[{"article_processing_charge":"No","file":[{"relation":"main_file","file_id":"11597","content_type":"application/pdf","date_created":"2022-07-18T08:15:24Z","success":1,"file_size":3146207,"creator":"dernst","file_name":"2022_GenomeBiology_Zhang.pdf","checksum":"2c30ef84151d257a6b835b4e069b70ac","access_level":"open_access","date_updated":"2022-07-18T08:15:24Z"}],"article_number":"149","date_published":"2022-07-07T00:00:00Z","_id":"11587","abstract":[{"lang":"eng","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."}],"publication_status":"published","oa":1,"file_date_updated":"2022-07-18T08:15:24Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":23,"article_type":"original","year":"2022","oa_version":"Published Version","has_accepted_license":"1","scopus_import":"1","external_id":{"isi":["000821915500002"]},"date_updated":"2023-08-03T12:04:18Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1474-760X"]},"month":"07","date_created":"2022-07-17T22:01:53Z","publisher":"BioMed Central","isi":1,"publication":"Genome Biology","department":[{"_id":"FyKo"}],"quality_controlled":"1","intvolume":"        23","status":"public","citation":{"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).","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>","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.","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.","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>."},"title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","day":"07","author":[{"last_name":"Zhang","first_name":"Runxuan","full_name":"Zhang, Runxuan"},{"last_name":"Kuo","first_name":"Richard","full_name":"Kuo, Richard"},{"full_name":"Coulter, Max","first_name":"Max","last_name":"Coulter"},{"last_name":"Calixto","full_name":"Calixto, Cristiane P.G.","first_name":"Cristiane P.G."},{"last_name":"Entizne","first_name":"Juan Carlos","full_name":"Entizne, Juan Carlos"},{"last_name":"Guo","full_name":"Guo, Wenbin","first_name":"Wenbin"},{"first_name":"Yamile","full_name":"Marquez, Yamile","last_name":"Marquez"},{"last_name":"Milne","first_name":"Linda","full_name":"Milne, Linda"},{"id":"FF6018E0-D806-11E9-8E43-0B14E6697425","orcid":"0000-0003-3413-1343","first_name":"Stefan","full_name":"Riegler, Stefan","last_name":"Riegler"},{"last_name":"Matsui","first_name":"Akihiro","full_name":"Matsui, Akihiro"},{"full_name":"Tanaka, Maho","first_name":"Maho","last_name":"Tanaka"},{"first_name":"Sarah","full_name":"Harvey, Sarah","last_name":"Harvey"},{"full_name":"Gao, Yubang","first_name":"Yubang","last_name":"Gao"},{"first_name":"Theresa","full_name":"Wießner-Kroh, Theresa","last_name":"Wießner-Kroh"},{"first_name":"Alejandro","full_name":"Paniagua, Alejandro","last_name":"Paniagua"},{"last_name":"Crespi","full_name":"Crespi, Martin","first_name":"Martin"},{"last_name":"Denby","first_name":"Katherine","full_name":"Denby, Katherine"},{"full_name":"Hur, Asa Ben","first_name":"Asa Ben","last_name":"Hur"},{"last_name":"Huq","full_name":"Huq, Enamul","first_name":"Enamul"},{"last_name":"Jantsch","first_name":"Michael","full_name":"Jantsch, Michael"},{"first_name":"Artur","full_name":"Jarmolowski, Artur","last_name":"Jarmolowski"},{"last_name":"Koester","first_name":"Tino","full_name":"Koester, Tino"},{"last_name":"Laubinger","first_name":"Sascha","full_name":"Laubinger, Sascha"},{"full_name":"Li, Qingshun Quinn","first_name":"Qingshun Quinn","last_name":"Li"},{"first_name":"Lianfeng","full_name":"Gu, Lianfeng","last_name":"Gu"},{"last_name":"Seki","first_name":"Motoaki","full_name":"Seki, Motoaki"},{"last_name":"Staiger","full_name":"Staiger, Dorothee","first_name":"Dorothee"},{"full_name":"Sunkar, Ramanjulu","first_name":"Ramanjulu","last_name":"Sunkar"},{"first_name":"Zofia","full_name":"Szweykowska-Kulinska, Zofia","last_name":"Szweykowska-Kulinska"},{"full_name":"Tu, Shih Long","first_name":"Shih Long","last_name":"Tu"},{"full_name":"Wachter, Andreas","first_name":"Andreas","last_name":"Wachter"},{"first_name":"Robbie","full_name":"Waugh, Robbie","last_name":"Waugh"},{"full_name":"Xiong, Liming","first_name":"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","first_name":"Anireddy S.N.","full_name":"Reddy, Anireddy S.N."