[{"author":[{"full_name":"Zhao, Lina","last_name":"Zhao","first_name":"Lina"},{"last_name":"Fenk","full_name":"Fenk, Lorenz A.","first_name":"Lorenz A."},{"first_name":"Lars","full_name":"Nilsson, Lars","last_name":"Nilsson"},{"id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","first_name":"Niko Paresh","full_name":"Amin-Wetzel, Niko Paresh","last_name":"Amin-Wetzel"},{"last_name":"Ramirez","full_name":"Ramirez, Nelson","first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"De Bono, Mario","last_name":"De Bono"},{"last_name":"Chen","full_name":"Chen, Changchun","first_name":"Changchun"}],"title":"ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans","_id":"11637","issue":"6","abstract":[{"lang":"eng","text":"The ability to detect and respond to acute oxygen (O2) shortages is indispensable to aerobic life. The molecular mechanisms and circuits underlying this capacity are poorly understood. Here, we characterize the behavioral responses of feeding Caenorhabditis elegans to approximately 1% O2. Acute hypoxia triggers a bout of turning maneuvers followed by a persistent switch to rapid forward movement as animals seek to avoid and escape hypoxia. While the behavioral responses to 1% O2 closely resemble those evoked by 21% O2, they have distinct molecular and circuit underpinnings. Disrupting phosphodiesterases (PDEs), specific G proteins, or BBSome function inhibits escape from 1% O2 due to increased cGMP signaling. A primary source of cGMP is GCY-28, the ortholog of the atrial natriuretic peptide (ANP) receptor. cGMP activates the protein kinase G EGL-4 and enhances neuroendocrine secretion to inhibit acute responses to 1% O2. Triggering a rise in cGMP optogenetically in multiple neurons, including AIA interneurons, rapidly and reversibly inhibits escape from 1% O2. Ca2+ imaging reveals that a 7% to 1% O2 stimulus evokes a Ca2+ decrease in several neurons. Defects in mitochondrial complex I (MCI) and mitochondrial complex I (MCIII), which lead to persistently high reactive oxygen species (ROS), abrogate acute hypoxia responses. In particular, repressing the expression of isp-1, which encodes the iron sulfur protein of MCIII, inhibits escape from 1% O2 without affecting responses to 21% O2. Both genetic and pharmacological up-regulation of mitochondrial ROS increase cGMP levels, which contribute to the reduced hypoxia responses. Our results implicate ROS and precise regulation of intracellular cGMP in the modulation of acute responses to hypoxia by C. elegans."}],"doi":"10.1371/journal.pbio.3001684","publication_identifier":{"eissn":["1545-7885"]},"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"}],"acknowledgement":" This work was funded by H2020 European Research Council (ERC Advanced grant, 269058 ACMO, https://erc.europa.eu/funding/advanced-grants) and Wellcome Trust UK (Wellcome Investigator Award, 209504/Z/17/Z, https://wellcome.org/grant-funding/people-and-projects/grants-awarded/molecular-mechanisms-neural-circuit-function-0) to M.d.B, and by H2020 European Research Council (ERC starting grant, 802653 OXYGEN SENSING, https://erc.europa.eu/funding/starting-grants) and Vetenskapsrådet (VR starting grant, 2018-02216, https://www.vr.se/english.html) to C.C. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","publication_status":"published","status":"public","day":"21","citation":{"apa":"Zhao, L., Fenk, L. A., Nilsson, L., Amin-Wetzel, N. P., Ramirez, N., de Bono, M., &#38; Chen, C. (2022). ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>","ieee":"L. Zhao <i>et al.</i>, “ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans,” <i>PLoS Biology</i>, vol. 20, no. 6. Public Library of Science, 2022.","ama":"Zhao L, Fenk LA, Nilsson L, et al. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. 2022;20(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>","ista":"Zhao L, Fenk LA, Nilsson L, Amin-Wetzel NP, Ramirez N, de Bono M, Chen C. 2022. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. PLoS Biology. 20(6), e3001684.","short":"L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono, C. Chen, PLoS Biology 20 (2022).","mla":"Zhao, Lina, et al. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>, vol. 20, no. 6, e3001684, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>.","chicago":"Zhao, Lina, Lorenz A. Fenk, Lars Nilsson, Niko Paresh Amin-Wetzel, Nelson Ramirez, Mario de Bono, and Changchun Chen. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>."},"file_date_updated":"2022-07-25T07:38:49Z","ddc":["570"],"month":"06","pmid":1,"oa_version":"Published Version","file":[{"file_size":3721585,"relation":"main_file","creator":"dernst","file_name":"2022_PLoSBiology_Zhao.pdf","content_type":"application/pdf","checksum":"df4902f854ad76769d3203bfdc69f16c","access_level":"open_access","date_updated":"2022-07-25T07:38:49Z","success":1,"date_created":"2022-07-25T07:38:49Z","file_id":"11643"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":20,"oa":1,"year":"2022","publication":"PLoS Biology","date_updated":"2023-08-03T12:11:44Z","article_type":"original","article_number":"e3001684","department":[{"_id":"MaDe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-06-21T00:00:00Z","external_id":{"pmid":["35727855"],"isi":["000828679600001"]},"scopus_import":"1","date_created":"2022-07-24T22:01:42Z","intvolume":"        20","publisher":"Public Library of Science","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1"},{"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","status":"public","acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030).","title":"Inferring couplings in networks across order-disorder phase transitions","author":[{"full_name":"Ngampruetikorn, Vudtiwat","last_name":"Ngampruetikorn","first_name":"Vudtiwat"},{"full_name":"Sachdeva, Vedant","last_name":"Sachdeva","first_name":"Vedant"},{"last_name":"Torrence","full_name":"Torrence, Johanna","first_name":"Johanna"},{"last_name":"Humplik","full_name":"Humplik, Jan","first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David J.","last_name":"Schwab","full_name":"Schwab, David J."