[{"article_processing_charge":"No","publisher":"Elsevier","acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","oa":1,"doi":"10.1016/j.jcp.2022.111439","volume":467,"author":[{"id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","first_name":"Aleksei","orcid":"0000-0003-2189-3904","full_name":"Kalinov, Aleksei","last_name":"Kalinov"},{"first_name":"A.I.","full_name":"Osinskiy, A.I.","last_name":"Osinskiy"},{"first_name":"S.A.","last_name":"Matveev","full_name":"Matveev, S.A."},{"first_name":"W.","last_name":"Otieno","full_name":"Otieno, W."},{"last_name":"Brilliantov","full_name":"Brilliantov, N.V.","first_name":"N.V."}],"article_type":"original","month":"10","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"arxiv":1,"publication_identifier":{"issn":["0021-9991"]},"keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","date_created":"2022-07-11T12:19:59Z","oa_version":"Preprint","publication_status":"published","status":"public","scopus_import":"1","publication":"Journal of Computational Physics","date_updated":"2024-10-21T06:01:47Z","isi":1,"article_number":"111439","intvolume":"       467","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["518"],"date_published":"2022-10-15T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.09481"}],"abstract":[{"lang":"eng","text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise."}],"_id":"11556","language":[{"iso":"eng"}],"external_id":{"arxiv":["2103.09481"],"isi":["000917225500013"]},"type":"journal_article","quality_controlled":"1","day":"15","citation":{"chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439.","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>.","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022.","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022)."}},{"pmid":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"BioMed Central","volume":23,"author":[{"full_name":"Zhang, Runxuan","last_name":"Zhang","first_name":"Runxuan"},{"full_name":"Kuo, Richard","last_name":"Kuo","first_name":"Richard"},{"first_name":"Max","last_name":"Coulter","full_name":"Coulter, Max"},{"first_name":"Cristiane P.G.","last_name":"Calixto","full_name":"Calixto, Cristiane P.G."},{"first_name":"Juan Carlos","last_name":"Entizne","full_name":"Entizne, Juan Carlos"},{"last_name":"Guo","full_name":"Guo, Wenbin","first_name":"Wenbin"},{"first_name":"Yamile","last_name":"Marquez","full_name":"Marquez, Yamile"},{"first_name":"Linda","last_name":"Milne","full_name":"Milne, Linda"},{"full_name":"Riegler, Stefan","last_name":"Riegler","orcid":"0000-0003-3413-1343","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","first_name":"Stefan"},{"last_name":"Matsui","full_name":"Matsui, Akihiro","first_name":"Akihiro"},{"full_name":"Tanaka, Maho","last_name":"Tanaka","first_name":"Maho"},{"first_name":"Sarah","last_name":"Harvey","full_name":"Harvey, Sarah"},{"full_name":"Gao, Yubang","last_name":"Gao","first_name":"Yubang"},{"full_name":"Wießner-Kroh, Theresa","last_name":"Wießner-Kroh","first_name":"Theresa"},{"first_name":"Alejandro","last_name":"Paniagua","full_name":"Paniagua, Alejandro"},{"first_name":"Martin","full_name":"Crespi, Martin","last_name":"Crespi"},{"last_name":"Denby","full_name":"Denby, Katherine","first_name":"Katherine"},{"last_name":"Hur","full_name":"Hur, Asa Ben","first_name":"Asa Ben"},{"first_name":"Enamul","full_name":"Huq, Enamul","last_name":"Huq"},{"last_name":"Jantsch","full_name":"Jantsch, Michael","first_name":"Michael"},{"full_name":"Jarmolowski, Artur","last_name":"Jarmolowski","first_name":"Artur"},{"last_name":"Koester","full_name":"Koester, Tino","first_name":"Tino"},{"first_name":"Sascha","last_name":"Laubinger","full_name":"Laubinger, Sascha"},{"first_name":"Qingshun Quinn","last_name":"Li","full_name":"Li, Qingshun Quinn"},{"full_name":"Gu, Lianfeng","last_name":"Gu","first_name":"Lianfeng"},{"last_name":"Seki","full_name":"Seki, Motoaki","first_name":"Motoaki"},{"first_name":"Dorothee","last_name":"Staiger","full_name":"Staiger, Dorothee"},{"last_name":"Sunkar","full_name":"Sunkar, Ramanjulu","first_name":"Ramanjulu"},{"last_name":"Szweykowska-Kulinska","full_name":"Szweykowska-Kulinska, Zofia","first_name":"Zofia"},{"first_name":"Shih Long","last_name":"Tu","full_name":"Tu, Shih Long"},{"last_name":"Wachter","full_name":"Wachter, Andreas","first_name":"Andreas"},{"last_name":"Waugh","full_name":"Waugh, Robbie","first_name":"Robbie"},{"first_name":"Liming","full_name":"Xiong, Liming","last_name":"Xiong"},{"last_name":"Zhang","full_name":"Zhang, Xiao Ning","first_name":"Xiao Ning"},{"last_name":"Conesa","full_name":"Conesa, Ana","first_name":"Ana"},{"last_name":"Reddy","full_name":"Reddy, Anireddy S.N.","first_name":"Anireddy S.N."},{"first_name":"Andrea","full_name":"Barta, Andrea","last_name":"Barta"},{"first_name":"Maria","last_name":"Kalyna","full_name":"Kalyna, Maria"},{"first_name":"John W.S.","last_name":"Brown","full_name":"Brown, John W.S."}],"article_type":"original","month":"07","department":[{"_id":"FyKo"}],"acknowledgement":"This work was jointly supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1 to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032 to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542 to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173) to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03 to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica to S.-L. T.","oa":1,"doi":"10.1186/s13059-022-02711-0","title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","date_created":"2022-07-17T22:01:53Z","oa_version":"Published Version","publication_identifier":{"eissn":["1474-760X"]},"file":[{"success":1,"content_type":"application/pdf","file_size":3146207,"date_created":"2022-07-18T08:15:24Z","access_level":"open_access","creator":"dernst","date_updated":"2022-07-18T08:15:24Z","file_id":"11597","relation":"main_file","checksum":"2c30ef84151d257a6b835b4e069b70ac","file_name":"2022_GenomeBiology_Zhang.pdf"}],"publication_status":"published","scopus_import":"1","status":"public","date_updated":"2025-06-11T13:37:00Z","publication":"Genome Biology","isi":1,"file_date_updated":"2022-07-18T08:15:24Z","date_published":"2022-07-07T00:00:00Z","intvolume":"        23","article_number":"149","year":"2022","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"ama":"Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. 2022;23. doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>","ista":"Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149.","chicago":"Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>. BioMed Central, 2022. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>.","mla":"Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>, vol. 23, 149, BioMed Central, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>.","short":"R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez, L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh, A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski, T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska, S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy, A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).","ieee":"R. Zhang <i>et al.</i>, “A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis,” <i>Genome Biology</i>, vol. 23. BioMed Central, 2022.","apa":"Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W., … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>"},"day":"07","_id":"11587","abstract":[{"text":"Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.