},{"full_name":"Barta, Andrea","first_name":"Andrea","last_name":"Barta"},{"first_name":"Maria","full_name":"Kalyna, Maria","last_name":"Kalyna"},{"full_name":"Brown, John W.S.","first_name":"John W.S.","last_name":"Brown"}],"type":"journal_article","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.","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1186/s13059-022-02711-0"},{"date_created":"2022-07-17T22:01:54Z","month":"07","page":"1669-1680","status":"public","intvolume":"       107","publication":"Haematologica","department":[{"_id":"MiSi"}],"quality_controlled":"1","isi":1,"publisher":"Ferrata Storti Foundation","author":[{"last_name":"Nicolai","full_name":"Nicolai, Leo","first_name":"Leo"},{"first_name":"Rainer","full_name":"Kaiser, Rainer","last_name":"Kaiser"},{"full_name":"Escaig, Raphael","first_name":"Raphael","last_name":"Escaig"},{"first_name":"Marie Louise","full_name":"Hoffknecht, Marie Louise","last_name":"Hoffknecht"},{"full_name":"Anjum, Afra","first_name":"Afra","last_name":"Anjum"},{"last_name":"Leunig","first_name":"Alexander","full_name":"Leunig, Alexander"},{"full_name":"Pircher, Joachim","first_name":"Joachim","last_name":"Pircher"},{"first_name":"Andreas","full_name":"Ehrlich, Andreas","last_name":"Ehrlich"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"first_name":"Hellen","full_name":"Ishikawa-Ankerhold, Hellen","last_name":"Ishikawa-Ankerhold"},{"last_name":"Aird","first_name":"William C.","full_name":"Aird, William C."},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","last_name":"Gärtner","full_name":"Gärtner, Florian R","first_name":"Florian R"}],"type":"journal_article","day":"01","title":"Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo","citation":{"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>.","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.","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.","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.","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>","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>"},"ec_funded":1,"ddc":["570"],"doi":"10.3324/haematol.2021.278896","language":[{"iso":"eng"}],"project":[{"grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"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]). ","abstract":[{"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.","lang":"eng"}],"_id":"11588","date_published":"2022-07-01T00:00:00Z","file":[{"content_type":"application/pdf","file_id":"11595","relation":"main_file","success":1,"date_created":"2022-07-18T07:51:55Z","file_name":"2022_Haematologica_Nicolai.pdf","file_size":1722094,"creator":"dernst","date_updated":"2022-07-18T07:51:55Z","access_level":"open_access","checksum":"9b47830945f3c30428fe9cfee2dc4a8a"}],"article_processing_charge":"No","issue":"7","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"volume":107,"file_date_updated":"2022-07-18T07:51:55Z","oa":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","has_accepted_license":"1","oa_version":"Published Version","year":"2022","article_type":"original","publication_identifier":{"eissn":["1592-8721"],"issn":["0390-6078"]},"scopus_import":"1","external_id":{"isi":["000823746100018"]},"date_updated":"2023-08-03T12:01:01Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"has_accepted_license":"1","year":"2022","oa_version":"Published Version","article_type":"original","publication_identifier":{"eissn":["1664-462X"]},"scopus_import":"1","external_id":{"isi":["000819250500001"],"pmid":["35783951"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:01:47Z","article_processing_charge":"No","_id":"11589","abstract":[{"lang":"eng","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."}],"date_published":"2022-06-16T00:00:00Z","article_number":"862398","file":[{"file_name":"2022_FrontiersPlantScience_Wang.pdf","creator":"dernst","file_size":5040638,"date_updated":"2022-07-18T08:05:15Z","access_level":"open_access","checksum":"95313515637c0f84de591d204375d764","content_type":"application/pdf","relation":"main_file","file_id":"11596","success":1,"date_created":"2022-07-18T08:05:15Z"}],"oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":13,"file_date_updated":"2022-07-18T08:05:15Z","title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","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.","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.","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>.","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>.","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022).","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>","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>"},"type":"journal_article","author":[{"full_name":"Wang, Ren","first_name":"Ren","last_name":"Wang"},{"first_name":"Ellie","full_name":"Himschoot, Ellie","last_name":"Himschoot"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"last_name":"Boudsocq","first_name":"Marie","full_name":"Boudsocq, Marie"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"}],"day":"16","pmid":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.3389/fpls.2022.1100792"}]},"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.","doi":"10.3389/fpls.2022.862398","ddc":["580"],"language":[{"iso":"eng"}],"date_created":"2022-07-17T22:01:54Z","month":"06","isi":1,"publisher":"Frontiers","intvolume":"        