},{"full_name":"Palmer, Stephanie E.","last_name":"Palmer","first_name":"Stephanie E."}],"_id":"11638","abstract":[{"text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data.","lang":"eng"}],"issue":"2","doi":"10.1103/PhysRevResearch.4.023240","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","file_size":1379683,"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","success":1,"date_updated":"2022-07-25T07:47:23Z","file_id":"11644","date_created":"2022-07-25T07:47:23Z"}],"arxiv":1,"has_accepted_license":"1","volume":4,"article_processing_charge":"No","citation":{"chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>.","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>.","ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. 2022;4(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>","ieee":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” <i>Physical Review Research</i>, vol. 4, no. 2. American Physical Society, 2022.","apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., &#38; Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>"},"day":"24","file_date_updated":"2022-07-25T07:47:23Z","ddc":["530"],"month":"06","oa_version":"Published Version","funded_apc":"1","publication":"Physical Review Research","date_updated":"2022-07-25T07:52:35Z","article_number":"023240","article_type":"original","oa":1,"year":"2022","publisher":"American Physical Society","intvolume":"         4","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2106.02349"]},"date_published":"2022-06-24T00:00:00Z","date_created":"2022-07-24T22:01:42Z","scopus_import":"1"},{"arxiv":1,"article_processing_charge":"No","volume":68,"citation":{"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.","ista":"Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786.","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>","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>.","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>."},"day":"01","month":"12","oa_version":"Preprint","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"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_status":"published","status":"public","title":"List decoding random Euclidean codes and Infinite constellations","author":[{"full_name":"Zhang, Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan"},{"last_name":"Vatedka","full_name":"Vatedka, Shashank","first_name":"Shashank"}],"_id":"11639","abstract":[{"lang":"eng","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."}],"issue":"12","doi":"10.1109/TIT.2022.3189542","publisher":"IEEE","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1901.03790","open_access":"1"}],"intvolume":"        68","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"MaMo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000891796100007"],"arxiv":["1901.03790"]},"date_published":"2022-12-01T00:00:00Z","date_created":"2022-07-24T22:01:42Z","scopus_import":"1","publication":"IEEE Transactions on Information Theory","date_updated":"2023-08-03T12:12:19Z","page":"7753-7786","article_type":"original","oa":1,"year":"2022"},{"citation":{"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.","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>","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","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.","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>","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>.","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>."},"day":"01","ddc":["570"],"month":"11","file_date_updated":"2023-02-02T08:11:23Z","oa_version":"Published Version","file":[{"relation":"main_file","file_size":6431779,"creator":"dernst","file_name":"2022_MolecularEcologyRes_Szep.pdf","date_updated":"2023-02-02T08:11:23Z","success":1,"content_type":"application/pdf","checksum":"3102e203e77b884bffffdbe8e548da88","access_level":"open_access","date_created":"2023-02-02T08:11:23Z","file_id":"12477"}],"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"has_accepted_license":"1","volume":22,"article_processing_charge":"Yes (via OA deal)","title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","author":[{"full_name":"Szep, Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko"},{"last_name":"Trubenova","full_name":"Trubenova, Barbora","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"last_name":"Csilléry","full_name":"Csilléry, Katalin","first_name":"Katalin"}],"_id":"11640","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."}],"issue":"8","doi":"10.1111/1755-0998.13676","publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"project":[{"call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172"}],"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.","status":"public","publication_status":"published","ec_funded":1,"department":[{"_id":"NiBa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-11-01T00:00:00Z","external_id":{"isi":["000825873600001"]},"date_created":"2022-07-24T22:01:43Z","scopus_import":"1","publisher":"Wiley","intvolume":"        22","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"year":"2022","publication":"Molecular Ecology