\r\nConclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["35799267"],"isi":["000821915500002"]},"type":"journal_article","quality_controlled":"1"},{"date_created":"2022-07-17T22:01:54Z","title":"Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo","oa_version":"Published Version","publication_identifier":{"issn":["0390-6078"],"eissn":["1592-8721"]},"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_size":1722094,"date_created":"2022-07-18T07:51:55Z","checksum":"9b47830945f3c30428fe9cfee2dc4a8a","file_name":"2022_Haematologica_Nicolai.pdf","file_id":"11595","date_updated":"2022-07-18T07:51:55Z","creator":"dernst","relation":"main_file"}],"publication_status":"published","corr_author":"1","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_processing_charge":"No","publisher":"Ferrata Storti Foundation","volume":107,"author":[{"full_name":"Nicolai, Leo","last_name":"Nicolai","first_name":"Leo"},{"first_name":"Rainer","last_name":"Kaiser","full_name":"Kaiser, Rainer"},{"full_name":"Escaig, Raphael","last_name":"Escaig","first_name":"Raphael"},{"first_name":"Marie Louise","full_name":"Hoffknecht, Marie Louise","last_name":"Hoffknecht"},{"first_name":"Afra","last_name":"Anjum","full_name":"Anjum, Afra"},{"last_name":"Leunig","full_name":"Leunig, Alexander","first_name":"Alexander"},{"last_name":"Pircher","full_name":"Pircher, Joachim","first_name":"Joachim"},{"first_name":"Andreas","last_name":"Ehrlich","full_name":"Ehrlich, Andreas"},{"first_name":"Michael","full_name":"Lorenz, Michael","last_name":"Lorenz"},{"first_name":"Hellen","full_name":"Ishikawa-Ankerhold, Hellen","last_name":"Ishikawa-Ankerhold"},{"first_name":"William C.","full_name":"Aird, William C.","last_name":"Aird"},{"last_name":"Massberg","full_name":"Massberg, Steffen","first_name":"Steffen"},{"orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","full_name":"Gärtner, Florian R","last_name":"Gärtner"}],"article_type":"original","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"department":[{"_id":"MiSi"}],"month":"07","acknowledgement":"This study was supported by the Deutsche Forschungsgemeinschaft (DFG) SFB 914 ( to SM [B02 and Z01]), the DFG SFB 1123 (to SM [B06]), the DFG FOR 2033 (to SM), the German\r\nCenter for Cardiovascular Research (DZHK) (Clinician Scientist Programme), MHA 1.4VD (to SM), Postdoc Start-up Grant, 81X3600213 (to FG), 81X3600222 (to LN), the FP7 program\r\n(project 260309, PRESTIGE [to SM]). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 83344, ERC-2018-ADG “IMMUNOTHROMBOSIS” [to SM] and the Marie Skłodowska Curie Individual Fellowship (EU project 747687, LamelliActin [to FG]). ","oa":1,"doi":"10.3324/haematol.2021.278896","date_published":"2022-07-01T00:00:00Z","intvolume":"       107","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"has_accepted_license":"1","day":"01","citation":{"apa":"Nicolai, L., Kaiser, R., Escaig, R., Hoffknecht, M. L., Anjum, A., Leunig, A., … Gärtner, F. R. (2022). Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. Ferrata Storti Foundation. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>","mla":"Nicolai, Leo, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>, vol. 107, no. 7, Ferrata Storti Foundation, 2022, pp. 1669–80, doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>.","short":"L. Nicolai, R. Kaiser, R. Escaig, M.L. Hoffknecht, A. Anjum, A. Leunig, J. Pircher, A. Ehrlich, M. Lorenz, H. Ishikawa-Ankerhold, W.C. Aird, S. Massberg, F.R. Gärtner, Haematologica 107 (2022) 1669–1680.","ieee":"L. Nicolai <i>et al.</i>, “Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo,” <i>Haematologica</i>, vol. 107, no. 7. Ferrata Storti Foundation, pp. 1669–1680, 2022.","chicago":"Nicolai, Leo, Rainer Kaiser, Raphael Escaig, Marie Louise Hoffknecht, Afra Anjum, Alexander Leunig, Joachim Pircher, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>. Ferrata Storti Foundation, 2022. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>.","ama":"Nicolai L, Kaiser R, Escaig R, et al. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. 2022;107(7):1669-1680. doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>","ista":"Nicolai L, Kaiser R, Escaig R, Hoffknecht ML, Anjum A, Leunig A, Pircher J, Ehrlich A, Lorenz M, Ishikawa-Ankerhold H, Aird WC, Massberg S, Gärtner FR. 2022. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. Haematologica. 107(7), 1669–1680."},"language":[{"iso":"eng"}],"_id":"11588","abstract":[{"lang":"eng","text":"Visualizing cell behavior and effector function on a single cell level has been crucial for understanding key aspects of mammalian biology. Due to their small size, large number and rapid recruitment into thrombi, there is a lack of data on fate and behavior of individual platelets in thrombosis and hemostasis. Here we report the use of platelet lineage restricted multi-color reporter mouse strains to delineate platelet function on a single cell level. We show that genetic labeling allows for single platelet and megakaryocyte (MK) tracking and morphological analysis in vivo and in vitro, while not affecting lineage functions. Using Cre-driven Confetti expression, we provide insights into temporal gene expression patterns as well as spatial clustering of MK in the bone marrow. In the vasculature, shape analysis of activated platelets recruited to thrombi identifies ubiquitous filopodia formation with no evidence of lamellipodia formation. Single cell tracking in complex thrombi reveals prominent myosin-dependent motility of platelets and highlights thrombus formation as a highly dynamic process amenable to modification and intervention of the acto-myosin cytoskeleton. Platelet function assays combining flow cytrometry, as well as in vivo, ex vivo and in vitro imaging show unaltered platelet functions of multicolor reporter mice compared to wild-type controls. In conclusion, platelet lineage multicolor reporter mice prove useful in furthering our understanding of platelet and MK biology on a single cell level."}],"external_id":{"isi":["000823746100018"]},"type":"journal_article","quality_controlled":"1","issue":"7","ec_funded":1,"scopus_import":"1","page":"1669-1680","status":"public","publication":"Haematologica","date_updated":"2025-04-14T07:43:16Z","isi":1,"file_date_updated":"2022-07-18T07:51:55Z"},{"quality_controlled":"1","type":"journal_article","external_id":{"pmid":["35783951"],"isi":["000819250500001"]},"_id":"11589","language":[{"iso":"eng"}],"abstract":[{"text":"Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana.","lang":"eng"}],"day":"16","citation":{"ista":"Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398.","ama":"Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. 2022;13. doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>","chicago":"Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>.","ieee":"R. Wang <i>et al.