratively constructs the geometry of each puzzle piece to expand the disassembly graph incrementally, aiming to achieve a user-specified level of difficulty. We show that our approach allows efficient generation of high-level interlocking puzzles of various shape complexities, including new solutions not attainable by state-of-the-art approaches.","lang":"eng"}],"quality_controlled":"1","publisher":"Association for Computing Machinery","volume":41,"department":[{"_id":"BeBi"}],"external_id":{"isi":["000830989200018"]},"publication_status":"published","date_created":"2022-08-07T22:01:57Z","month":"07","issue":"4","scopus_import":"1","_id":"11735","article_number":"150","article_type":"original","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"acknowledgement":"We thank the reviewers for the valuable comments, David Gontier for sharing the source code of the baseline design approach, Christian Hafner for proofreading the paper, Keenan Crane for the 3D model of Cow, and Thingiverse for the 3D models of Moai and Owl. This work was supported by the SUTD Start-up Research Grant (Number: SRG ISTD 2019 148), the Swiss National Science Foundation (NCCR Digital Fabrication Agreement #51NF40-141853), and\r\nthe European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 715767 – MATERIALIZABLE).","year":"2022","ec_funded":1,"oa":1,"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"0b51651be45b1b33f2072bd5d2686c69","file_id":"11992","date_updated":"2022-08-28T07:56:19Z","access_level":"open_access","file_size":16896871,"creator":"bbickel","file_name":"Chen-2022-High-LevelPuzzle_authorVersion.pdf","date_created":"2022-08-28T07:56:19Z","success":1}],"day":"22","doi":"10.1145/3528223.3530071","date_published":"2022-07-22T00:00:00Z","intvolume":"        41","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"ddc":["000"],"isi":1,"publication":"ACM Transactions on Graphics","oa_version":"Submitted Version","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2022-08-28T07:56:19Z","title":"Computational design of high-level interlocking puzzles","author":[{"last_name":"Chen","full_name":"Chen, Rulin","first_name":"Rulin"},{"full_name":"Wang, Ziqi","last_name":"Wang","first_name":"Ziqi"},{"first_name":"Peng","last_name":"Song","full_name":"Song, Peng"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"date_updated":"2025-04-14T07:28:57Z","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/unlocking-interlocking-riddles/","relation":"press_release"}]}}]