Resources","date_updated":"2023-08-03T12:11:01Z","page":"2941-2955","article_type":"original"},{"publication_identifier":{"eissn":["2050-5701"],"issn":["2050-5698"]},"status":"public","publication_status":"published","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.","author":[{"first_name":"Christoph","full_name":"Gerle, Christoph","last_name":"Gerle"},{"full_name":"Kishikawa, Jun-ichi","last_name":"Kishikawa","first_name":"Jun-ichi"},{"first_name":"Tomoko","full_name":"Yamaguchi, Tomoko","last_name":"Yamaguchi"},{"full_name":"Nakanishi, Atsuko","last_name":"Nakanishi","first_name":"Atsuko"},{"last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun","first_name":"Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","orcid":"0000-0002-3219-2022"},{"full_name":"Makino, Fumiaki","last_name":"Makino","first_name":"Fumiaki"},{"first_name":"Tomoko","last_name":"Miyata","full_name":"Miyata, Tomoko"},{"full_name":"Kawamoto, Akihiro","last_name":"Kawamoto","first_name":"Akihiro"},{"full_name":"Yokoyama, Ken","last_name":"Yokoyama","first_name":"Ken"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"full_name":"Kurisu, Genji","last_name":"Kurisu","first_name":"Genji"},{"full_name":"Kato, Takayuki","last_name":"Kato","first_name":"Takayuki"}],"title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","_id":"11648","issue":"5","abstract":[{"lang":"eng","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."}],"doi":"10.1093/jmicro/dfac037","file":[{"file_name":"2022_Microscopy_Gerle.pdf","creator":"dernst","file_size":7812696,"relation":"main_file","success":1,"date_updated":"2023-02-03T08:34:48Z","access_level":"open_access","checksum":"23b51c163636bf9313f7f0818312e67e","content_type":"application/pdf","file_id":"12498","date_created":"2023-02-03T08:34:48Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":71,"day":"01","citation":{"apa":"Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino, F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>","ieee":"C. Gerle <i>et al.</i>, “Structures of multisubunit membrane complexes with the CRYO ARM 200,” <i>Microscopy</i>, vol. 71, no. 5. Oxford University Press, pp. 249–261, 2022.","short":"C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino, T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy 71 (2022) 249–261.","ista":"Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.","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>","chicago":"Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>.","mla":"Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>, vol. 71, no. 5, Oxford University Press, 2022, pp. 249–61, doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>."},"ddc":["570"],"file_date_updated":"2023-02-03T08:34:48Z","pmid":1,"month":"10","oa_version":"Published Version","publication":"Microscopy","date_updated":"2023-08-03T12:13:37Z","article_type":"original","page":"249-261","oa":1,"year":"2022","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"intvolume":"        71","publisher":"Oxford University Press","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"LeSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["35861182"],"isi":["000837950900001"]},"date_published":"2022-10-01T00:00:00Z","scopus_import":"1","date_created":"2022-07-25T10:04:58Z"},{"author":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231"}],"oa":1,"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","_id":"11653","year":"2022","abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"doi":"10.15479/AT:ISTA:11653","date_updated":"2024-02-21T12:35:53Z","status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12248"}]},"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"day":"05","citation":{"ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","short":"M.N. Elkrewi, (2022).","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>."},"file_date_updated":"2022-08-08T22:30:04Z","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_published":"2022-08-05T00:00:00Z","date_created":"2022-07-26T11:01:47Z","oa_version":"Published Version","file":[{"date_created":"2022-07-26T12:37:52Z","file_id":"11655","title":"Supplementary Datasets","embargo":"2022-08-07","relation":"main_file","creator":"melkrewi","file_size":2209382998,"file_name":"Data.zip","date_updated":"2022-08-08T22:30:04Z","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","content_type":"application/x-zip-compressed","access_level":"open_access","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","contributor":[{"last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"Sax","first_name":"Luca"},{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans"},{"first_name":"Francisco","last_name":"Hontoria "},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"type":"research_data","article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"date_created":"2022-07-27T09:27:34Z","date_published":"2022-07-27T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","oa":1,"year":"2022","date_updated":"2022-07-28T07:57:48Z","publication":"Leibniz International Proceedings on Mathematics","file_date_updated":"2022-07-27T09:25:53Z","ddc":["510"],"month":"07","citation":{"mla":"Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>, Schloss Dagstuhl - Leibniz Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik, n.d.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth in arrangements: Dehn–Sommerville–Euler relations with applications,” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.).","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings on Mathematics.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>."