</i>, “Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana,” <i>Frontiers in Plant Science</i>, vol. 13. Frontiers, 2022.","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022).","mla":"Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>, vol. 13, 862398, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>.","apa":"Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste, S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>"},"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["580"],"year":"2022","intvolume":"        13","article_number":"862398","date_published":"2022-06-16T00:00:00Z","file_date_updated":"2022-07-18T08:05:15Z","isi":1,"date_updated":"2023-08-03T12:01:47Z","publication":"Frontiers in Plant Science","status":"public","scopus_import":"1","publication_status":"published","file":[{"date_updated":"2022-07-18T08:05:15Z","relation":"main_file","file_id":"11596","creator":"dernst","checksum":"95313515637c0f84de591d204375d764","file_name":"2022_FrontiersPlantScience_Wang.pdf","content_type":"application/pdf","success":1,"file_size":5040638,"date_created":"2022-07-18T08:05:15Z","access_level":"open_access"}],"publication_identifier":{"eissn":["1664-462X"]},"oa_version":"Published Version","date_created":"2022-07-17T22:01:54Z","title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","doi":"10.3389/fpls.2022.862398","oa":1,"acknowledgement":"RW and JC predoctoral fellows that were supported by the Chinese Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing the CKP family clone sets, and for providing useful feedback on the manuscript.","month":"06","department":[{"_id":"JiFr"}],"article_type":"original","volume":13,"author":[{"first_name":"Ren","last_name":"Wang","full_name":"Wang, Ren"},{"first_name":"Ellie","last_name":"Himschoot","full_name":"Himschoot, Ellie"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"first_name":"Marie","full_name":"Boudsocq, Marie","last_name":"Boudsocq"},{"first_name":"Danny","full_name":"Geelen, Danny","last_name":"Geelen"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"}],"publisher":"Frontiers","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"link":[{"url":"https://doi.org/10.3389/fpls.2022.1100792","relation":"erratum"}]},"pmid":1},{"file":[{"checksum":"dc67b60f2e50e9ef2bd820ca0d7333d2","file_name":"2022_NewJournalPhysics_Brauneis.pdf","date_updated":"2022-07-18T06:33:13Z","file_id":"11594","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_size":3415721,"date_created":"2022-07-18T06:33:13Z"}],"publication_status":"published","title":"Artificial atoms from cold bosons in one dimension","date_created":"2022-07-17T22:01:55Z","oa_version":"Published Version","publication_identifier":{"issn":["1367-2630"]},"author":[{"full_name":"Brauneis, Fabian","last_name":"Brauneis","first_name":"Fabian"},{"first_name":"Timothy G.","last_name":"Backert","full_name":"Backert, Timothy G."},{"first_name":"Simeon I.","last_name":"Mistakidis","full_name":"Mistakidis, Simeon I."},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"full_name":"Hammer, Hans Werner","last_name":"Hammer","first_name":"Hans Werner"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem","last_name":"Volosniev"}],"volume":24,"article_type":"original","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"department":[{"_id":"MiLe"}],"month":"06","acknowledgement":"This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (FB, H-WH, AGV) and European Union's Horizon 2020 research and innovation programme under the Marie Skĺodowska-Curie Grant Agreement No. 754411 (AGV). ML acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). SIM acknowledges support from the NSF through a grant for ITAMP at Harvard University.","doi":"10.1088/1367-2630/ac78d8","oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"IOP Publishing","has_accepted_license":"1","day":"01","citation":{"chicago":"Brauneis, Fabian, Timothy G. Backert, Simeon I. Mistakidis, Mikhail Lemeshko, Hans Werner Hammer, and Artem Volosniev. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>.","ista":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. 2022. Artificial atoms from cold bosons in one dimension. New Journal of Physics. 24(6), 063036.","ama":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. 2022;24(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>","apa":"Brauneis, F., Backert, T. G., Mistakidis, S. I., Lemeshko, M., Hammer, H. W., &#38; Volosniev, A. (2022). Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>","short":"F. Brauneis, T.G. Backert, S.I. Mistakidis, M. Lemeshko, H.W. Hammer, A. Volosniev, New Journal of Physics 24 (2022).","ieee":"F. Brauneis, T. G. Backert, S. I. Mistakidis, M. Lemeshko, H. W. Hammer, and A. Volosniev, “Artificial atoms from cold bosons in one dimension,” <i>New Journal of Physics</i>, vol. 24, no. 6. IOP Publishing, 2022.","mla":"Brauneis, Fabian, et al. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>, vol. 24, no. 6, 063036, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>."},"abstract":[{"text":"We investigate the ground-state properties of weakly repulsive one-dimensional bosons in the presence of an attractive zero-range impurity potential. First, we derive mean-field solutions to the problem on a finite ring for the two asymptotic cases: (i) all bosons are bound to the impurity and (ii) all bosons are in a scattering state. Moreover, we derive the critical line that separates these regimes in the parameter space. In the thermodynamic limit, this critical line determines the maximum number of bosons that can be bound by the impurity potential, forming an artificial atom. Second, we validate the mean-field results using the flow equation approach and the multi-layer multi-configuration time-dependent Hartree method for atomic mixtures. While beyond-mean-field effects destroy long-range order in the Bose gas, the critical boson number is unaffected. Our findings are important for understanding such artificial atoms in low-density Bose gases with static and mobile impurities.","lang":"eng"}],"_id":"11590","language":[{"iso":"eng"}],"external_id":{"isi":["000818530000001"]},"type":"journal_article","quality_controlled":"1","date_published":"2022-06-01T00:00:00Z","article_number":"063036","intvolume":"        24","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"publication":"New Journal of Physics","date_updated":"2025-04-14T07:43:58Z","isi":1,"file_date_updated":"2022-07-18T06:33:13Z","ec_funded":1,"issue":"6","scopus_import":"1","status":"public"},{"publication_status":"published","arxiv":1,"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"date_created":"2022-07-17T22:01:55Z","title":"Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams","oa_version":"Preprint","doi":"10.1103/PhysRevA.105.062454","oa":1,"acknowledgement":"We thank T. Mavrogordatos and D. Zhu for initial contribution on the presented topic and K. Fedorov for stimulating discussions on entangled microwave beams. This work was supported by the Austrian Science Fund (FWF) through Grant No. P32299 (PHONED) and the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 899354 (SuperQuLAN). Most of the computational results presented were obtained using the CLIP cluster [65].","volume":105,"author":[{"full_name":"Agustí, J.","last_name":"Agustí","first_name":"J."},{"first_name":"Y.","last_name":"Minoguchi","full_name":"Minoguchi, Y."},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink"},{"first_name":"P.","full_name":"Rabl, P.","last_name":"Rabl"}],"department":[{"_id":"JoFi"}],"month":"06","project":[{"call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits"}],"article_type":"original","article_processing_charge":"No","publisher":"American Physical Society","external_id":{"arxiv":["2204.02993"],"isi":["000824330200003"]},"_id":"11591","abstract":[{"lang":"eng","text":"We investigate the deterministic generation and distribution of entanglement in large quantum networks by driving distant qubits with the output fields of a nondegenerate parametric amplifier. In this setting, the amplifier produces a continuous Gaussian two-mode squeezed state, which acts as a quantum-correlated reservoir for the qubits and relaxes them into a highly entangled steady state. Here we are interested in the maximal amount of entanglement and the optimal entanglement generation rates that can be achieved with this scheme under realistic conditions taking, in particular, the finite amplifier bandwidth, waveguide losses, and propagation delays into account. By combining exact numerical simulations of the full network with approximate analytic results, we predict the optimal working point for the amplifier and the corresponding qubit-qubit entanglement under various conditions. Our findings show that this passive conversion of Gaussian into discrete-variable entanglement offers a robust and experimentally very attractive approach for operating large optical, microwave, or hybrid quantum networks, for which efficient parametric amplifiers are currently developed."