},"day":"27","oa_version":"Submitted Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"checksum":"b2f511e8b1cae5f1892b0cdec341acac","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-07-27T09:25:53Z","creator":"scultrer","file_size":639266,"relation":"main_file","file_name":"D-S-E.pdf","date_created":"2022-07-27T09:25:53Z","file_id":"11659"}],"article_processing_charge":"No","has_accepted_license":"1","_id":"11658","title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","author":[{"first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890"},{"orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"abstract":[{"lang":"eng","text":"The depth of a cell in an arrangement of n (non-vertical) great-spheres in Sd is the number of great-spheres that pass above the cell. We prove Euler-type relations, which imply extensions of the classic Dehn–Sommerville relations for convex polytopes to sublevel sets of the depth function, and we use the relations to extend the expressions for the number of faces of neighborly polytopes to the number of cells of levels in neighborly arrangements."}],"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publication_status":"submitted","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","status":"public"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"date_created":"2022-07-27T09:31:15Z","date_published":"2022-07-25T00:00:00Z","date_updated":"2022-07-28T08:05:34Z","publication":"LIPIcs","oa":1,"year":"2022","alternative_title":["LIPIcs"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","checksum":"95903f9d1649e8e437a967b6f2f64730","content_type":"application/pdf","date_updated":"2022-07-27T09:30:30Z","file_name":"window 1.pdf","relation":"main_file","file_size":564836,"creator":"scultrer","file_id":"11661","date_created":"2022-07-27T09:30:30Z"}],"article_processing_charge":"No","has_accepted_license":"1","ddc":["510"],"month":"07","file_date_updated":"2022-07-27T09:30:30Z","citation":{"mla":"Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs,” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. LIPIcs.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs (n.d.)."},"day":"25","oa_version":"Submitted Version","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35. ","status":"public","publication_status":"submitted","_id":"11660","title":"A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs","author":[{"orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","full_name":"Biswas, Ranita","last_name":"Biswas"},{"orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","first_name":"Morteza"}],"abstract":[{"text":"We characterize critical points of 1-dimensional maps paired in persistent homology geometrically and this way get elementary proofs of theorems about the symmetry of persistence diagrams and the variation of such maps. In particular, we identify branching points and endpoints of networks as the sole source of asymmetry and relate the cycle basis in persistent homology with a version of the stable marriage problem. Our analysis provides the foundations of fast algorithms for maintaining collections of interrelated sorted lists together with their persistence diagrams. ","lang":"eng"}]},{"related_material":{"record":[{"id":"10604","relation":"used_in_publication","status":"public"}]},"status":"public","acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","date_updated":"2023-08-02T13:50:08Z","doi":"10.25338/B81931","keyword":["Biological sciences"],"abstract":[{"text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes.","lang":"eng"}],"year":"2022","_id":"11686","oa":1,"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"article_processing_charge":"No","type":"research_data_reference","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25338/B81931"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"date_created":"2022-07-29T06:45:41Z","oa_version":"Published Version","date_published":"2022-01-06T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","ddc":["570"],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"01","citation":{"apa":"Turelli, M., &#38; Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","ista":"Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control, Dryad, <a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","ama":"Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>","short":"M. Turelli, N.H. Barton, (2022).","mla":"Turelli, Michael, and Nicholas H. Barton. <i>Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","chicago":"Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>."},"department":[{"_id":"NiBa"}],"day":"06"},{"citation":{"ieee":"M. Parvizian <i>et al.</i>, “Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals.’” Zenodo, 2022.","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>","short":"M. Parvizian, A. Duran Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, (2022).","ista":"Parvizian M, Duran Balsa A, Pokratath R, Kalha C, Lee S, Van den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","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>","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>.","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>."},"day":"12","department":[{"_id":"MaIb"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"05","ddc":["540"],"date_published":"2022-05-12T00:00:00Z","oa_version":"Published Version","date_created":"2022-07-29T09:31:13Z","publisher":"Zenodo","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6542908"}],"article_processing_charge":"No","type":"research_data_reference","oa":1,"title":"Data for \"The chemistry of Cu3N and Cu3PdN nanocrystals\"","author":[{"first_name":"Mahsa","full_name":"Parvizian, Mahsa","last_name":"Parvizian"},{"last_name":"Duran Balsa","full_name":"Duran Balsa, Alejandra","first_name":"Alejandra"},{"last_name":"Pokratath","full_name":"Pokratath, Rohan","first_name":"Rohan"},{"last_name":"Kalha","full_name":"Kalha, Curran","first_name":"Curran"},{"full_name":"Lee, Seungho","last_name":"Lee","first_name":"Seungho"},{"first_name":"Dietger","full_name":"Van den Eynden, Dietger","last_name":"Van den Eynden"},{"orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Regoutz","full_name":"Regoutz, Anna","first_name":"Anna"},{"first_name":"Jonathan","last_name":"De