}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","day":"29","citation":{"ista":"Agustí J, Minoguchi Y, Fink JM, Rabl P. 2022. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. Physical Review A. 105(6), 062454.","ama":"Agustí J, Minoguchi Y, Fink JM, Rabl P. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>","chicago":"Agustí, J., Y. Minoguchi, Johannes M Fink, and P. Rabl. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>.","ieee":"J. Agustí, Y. Minoguchi, J. M. Fink, and P. Rabl, “Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022.","short":"J. Agustí, Y. Minoguchi, J.M. Fink, P. Rabl, Physical Review A 105 (2022).","mla":"Agustí, J., et al. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>, vol. 105, no. 6, 062454, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>.","apa":"Agustí, J., Minoguchi, Y., Fink, J. M., &#38; Rabl, P. (2022). Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>"},"intvolume":"       105","article_number":"062454","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","date_published":"2022-06-29T00:00:00Z","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2204.02993","open_access":"1"}],"publication":"Physical Review A","date_updated":"2025-04-14T07:53:28Z","isi":1,"status":"public","ec_funded":1,"issue":"6","scopus_import":"1"},{"date_published":"2022-06-30T00:00:00Z","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2206.03924","open_access":"1"}],"article_number":"063329","intvolume":"       105","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","citation":{"ama":"Bighin G, Cappellaro A, Salasnich L. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>","ista":"Bighin G, Cappellaro A, Salasnich L. 2022. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. Physical Review A. 105(6), 063329.","chicago":"Bighin, Giacomo, Alberto Cappellaro, and L. Salasnich. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>.","mla":"Bighin, Giacomo, et al. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>, vol. 105, no. 6, 063329, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>.","short":"G. Bighin, A. Cappellaro, L. Salasnich, Physical Review A 105 (2022).","ieee":"G. Bighin, A. Cappellaro, and L. Salasnich, “Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022.","apa":"Bighin, G., Cappellaro, A., &#38; Salasnich, L. (2022). Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>"},"day":"30","external_id":{"isi":["000829758500010"],"arxiv":["2206.03924"]},"abstract":[{"lang":"eng","text":"We compare recent experimental results [Science 375, 528 (2022)] of the superfluid unitary Fermi gas near the critical temperature with a thermodynamic model based on the elementary excitations of the system. We find good agreement between experimental data and our theory for several quantities such as first sound, second sound, and superfluid fraction. We also show that mode mixing between first and second sound occurs. Finally, we characterize the response amplitude to a density perturbation: Close to the critical temperature both first and second sound can be excited through a density perturbation, whereas at lower temperatures only the first sound mode exhibits a significant response."}],"_id":"11592","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","issue":"6","scopus_import":"1","status":"public","publication":"Physical Review A","date_updated":"2023-08-03T12:00:11Z","isi":1,"date_created":"2022-07-17T22:01:55Z","title":"Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations","oa_version":"Preprint","arxiv":1,"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"publication_status":"published","article_processing_charge":"No","publisher":"American Physical Society","author":[{"last_name":"Bighin","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","orcid":"0000-0001-8823-9777"},{"full_name":"Cappellaro, Alberto","last_name":"Cappellaro","orcid":"0000-0001-6110-2359","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto"},{"last_name":"Salasnich","full_name":"Salasnich, L.","first_name":"L."}],"volume":105,"department":[{"_id":"MiLe"}],"month":"06","article_type":"original","doi":"10.1103/PhysRevA.105.063329","oa":1,"acknowledgement":"The authors gratefully acknowledge stimulating discussions with T. Enss, and thank an anonymous referee for suggestions and remarks that allowed us to improve the original manuscript. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster)."},{"scopus_import":"1","page":"425-447","status":"public","publication":"Discrete and Computational Geometry","date_updated":"2025-04-14T13:52:37Z","isi":1,"date_published":"2022-09-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"intvolume":"        68","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","citation":{"short":"R. Fulek, J. Kynčl, Discrete and Computational Geometry 68 (2022) 425–447.","ieee":"R. Fulek and J. Kynčl, “The Z2-Genus of Kuratowski minors,” <i>Discrete and Computational Geometry</i>, vol. 68. Springer Nature, pp. 425–447, 2022.","mla":"Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” <i>Discrete and Computational Geometry</i>, vol. 68, Springer Nature, 2022, pp. 425–47, doi:<a href=\"https://doi.org/10.1007/s00454-022-00412-w\">10.1007/s00454-022-00412-w</a>.","apa":"Fulek, R., &#38; Kynčl, J. (2022). The Z2-Genus of Kuratowski minors. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00412-w\">https://doi.org/10.1007/s00454-022-00412-w</a>","ista":"Fulek R, Kynčl J. 2022. The Z2-Genus of Kuratowski minors. Discrete and Computational Geometry. 68, 425–447.","ama":"Fulek R, Kynčl J. The Z2-Genus of Kuratowski minors. <i>Discrete and Computational Geometry</i>. 2022;68:425-447. doi:<a href=\"https://doi.org/10.1007/s00454-022-00412-w\">10.1007/s00454-022-00412-w</a>","chicago":"Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-022-00412-w\">https://doi.org/10.1007/s00454-022-00412-w</a>."},"language":[{"iso":"eng"}],"_id":"11593","abstract":[{"lang":"eng","text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z2 -genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t×t grid or one of the following so-called t -Kuratowski graphs: K3,t, or t copies of K5 or K3,3 sharing at most two common vertices. We show that the Z2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its Z2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani–Tutte theorem on orientable surfaces. We also obtain an analogous result for Euler genus and Euler Z2-genus of graphs."}],"external_id":{"isi":["000825014500001"],"arxiv":["1803.05085"]},"type":"journal_article","quality_controlled":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"186"}]},"article_processing_charge":"No","publisher":"Springer Nature","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek","full_name":"Fulek, Radoslav"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"}],"volume":68,"article_type":"original","project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"UlWa"}],"month":"09","acknowledgement":"We thank Zdeněk Dvořák, Xavier Goaoc, and Pavel Paták for helpful discussions. We also thank Bojan Mohar, Paul Seymour, Gelasio Salazar, Jim Geelen, and John Maharry for information about their unpublished results related to Conjecture 3.1. Finally we thank the reviewers for corrections and suggestions for improving the presentation.