Roo","full_name":"De Roo, Jonathan"}],"_id":"11695","abstract":[{"text":"Data underlying the figures in the publication \"The chemistry of Cu3N and Cu3PdN nanocrystals\" ","lang":"eng"}],"year":"2022","doi":"10.5281/ZENODO.6542908","date_updated":"2023-08-03T07:19:12Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11451"}]},"status":"public"},{"publication":"Networks and Heterogeneous Media","date_updated":"2023-08-03T12:25:49Z","article_type":"original","page":"687-717","oa":1,"year":"2022","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.05677","open_access":"1"}],"intvolume":"        17","publisher":"American Institute of Mathematical Sciences","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"JaMa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000812422100001"],"arxiv":["2105.05677"]},"date_published":"2022-10-01T00:00:00Z","scopus_import":"1","date_created":"2022-07-31T22:01:46Z","publication_identifier":{"issn":["1556-1801"],"eissn":["1556-181X"]},"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"status":"public","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.","publication_status":"published","ec_funded":1,"author":[{"first_name":"Matthias","last_name":"Erbar","full_name":"Erbar, Matthias"},{"last_name":"Forkert","full_name":"Forkert, Dominik L","first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan"},{"first_name":"Delio","full_name":"Mugnolo, Delio","last_name":"Mugnolo"}],"title":"Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph","_id":"11700","issue":"5","abstract":[{"text":"This paper contains two contributions in the study of optimal transport on metric graphs. Firstly, we prove a Benamou–Brenier formula for the Wasserstein distance, which establishes the equivalence of static and dynamical optimal transport. Secondly, in the spirit of Jordan–Kinderlehrer–Otto, we show that McKean–Vlasov equations can be formulated as gradient flow of the free energy in the Wasserstein space of probability measures. The proofs of these results are based on careful regularisation arguments to circumvent some of the difficulties arising in metric graphs, namely, branching of geodesics and the failure of semi-convexity of entropy functionals in the Wasserstein space.","lang":"eng"}],"doi":"10.3934/nhm.2022023","arxiv":1,"volume":17,"article_processing_charge":"No","day":"01","citation":{"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>.","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>.","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>","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.","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>","short":"M. Erbar, D.L. Forkert, J. Maas, D. Mugnolo, Networks and Heterogeneous Media 17 (2022) 687–717."},"month":"10","oa_version":"Preprint"},{"arxiv":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"file":[{"file_size":2122096,"creator":"dernst","relation":"main_file","file_name":"2022_Nonlinearity_Agresti.pdf","content_type":"application/pdf","checksum":"997a4bff2dfbee3321d081328c2f1e1a","access_level":"open_access","date_updated":"2022-08-01T10:39:36Z","success":1,"date_created":"2022-08-01T10:39:36Z","file_id":"11715"}],"has_accepted_license":"1","article_processing_charge":"No","volume":35,"citation":{"mla":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.” <i>Nonlinearity</i>, vol. 35, no. 8, IOP Publishing, 2022, pp. 4100–210, doi:<a href=\"https://doi.org/10.1088/1361-6544/abd613\">10.1088/1361-6544/abd613</a>.","chicago":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.” <i>Nonlinearity</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1361-6544/abd613\">https://doi.org/10.1088/1361-6544/abd613</a>.","ama":"Agresti A, Veraar M. Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence. <i>Nonlinearity</i>. 2022;35(8):4100-4210. doi:<a href=\"https://doi.org/10.1088/1361-6544/abd613\">10.1088/1361-6544/abd613</a>","short":"A. Agresti, M. Veraar, Nonlinearity 35 (2022) 4100–4210.","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.","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.","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>"},"day":"04","month":"08","file_date_updated":"2022-08-01T10:39:36Z","ddc":["510"],"license":"https://creativecommons.org/licenses/by/3.0/","oa_version":"Published Version","publication_identifier":{"issn":["0951-7715"],"eissn":["1361-6544"]},"status":"public","acknowledgement":"The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","publication_status":"published","title":"Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence","author":[{"last_name":"Agresti","full_name":"Agresti, Antonio","first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"_id":"11701","abstract":[{"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.","lang":"eng"}],"issue":"8","doi":"10.1088/1361-6544/abd613","publisher":"IOP Publishing","intvolume":"        35","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JuFi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000826695900001"],"arxiv":["2001.00512"]},"date_published":"2022-08-04T00:00:00Z","date_created":"2022-07-31T22:01:47Z","scopus_import":"1","publication":"Nonlinearity","date_updated":"2023-08-03T12:25:08Z","page":"4100-4210","article_type":"original","oa":1,"year":"2022"},{"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"title":"The \"New Synthesis\"","_id":"11702","issue":"30","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."}],"doi":"10.1073/pnas.2122147119","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","status":"public","publication_status":"published","day":"18","citation":{"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, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>.","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>.","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119.","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>","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","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. Proceedings of the National Academy of Sciences, 2022.","apa":"Barton, N. H. (2022). The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>"},"month":"07","pmid":1,"ddc":["570"],"file_date_updated":"2022-08-01T10:58:28Z","oa_version":"Published Version","file":[{"date_created":"2022-08-01T10:58:28Z","file_id":"11716","date_updated":"2022-08-01T10:58:28Z","success":1,"content_type":"application/pdf","checksum":"06c866196a8957f0c37b8a121771c885","access_level":"open_access","file_size":848511,"relation":"main_file","creator":"dernst","file_name":"2022_PNAS_Barton.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":119,"article_processing_charge":"No","oa":1,"year":"2022","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_updated":"2022-08-01T11:00:25Z","article_type":"original","article_number":"e2122147119","department":[{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-07-18T00:00:00Z","external_id":{"pmid":["35858408"]},"scopus_import":"1","date_created":"2022-07-31T22:01:47Z","intvolume":"       119","publisher":"Proceedings of the National Academy of Sciences","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}]},{"publication":"PLoS Genetics","date_updated":"2023-08-03T12:17:12Z","article_number":"e1010226","article_type":"original","oa":1,"year":"2022","publisher":"Public Library of Science","intvolume":"        18","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"BeVi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-07-06T00:00:00Z","external_id":{"pmid":["35793353"],"isi":["000886643100006"]},"date_created":"2022-07-31T22:01:48Z","scopus_import":"1","publication_identifier":{"eissn":["1553-7404"]},"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"publication_status":"published","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.","status":"public","ec_funded":1,"title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","author":[{"orcid":"0000-0002-9752-7380","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","full_name":"Toups, Melissa A"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"},{"first_name":"John R.","last_name":"Pannell","full_name":"Pannell, John R."}],"_id":"11703","abstract":[{"lang":"eng","text":"Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism."}],"issue":"7","doi":"10.1371/journal.pgen.1010226","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","creator":"dernst","file_size":1620272,"file_name":"2022_PLoSGenetics_Toups.pdf","date_updated":"2022-08-01T07:49:25Z","success":1,"content_type":"application/pdf","checksum":"aa4c137f82635e700856c359dccfaa0a","access_level":"open_access","date_created":"2022-08-01T07:49:25Z","file_id":"11708"}],"has_accepted_license":"1","article_processing_charge":"No","volume":18,"citation":{"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>.","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>.","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>","short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022).","ista":"Toups MA, Vicoso B, Pannell JR. 2022. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. 18(7), e1010226.","apa":"Toups, M. A., Vicoso, B., &#38; Pannell, J. R. (2022). Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>","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."},"day":"06","ddc":["570"],"file_date_updated":"2022-08-01T07:49:25Z","pmid":1,"month":"07","oa_version":"Published Version"},{"has_accepted_license":"1","article_processing_charge":"No","volume":17,"file":[{"creator":"dernst","relation":"main_file","file_size":1421256,"file_name":"2022_PLoSONE_Budanur.pdf","date_updated":"2022-08-01T08:02:38Z","success":1,"content_type":"application/pdf","checksum":"1ddd9b91e6dec31ab0e7a8433ca2d452","access_level":"open_access","date_created":"2022-08-01T08:02:38Z","file_id":"11712"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","day":"18","citation":{"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>.","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>.","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.","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>","ista":"Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating epidemics. PLoS ONE. 17(7), e0269975.","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>","short":"N.B. Budanur, B. Hof, PLoS ONE 17 (2022)."},"file_date_updated":"2022-08-01T08:02:38Z","month":"07","ddc":["510"],"publication_status":"published","status":"public","publication_identifier":{"eissn":["1932-6203"]},"issue":"7","abstract":[{"lang":"eng","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."}],"doi":"10.1371/journal.pone.0269975","author":[{"orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","last_name":"Budanur"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"title":"An autonomous compartmental model for accelerating epidemics","_id":"11704","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        17","publisher":"Public Library of Science","date_published":"2022-07-18T00:00:00Z","external_id":{"isi":["000911392100055"]},"scopus_import":"1","date_created":"2022-07-31T22:01:48Z","department":[{"_id":"BjHo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"id":"11711","relation":"research_data","status":"public"}]},"article_type":"original","article_number":"e0269975","publication":"PLoS ONE","date_updated":"2023-08-03T12:24:22Z","year":"2022","oa":1},{"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Wiley","intvolume":"        