\r\nSupported by Austrian Science Fund (FWF): M2281-N35. Supported by project 19-04113Y of the Czech Science Foundation (GAČR), by the Czech-French collaboration project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM), and by Charles University project UNCE/SCI/004.","oa":1,"doi":"10.1007/s00454-022-00412-w","date_created":"2022-07-17T22:01:56Z","title":"The Z2-Genus of Kuratowski minors","oa_version":"Preprint","arxiv":1,"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"publication_status":"published"},{"file":[{"checksum":"3ca88decb1011180dc6de7e0862153e1","file_name":"2022_FiniteFields_Kmentt.pdf","creator":"dernst","file_id":"12475","date_updated":"2023-02-02T07:56:34Z","relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","file_size":247615,"date_created":"2023-02-02T07:56:34Z"}],"publication_status":"published","date_created":"2022-07-24T22:01:41Z","title":"The Bertini irreducibility theorem for higher codimensional slices","oa_version":"Published Version","arxiv":1,"publication_identifier":{"eissn":["1090-2465"],"issn":["1071-5797"]},"volume":83,"author":[{"id":"c90670c9-0bf0-11ed-86f5-ed522ece2fac","first_name":"Philip","last_name":"Kmentt","full_name":"Kmentt, Philip"},{"orcid":"0000-0002-1812-2810","id":"440EB050-F248-11E8-B48F-1D18A9856A87","first_name":"Alec L","last_name":"Shute","full_name":"Shute, Alec L"}],"month":"10","department":[{"_id":"TiBr"}],"article_type":"original","doi":"10.1016/j.ffa.2022.102085","oa":1,"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","publisher":"Elsevier","citation":{"ieee":"P. Kmentt and A. L. Shute, “The Bertini irreducibility theorem for higher codimensional slices,” <i>Finite Fields and their Applications</i>, vol. 83, no. 10. Elsevier, 2022.","short":"P. Kmentt, A.L. Shute, Finite Fields and Their Applications 83 (2022).","mla":"Kmentt, Philip, and Alec L. Shute. “The Bertini Irreducibility Theorem for Higher Codimensional Slices.” <i>Finite Fields and Their Applications</i>, vol. 83, no. 10, 102085, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">10.1016/j.ffa.2022.102085</a>.","apa":"Kmentt, P., &#38; Shute, A. L. (2022). The Bertini irreducibility theorem for higher codimensional slices. <i>Finite Fields and Their Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">https://doi.org/10.1016/j.ffa.2022.102085</a>","ista":"Kmentt P, Shute AL. 2022. The Bertini irreducibility theorem for higher codimensional slices. Finite Fields and their Applications. 83(10), 102085.","ama":"Kmentt P, Shute AL. The Bertini irreducibility theorem for higher codimensional slices. <i>Finite Fields and their Applications</i>. 2022;83(10). doi:<a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">10.1016/j.ffa.2022.102085</a>","chicago":"Kmentt, Philip, and Alec L Shute. “The Bertini Irreducibility Theorem for Higher Codimensional Slices.” <i>Finite Fields and Their Applications</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">https://doi.org/10.1016/j.ffa.2022.102085</a>."},"day":"01","has_accepted_license":"1","external_id":{"isi":["000835490600001"],"arxiv":["2111.06697"]},"language":[{"iso":"eng"}],"_id":"11636","abstract":[{"text":"In [3], Poonen and Slavov recently developed a novel approach to Bertini irreducibility theorems over an arbitrary field, based on random hyperplane slicing. In this paper, we extend their work by proving an analogous bound for the dimension of the exceptional locus in the setting of linear subspaces of higher codimensions.","lang":"eng"}],"quality_controlled":"1","type":"journal_article","date_published":"2022-10-01T00:00:00Z","intvolume":"        83","article_number":"102085","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","date_updated":"2025-07-10T11:50:13Z","publication":"Finite Fields and their Applications","isi":1,"file_date_updated":"2023-02-02T07:56:34Z","issue":"10","scopus_import":"1","status":"public"},{"publication_identifier":{"eissn":["1545-7885"]},"date_created":"2022-07-24T22:01:42Z","title":"ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans","oa_version":"Published Version","publication_status":"published","file":[{"checksum":"df4902f854ad76769d3203bfdc69f16c","file_name":"2022_PLoSBiology_Zhao.pdf","file_id":"11643","relation":"main_file","creator":"dernst","date_updated":"2022-07-25T07:38:49Z","access_level":"open_access","content_type":"application/pdf","success":1,"file_size":3721585,"date_created":"2022-07-25T07:38:49Z"}],"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","publisher":"Public Library of Science","pmid":1,"doi":"10.1371/journal.pbio.3001684","oa":1,"acknowledgement":" This work was funded by H2020 European Research Council (ERC Advanced grant, 269058 ACMO, https://erc.europa.eu/funding/advanced-grants) and Wellcome Trust UK (Wellcome Investigator Award, 209504/Z/17/Z, https://wellcome.org/grant-funding/people-and-projects/grants-awarded/molecular-mechanisms-neural-circuit-function-0) to M.d.B, and by H2020 European Research Council (ERC starting grant, 802653 OXYGEN SENSING, https://erc.europa.eu/funding/starting-grants) and Vetenskapsrådet (VR starting grant, 2018-02216, https://www.vr.se/english.html) to C.C. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","author":[{"first_name":"Lina","last_name":"Zhao","full_name":"Zhao, Lina"},{"last_name":"Fenk","full_name":"Fenk, Lorenz A.","first_name":"Lorenz A."},{"full_name":"Nilsson, Lars","last_name":"Nilsson","first_name":"Lars"},{"full_name":"Amin-Wetzel, Niko Paresh","last_name":"Amin-Wetzel","first_name":"Niko Paresh","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425"},{"first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425","full_name":"Ramirez, Nelson","last_name":"Ramirez"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono","full_name":"De Bono, Mario"},{"full_name":"Chen, Changchun","last_name":"Chen","first_name":"Changchun"}],"volume":20,"month":"06","department":[{"_id":"MaDe"}],"project":[{"grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function"}],"article_type":"original","article_number":"e3001684","intvolume":"        20","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","date_published":"2022-06-21T00:00:00Z","external_id":{"isi":["000828679600001"],"pmid":["35727855"]},"_id":"11637","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."}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","day":"21","citation":{"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.","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>","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>.","short":"L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono, C. Chen, PLoS Biology 20 (2022).","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.","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>.","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>"},"has_accepted_license":"1","status":"public","issue":"6","scopus_import":"1","file_date_updated":"2022-07-25T07:38:49Z","date_updated":"2025-04-15T07:32:21Z","publication":"PLoS Biology","isi":1},{"file_date_updated":"2022-07-25T07:47:23Z","publication":"Physical Review Research","date_updated":"2025-03-06T14:09:21Z","status":"public","issue":"2","scopus_import":"1","_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"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["2106.02349"],"pmid":["37576946"]},"type":"journal_article","quality_controlled":"1","has_accepted_license":"1","citation":{"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>","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>.","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.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","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>.","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>","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."},"day":"24","intvolume":"         4","article_number":"023240","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"date_published":"2022-06-24T00:00:00Z","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).","oa":1,"doi":"10.1103/PhysRevResearch.4.023240","volume":4,"author":[{"first_name":"Vudtiwat","last_name":"Ngampruetikorn","full_name":"Ngampruetikorn, Vudtiwat"},{"last_name":"Sachdeva","full_name":"Sachdeva, Vedant","first_name":"Vedant"},{"first_name":"Johanna","full_name":"Torrence, Johanna","last_name":"Torrence"},{"last_name":"Humplik","full_name":"Humplik, Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"David J.","last_name":"Schwab","full_name":"Schwab, David J."},{"last_name":"Palmer","full_name":"Palmer, Stephanie E.","first_name":"Stephanie E."}],"article_type":"original","month":"06","department":[{"_id":"GaTk"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"American Physical Society","pmid":1,"publication_status":"published","file":[{"access_level":"open_access","file_size":1379683,"date_created":"2022-07-25T07:47:23Z","content_type":"application/pdf","success":1,"file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","relation":"main_file","file_id":"11644","date_updated":"2022-07-25T07:47:23Z","creator":"dernst"}],"publication_identifier":{"issn":["2643-1564"]},"arxiv":1,"title":"Inferring couplings in networks across order-disorder phase transitions","date_created":"2022-07-24T22:01:42Z","oa_version":"Published Version"},{"scopus_import":"1","issue":"12","page":"7753-7786","status":"public","isi":1,"date_updated":"2024-10-09T21:02:55Z","publication":"IEEE Transactions on Information Theory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1901.03790"}],"date_published":"2022-12-01T00:00:00Z","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        68","day":"01","citation":{"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>.","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>","ista":"Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.","apa":"Zhang, Y., &#38; Vatedka, S. (2022). List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2022.3189542\">https://doi.org/10.1109/TIT.2022.3189542</a>","mla":"Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12, IEEE, 2022, pp. 7753–86, doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786.","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."},"type":"journal_article","quality_controlled":"1","_id":"11639","abstract":[{"text":"We study the list decodability of different ensembles of codes over the real alphabet under the assumption of an omniscient adversary. It is a well-known result that when the source and the adversary have power constraints P and N respectively, the list decoding capacity is equal to 1/2logP/N. Random spherical codes achieve constant list sizes, and the goal of the present paper is to obtain a better understanding of the smallest achievable list size as a function of the gap to capacity. We show a reduction from arbitrary codes to spherical codes, and derive a lower bound on the list size of typical random spherical codes. We also give an upper bound on the list size achievable using nested Construction-A lattices and infinite Construction-A lattices. We then define and study a class of infinite constellations that generalize Construction-A lattices and prove upper and lower bounds for the same. Other goodness properties such as packing goodness and AWGN goodness of infinite constellations are proved along the way. Finally, we consider random lattices sampled from the Haar distribution and show that if a certain conjecture that originates in analytic number theory is true, then the list size grows as a polynomial function of the gap-to-capacity.","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000891796100007"],"arxiv":["1901.03790"]},"publisher":"IEEE","corr_author":"1","article_processing_charge":"No","article_type":"original","month":"12","department":[{"_id":"MaMo"}],"author":[{"orcid":"0000-0002-6465-6258","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","last_name":"Zhang","full_name":"Zhang, Yihan"},{"last_name":"Vatedka","full_name":"Vatedka, Shashank","first_name":"Shashank"}],"volume":68,"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].","doi":"10.1109/TIT.2022.3189542","oa":1,"oa_version":"Preprint","date_created":"2022-07-24T22:01:42Z","title":"List decoding random Euclidean codes and Infinite constellations","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"arxiv":1,"publication_status":"published"},{"ec_funded":1,"issue":"8","scopus_import":"1","status":"public","page":"2941-2955","date_updated":"2025-06-11T14:01:43Z","publication":"Molecular Ecology Resources","isi":1,"file_date_updated":"2023-02-02T08:11:23Z","date_published":"2022-11-01T00:00:00Z","intvolume":"        22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"year":"2022","day":"01","citation":{"ieee":"E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size,” <i>Molecular Ecology Resources</i>, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","mla":"Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>.","apa":"Szep, E., Trubenova, B., &#38; Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>","ista":"Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 22(8), 2941–2955.","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>","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>."},"has_accepted_license":"1","external_id":{"pmid":["35765749"],"isi":["000825873600001"]},"_id":"11640","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","pmid":1,"article_processing_charge":"Yes (via OA deal)","corr_author":"1","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"publisher":"Wiley","volume":22,"author":[{"last_name":"Szep","full_name":"Szep, Eniko","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Trubenova","full_name":"Trubenova, Barbora","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"first_name":"Katalin","last_name":"Csilléry","full_name":"Csilléry, Katalin"}],"month":"11","department":[{"_id":"NiBa"}],"project":[{"grant_number":"704172","call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","name":"Rate of Adaptation in Changing Environment"}],"article_type":"original","oa":1,"doi":"10.1111/1755-0998.13676","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.","title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","date_created":"2022-07-24T22:01:43Z","oa_version":"Published Version","publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"file":[{"file_size":6431779,"date_created":"2023-02-02T08:11:23Z","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12477","creator":"dernst","date_updated":"2023-02-02T08:11:23Z","file_name":"2022_MolecularEcologyRes_Szep.pdf","checksum":"3102e203e77b884bffffdbe8e548da88"}],"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.","doi":"10.1093/jmicro/dfac037","oa":1,"article_type":"original","department":[{"_id":"LeSa"}],"month":"10","author":[{"first_name":"Christoph","full_name":"Gerle, Christoph","last_name":"Gerle"},{"first_name":"Jun-ichi","last_name":"Kishikawa","full_name":"Kishikawa, Jun-ichi"},{"last_name":"Yamaguchi","full_name":"Yamaguchi, Tomoko","first_name":"Tomoko"},{"first_name":"Atsuko","last_name":"Nakanishi","full_name":"Nakanishi, Atsuko"},{"full_name":"Çoruh, Mehmet Orkun","last_name":"Çoruh","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","first_name":"Mehmet