61","date_created":"2022-07-31T22:01:48Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"scopus_import":"1","external_id":{"isi":["000828274200001"]},"date_published":"2022-08-26T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"article_number":"e202207002","article_type":"original","date_updated":"2023-08-03T12:23:52Z","publication":"Angewandte Chemie - International Edition","year":"2022","oa":1,"volume":61,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"12476","date_created":"2023-02-02T08:01:00Z","success":1,"date_updated":"2023-02-02T08:01:00Z","access_level":"open_access","content_type":"application/pdf","checksum":"ad601f2b9e26e46ab4785162be58b5ed","file_name":"2022_AngewandteChemieInternat_Chang.pdf","creator":"dernst","file_size":4072650,"relation":"main_file"}],"oa_version":"Published Version","ddc":["540"],"month":"08","file_date_updated":"2023-02-02T08:01:00Z","citation":{"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>","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).","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.","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>","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>.","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>."},"day":"26","ec_funded":1,"status":"public","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.","publication_status":"published","project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"doi":"10.1002/anie.202207002","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"}],"issue":"35","_id":"11705","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","first_name":"Cheng","full_name":"Chang, Cheng","last_name":"Chang"},{"orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu"},{"last_name":"Lee","full_name":"Lee, Seungho","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598"},{"first_name":"Maria","full_name":"Spadaro, Maria","last_name":"Spadaro"},{"first_name":"Kristopher M.","last_name":"Koskela","full_name":"Koskela, Kristopher M."},{"full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"orcid":"0000-0001-9732-3815","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","full_name":"Costanzo, Tommaso"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"first_name":"Richard L.","full_name":"Brutchey, Richard L.","last_name":"Brutchey"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}]},{"page":"1-20","publication":"International Colloquium on Structural Information and Communication Complexity","date_updated":"2023-08-03T12:16:29Z","year":"2022","oa":1,"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","series_title":"LNCS","publisher":"Springer Nature","main_file_link":[{"url":"https://arxiv.org/abs/2102.08703","open_access":"1"}],"intvolume":"     13298","external_id":{"arxiv":["2102.08703"],"isi":["000876977400001"]},"date_published":"2022-06-25T00:00:00Z","date_created":"2022-07-31T22:01:49Z","scopus_import":"1","department":[{"_id":"DaAl"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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_status":"published","status":"public","ec_funded":1,"publication_identifier":{"isbn":["9783031099922"],"issn":["0302-9743"],"eissn":["1611-3349"]},"project":[{"call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems","grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"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."}],"doi":"10.1007/978-3-031-09993-9_1","title":"Local mending","author":[{"last_name":"Balliu","full_name":"Balliu, Alkida","first_name":"Alkida"},{"full_name":"Hirvonen, Juho","last_name":"Hirvonen","first_name":"Juho"},{"full_name":"Melnyk, Darya","last_name":"Melnyk","first_name":"Darya"},{"first_name":"Dennis","last_name":"Olivetti","full_name":"Olivetti, Dennis"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","full_name":"Rybicki, Joel","last_name":"Rybicki","orcid":"0000-0002-6432-6646"},{"first_name":"Jukka","full_name":"Suomela, Jukka","last_name":"Suomela"}],"editor":[{"last_name":"Parter","full_name":"Parter, Merav","first_name":"Merav"}],"_id":"11707","article_processing_charge":"No","volume":13298,"arxiv":1,"oa_version":"Preprint","conference":{"name":"SIROCCO: Structural Information and Communication Complexity","start_date":"2022-06-27","location":"Paderborn, Germany","end_date":"2022-06-29"},"citation":{"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.","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>","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.","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.","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>","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>."},"day":"25","month":"06"},{"date_published":"2022-07-06T00:00:00Z","date_created":"2022-08-01T08:06:33Z","oa_version":"Published Version","department":[{"_id":"BjHo"}],"day":"06","citation":{"chicago":"Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>.","mla":"Budanur, Nazmi B. <i>Burakbudanur/Autoacc-Public</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">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>.","short":"N.B. Budanur, (2022).","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","apa":"Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","ddc":["000"],"month":"07","has_accepted_license":"1","type":"research_data_reference","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6802720"}],"publisher":"Zenodo","year":"2022","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\""}],"doi":"10.5281/ZENODO.6802720","author":[{"orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"}],"oa":1,"title":"burakbudanur/autoacc-public","_id":"11711","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11704"}]},"date_updated":"2023-08-03T12:24:21Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"}],"scopus_import":"1","date_created":"2022-08-01T09:04:27Z","date_published":"2022-05-13T00:00:00Z","external_id":{"pmid":["35562780"]},"intvolume":"        