Orkun","orcid":"0000-0002-3219-2022"},{"first_name":"Fumiaki","full_name":"Makino, Fumiaki","last_name":"Makino"},{"last_name":"Miyata","full_name":"Miyata, Tomoko","first_name":"Tomoko"},{"first_name":"Akihiro","last_name":"Kawamoto","full_name":"Kawamoto, Akihiro"},{"first_name":"Ken","last_name":"Yokoyama","full_name":"Yokoyama, Ken"},{"last_name":"Namba","full_name":"Namba, Keiichi","first_name":"Keiichi"},{"full_name":"Kurisu, Genji","last_name":"Kurisu","first_name":"Genji"},{"first_name":"Takayuki","last_name":"Kato","full_name":"Kato, Takayuki"}],"volume":71,"publisher":"Oxford University Press","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","pmid":1,"publication_status":"published","file":[{"file_size":7812696,"date_created":"2023-02-03T08:34:48Z","content_type":"application/pdf","success":1,"access_level":"open_access","creator":"dernst","date_updated":"2023-02-03T08:34:48Z","relation":"main_file","file_id":"12498","file_name":"2022_Microscopy_Gerle.pdf","checksum":"23b51c163636bf9313f7f0818312e67e"}],"publication_identifier":{"issn":["2050-5698"],"eissn":["2050-5701"]},"keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"oa_version":"Published Version","title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","date_created":"2022-07-25T10:04:58Z","file_date_updated":"2023-02-03T08:34:48Z","isi":1,"publication":"Microscopy","date_updated":"2023-08-03T12:13:37Z","page":"249-261","status":"public","scopus_import":"1","issue":"5","type":"journal_article","quality_controlled":"1","_id":"11648","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."}],"language":[{"iso":"eng"}],"external_id":{"pmid":["35861182"],"isi":["000837950900001"]},"has_accepted_license":"1","day":"01","citation":{"mla":"Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>, vol. 71, no. 5, Oxford University Press, 2022, pp. 249–61, doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>.","ieee":"C. Gerle <i>et al.</i>, “Structures of multisubunit membrane complexes with the CRYO ARM 200,” <i>Microscopy</i>, vol. 71, no. 5. Oxford University Press, pp. 249–261, 2022.","short":"C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino, T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy 71 (2022) 249–261.","apa":"Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino, F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>","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>","ista":"Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.","chicago":"Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>."},"year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"intvolume":"        71","date_published":"2022-10-01T00:00:00Z"},{"department":[{"_id":"NiBa"}],"month":"01","date_updated":"2025-06-11T13:45:56Z","author":[{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","oa":1,"doi":"10.25338/B81931","related_material":{"record":[{"relation":"used_in_publication","id":"10604","status":"public"}]},"license":"https://creativecommons.org/publicdomain/zero/1.0/","publisher":"Dryad","status":"public","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"corr_author":"1","article_processing_charge":"No","day":"06","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>","mla":"Turelli, Michael, and Nicholas H. Barton. <i>Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","short":"M. Turelli, N.H. Barton, (2022).","chicago":"Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>.","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>","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>."},"type":"research_data_reference","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"}],"_id":"11686","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25338/B81931"}],"date_published":"2022-01-06T00:00:00Z","date_created":"2022-07-29T06:45:41Z","title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","year":"2022","ddc":["570"],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","keyword":["Biological sciences"]},{"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","publisher":"Zenodo","related_material":{"record":[{"id":"11451","status":"public","relation":"used_in_publication"}]},"oa":1,"doi":"10.5281/ZENODO.6542908","author":[{"first_name":"Mahsa","full_name":"Parvizian, Mahsa","last_name":"Parvizian"},{"last_name":"Duran Balsa","full_name":"Duran Balsa, Alejandra","first_name":"Alejandra"},{"full_name":"Pokratath, Rohan","last_name":"Pokratath","first_name":"Rohan"},{"full_name":"Kalha, Curran","last_name":"Kalha","first_name":"Curran"},{"last_name":"Lee","full_name":"Lee, Seungho","first_name":"Seungho"},{"first_name":"Dietger","last_name":"Van den Eynden","full_name":"Van den Eynden, Dietger"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","last_name":"Regoutz","full_name":"Regoutz, Anna"},{"full_name":"De Roo, Jonathan","last_name":"De Roo","first_name":"Jonathan"}],"date_updated":"2023-08-03T07:19:12Z","department":[{"_id":"MaIb"}],"month":"05","ddc":["540"],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2022","date_created":"2022-07-29T09:31:13Z","title":"Data for \"The chemistry of Cu3N and Cu3PdN nanocrystals\"","date_published":"2022-05-12T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.6542908","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Data underlying the figures in the publication \"The chemistry of Cu3N and Cu3PdN nanocrystals\" ","lang":"eng"}],"_id":"11695","type":"research_data_reference","day":"12","citation":{"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>","mla":"Parvizian, Mahsa, et al. <i>Data for “The Chemistry of Cu3N and Cu3PdN Nanocrystals.”</i> Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","ieee":"M. Parvizian <i>et al.</i>, “Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals.’” Zenodo, 2022.","short":"M. Parvizian, A. Duran Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, (2022).","chicago":"Parvizian, Mahsa, Alejandra Duran Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “Data for ‘The Chemistry of Cu3N and Cu3PdN Nanocrystals.’” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6542908\">https://doi.org/10.5281/ZENODO.6542908</a>.","ama":"Parvizian M, Duran Balsa A, Pokratath R, et al. Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>","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>."}},{"volume":17,"author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"last_name":"Forkert","full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L"},{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Maas, Jan","last_name":"Maas"},{"last_name":"Mugnolo","full_name":"Mugnolo, Delio","first_name":"Delio"}],"project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"article_type":"original","department":[{"_id":"JaMa"}],"month":"10","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.","oa":1,"doi":"10.3934/nhm.2022023","corr_author":"1","article_processing_charge":"No","publisher":"American Institute of Mathematical Sciences","publication_status":"published","date_created":"2022-07-31T22:01:46Z","title":"Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph","oa_version":"Preprint","arxiv":1,"publication_identifier":{"issn":["1556-1801"],"eissn":["1556-181X"]},"publication":"Networks and Heterogeneous Media","date_updated":"2025-04-14T07:27:47Z","isi":1,"issue":"5","ec_funded":1,"scopus_import":"1","status":"public","page":"687-717","day":"01","citation":{"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.","short":"M. Erbar, D.L. Forkert, J. Maas, D. Mugnolo, Networks and Heterogeneous Media 17 (2022) 687–717.","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>.","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>","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>."