15","publisher":"Springer Nature","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","oa":1,"keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"year":"2022","date_updated":"2022-08-01T09:27:40Z","publication":"BMC Research Notes","article_type":"letter_note","article_number":"173","related_material":{"link":[{"url":"https://doi.org/10.1186/s13104-022-06152-7","relation":"erratum"}]},"ddc":["570"],"file_date_updated":"2022-08-01T09:24:42Z","pmid":1,"month":"05","day":"13","citation":{"chicago":"Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>.","mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>.","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.","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","ama":"Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. 2022;15. doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>","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."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2022-08-01T09:24:42Z","file_id":"11714","creator":"dernst","relation":"main_file","file_size":1545310,"file_name":"2022_BMCResearchNotes_Nikolic.pdf","content_type":"application/pdf","checksum":"008156e5340e9789f0f6d82bde4d347a","access_level":"open_access","date_updated":"2022-08-01T09:24:42Z","success":1}],"volume":15,"article_processing_charge":"No","has_accepted_license":"1","_id":"11713","author":[{"orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"},{"first_name":"Martina","last_name":"Sauert","full_name":"Sauert, Martina"},{"first_name":"Tanino G.","last_name":"Albanese","full_name":"Albanese, Tanino G."},{"first_name":"Isabella","full_name":"Moll, Isabella","last_name":"Moll"}],"title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","doi":"10.1186/s13104-022-06061-9","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"}],"project":[{"grant_number":"V00738","_id":"26956E74-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms"}],"publication_identifier":{"issn":["1756-0500"]},"publication_status":"published","status":"public","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."},{"ddc":["510"],"month":"10","file_date_updated":"2023-02-02T07:39:09Z","citation":{"mla":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>, vol. 408, no. Part A, 108591, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>.","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>.","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>","ieee":"K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” <i>Advances in Mathematics</i>, vol. 408, no. Part A. Elsevier, 2022.","short":"K. Drach, D. Schleicher, Advances in Mathematics 408 (2022).","ista":"Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics. 408(Part A), 108591.","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>"},"day":"29","oa_version":"Published Version","file":[{"success":1,"date_updated":"2023-02-02T07:39:09Z","access_level":"open_access","checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","content_type":"application/pdf","file_name":"2022_AdvancesMathematics_Drach.pdf","relation":"main_file","file_size":2164036,"creator":"dernst","file_id":"12474","date_created":"2023-02-02T07:39:09Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","volume":408,"has_accepted_license":"1","_id":"11717","title":"Rigidity of Newton dynamics","author":[{"first_name":"Kostiantyn","id":"fe8209e2-906f-11eb-847d-950f8fc09115","last_name":"Drach","full_name":"Drach, Kostiantyn","orcid":"0000-0002-9156-8616"},{"first_name":"Dierk","last_name":"Schleicher","full_name":"Schleicher, Dierk"}],"doi":"10.1016/j.aim.2022.108591","abstract":[{"text":"We study rigidity of rational maps that come from Newton's root finding method for polynomials of arbitrary degrees. We establish dynamical rigidity of these maps: each point in the Julia set of a Newton map is either rigid (i.e. its orbit can be distinguished in combinatorial terms from all other orbits), or the orbit of this point eventually lands in the filled-in Julia set of a polynomial-like restriction of the original map. As a corollary, we show that the Julia sets of Newton maps in many non-trivial cases are locally connected; in particular, every cubic Newton map without Siegel points has locally connected Julia set.\r\nIn the parameter space of Newton maps of arbitrary degree we obtain the following rigidity result: any two combinatorially equivalent Newton maps are quasiconformally conjugate in a neighborhood of their Julia sets provided that they either non-renormalizable, or they are both renormalizable “in the same way”.\r\nOur main tool is a generalized renormalization concept called “complex box mappings” for which we extend a dynamical rigidity result by Kozlovski and van Strien so as to include irrationally indifferent and renormalizable situations.","lang":"eng"}],"issue":"Part A","project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","grant_number":"885707","call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows"}],"publication_identifier":{"issn":["0001-8708"]},"ec_funded":1,"status":"public","publication_status":"published","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).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"VaKa"}],"date_created":"2022-08-01T17:08:16Z","scopus_import":"1","date_published":"2022-10-29T00:00:00Z","external_id":{"isi":["000860924200005"]},"publisher":"Elsevier","intvolume":"       408","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"oa":1,"keyword":["General Mathematics"],"year":"2022","date_updated":"2023-08-03T12:36:07Z","publication":"Advances in Mathematics","article_number":"108591","article_type":"original"}]