},"abstract":[{"lang":"eng","text":"This paper contains two contributions in the study of optimal transport on metric graphs. Firstly, we prove a Benamou–Brenier formula for the Wasserstein distance, which establishes the equivalence of static and dynamical optimal transport. Secondly, in the spirit of Jordan–Kinderlehrer–Otto, we show that McKean–Vlasov equations can be formulated as gradient flow of the free energy in the Wasserstein space of probability measures. The proofs of these results are based on careful regularisation arguments to circumvent some of the difficulties arising in metric graphs, namely, branching of geodesics and the failure of semi-convexity of entropy functionals in the Wasserstein space."}],"_id":"11700","language":[{"iso":"eng"}],"external_id":{"arxiv":["2105.05677"],"isi":["000812422100001"]},"type":"journal_article","quality_controlled":"1","date_published":"2022-10-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.05677"}],"intvolume":"        17","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","short":"CC BY (3.0)"},"article_processing_charge":"No","publisher":"IOP Publishing","acknowledgement":"The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","doi":"10.1088/1361-6544/abd613","oa":1,"author":[{"orcid":"0000-0002-9573-2962","first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio","last_name":"Agresti"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"volume":35,"article_type":"original","month":"08","department":[{"_id":"JuFi"}],"publication_identifier":{"eissn":["1361-6544"],"issn":["0951-7715"]},"arxiv":1,"title":"Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence","date_created":"2022-07-31T22:01:47Z","oa_version":"Published Version","publication_status":"published","file":[{"date_updated":"2022-08-01T10:39:36Z","creator":"dernst","file_id":"11715","relation":"main_file","file_name":"2022_Nonlinearity_Agresti.pdf","checksum":"997a4bff2dfbee3321d081328c2f1e1a","file_size":2122096,"date_created":"2022-08-01T10:39:36Z","success":1,"content_type":"application/pdf","access_level":"open_access"}],"status":"public","page":"4100-4210","issue":"8","scopus_import":"1","file_date_updated":"2022-08-01T10:39:36Z","date_updated":"2023-08-03T12:25:08Z","publication":"Nonlinearity","isi":1,"intvolume":"        35","year":"2022","ddc":["510"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-08-04T00:00:00Z","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"}],"_id":"11701","language":[{"iso":"eng"}],"external_id":{"arxiv":["2001.00512"],"isi":["000826695900001"]},"type":"journal_article","quality_controlled":"1","has_accepted_license":"1","citation":{"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.","ama":"Agresti A, Veraar M. Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence. <i>Nonlinearity</i>. 2022;35(8):4100-4210. doi:<a href=\"https://doi.org/10.1088/1361-6544/abd613\">10.1088/1361-6544/abd613</a>","chicago":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.” <i>Nonlinearity</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1361-6544/abd613\">https://doi.org/10.1088/1361-6544/abd613</a>.","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.","short":"A. Agresti, M. Veraar, Nonlinearity 35 (2022) 4100–4210.","mla":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.” <i>Nonlinearity</i>, vol. 35, no. 8, IOP Publishing, 2022, pp. 4100–210, doi:<a href=\"https://doi.org/10.1088/1361-6544/abd613\">10.1088/1361-6544/abd613</a>.","apa":"Agresti, A., &#38; Veraar, M. (2022). Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6544/abd613\">https://doi.org/10.1088/1361-6544/abd613</a>"},"day":"04"},{"status":"public","scopus_import":"1","issue":"30","file_date_updated":"2022-08-01T10:58:28Z","date_updated":"2025-05-14T11:01:10Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","article_number":"e2122147119","intvolume":"       119","date_published":"2022-07-18T00:00:00Z","quality_controlled":"1","type":"journal_article","external_id":{"pmid":["35858408"]},"_id":"11702","language":[{"iso":"eng"}],"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."}],"day":"18","citation":{"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>","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>.","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ieee":"N. H. Barton, “The ‘New Synthesis,’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30. National Academy of Sciences, 2022.","mla":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30, e2122147119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>.","apa":"Barton, N. H. (2022). The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>"},"has_accepted_license":"1","publisher":"National Academy of Sciences","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","pmid":1,"doi":"10.1073/pnas.2122147119","oa":1,"acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","department":[{"_id":"NiBa"}],"month":"07","article_type":"original","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"volume":119,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa_version":"Published Version","title":"The \"New Synthesis\"","date_created":"2022-07-31T22:01:47Z","publication_status":"published","file":[{"date_created":"2022-08-01T10:58:28Z","file_size":848511,"success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"11716","relation":"main_file","creator":"dernst","date_updated":"2022-08-01T10:58:28Z","file_name":"2022_PNAS_Barton.pdf","checksum":"06c866196a8957f0c37b8a121771c885"}]},{"pmid":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","publisher":"Public Library of Science","volume":18,"author":[{"full_name":"Toups, Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"},{"first_name":"John R.","full_name":"Pannell, John R.","last_name":"Pannell"}],"department":[{"_id":"BeVi"}],"month":"07","article_type":"original","project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"oa":1,"doi":"10.1371/journal.pgen.1010226","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.","title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","date_created":"2022-07-31T22:01:48Z","oa_version":"Published Version","publication_identifier":{"eissn":["1553-7404"]},"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2022-08-01T07:49:25Z","file_size":1620272,"checksum":"aa4c137f82635e700856c359dccfaa0a","file_name":"2022_PLoSGenetics_Toups.pdf","file_id":"11708","relation":"main_file","date_updated":"2022-08-01T07:49:25Z","creator":"dernst"}],"publication_status":"published","issue":"7","ec_funded":1,"scopus_import":"1","status":"public","publication":"PLoS Genetics","date_updated":"2025-04-14T07:41:20Z","isi":1,"file_date_updated":"2022-08-01T07:49:25Z","date_published":"2022-07-06T00:00:00Z","article_number":"e1010226","intvolume":"        18","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","day":"06","citation":{"short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022).","ieee":"M. A. Toups, B. Vicoso, and J. R. Pannell, “Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis,” <i>PLoS Genetics</i>, vol. 18, no. 7. Public Library of Science, 2022.","mla":"Toups, Melissa A., et al. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>, vol. 18, no. 7, e1010226, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>.","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>","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.","ama":"Toups MA, Vicoso B, Pannell JR. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. 2022;18(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>","chicago":"Toups, Melissa A, Beatriz Vicoso, and John R. Pannell. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>."},"has_accepted_license":"1","external_id":{"pmid":["35793353"],"isi":["000886643100006"]},"_id":"11703","abstract":[{"text":"Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.","lang":"eng"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article"}]