13","status":"public","publication":"Frontiers in Plant Science","quality_controlled":"1","department":[{"_id":"JiFr"}]},{"date_created":"2022-07-17T22:01:55Z","month":"06","isi":1,"publisher":"IOP Publishing","intvolume":"        24","status":"public","quality_controlled":"1","department":[{"_id":"MiLe"}],"publication":"New Journal of Physics","title":"Artificial atoms from cold bosons in one dimension","ec_funded":1,"citation":{"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>.","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.","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.","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)."},"type":"journal_article","author":[{"full_name":"Brauneis, Fabian","first_name":"Fabian","last_name":"Brauneis"},{"last_name":"Backert","first_name":"Timothy G.","full_name":"Backert, Timothy G."},{"first_name":"Simeon I.","full_name":"Mistakidis, Simeon I.","last_name":"Mistakidis"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"full_name":"Hammer, Hans Werner","first_name":"Hans Werner","last_name":"Hammer"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","full_name":"Volosniev, Artem","last_name":"Volosniev"}],"day":"01","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.","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ddc":["530"],"doi":"10.1088/1367-2630/ac78d8","language":[{"iso":"eng"}],"issue":"6","article_processing_charge":"No","date_published":"2022-06-01T00:00:00Z","_id":"11590","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"}],"article_number":"063036","file":[{"date_updated":"2022-07-18T06:33:13Z","access_level":"open_access","checksum":"dc67b60f2e50e9ef2bd820ca0d7333d2","file_name":"2022_NewJournalPhysics_Brauneis.pdf","file_size":3415721,"creator":"dernst","success":1,"date_created":"2022-07-18T06:33:13Z","content_type":"application/pdf","relation":"main_file","file_id":"11594"}],"oa":1,"publication_status":"published","volume":24,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2022-07-18T06:33:13Z","has_accepted_license":"1","year":"2022","oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["1367-2630"]},"date_updated":"2023-08-03T11:57:41Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000818530000001"]}},{"oa_version":"Preprint","year":"2022","article_type":"original","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"date_updated":"2023-08-03T11:58:16Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000824330200003"],"arxiv":["2204.02993"]},"scopus_import":"1","issue":"6","article_processing_charge":"No","arxiv":1,"_id":"11591","date_published":"2022-06-29T00:00:00Z","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."}],"article_number":"062454","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2204.02993"}],"oa":1,"publication_status":"published","volume":105,"title":"Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams","ec_funded":1,"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.","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.","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>.","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>.","short":"J. Agustí, Y. Minoguchi, J.M. Fink, P. Rabl, Physical Review A 105 (2022).","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>","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>"},"author":[{"last_name":"Agustí","full_name":"Agustí, J.","first_name":"J."},{"last_name":"Minoguchi","first_name":"Y.","full_name":"Minoguchi, Y."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink"},{"full_name":"Rabl, P.","first_name":"P.","last_name":"Rabl"}],"type":"journal_article","day":"29","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].","project":[{"call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits"}],"doi":"10.1103/PhysRevA.105.062454","language":[{"iso":"eng"}],"date_created":"2022-07-17T22:01:55Z","month":"06","isi":1,"publisher":"American Physical Society","intvolume":"       105","status":"public","quality_controlled":"1","department":[{"_id":"JoFi"}],"publication":"Physical Review A"},{"scopus_import":"1","external_id":{"arxiv":["2206.03924"],"isi":["000829758500010"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:00:11Z","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"article_type":"original","oa_version":"Preprint","year":"2022","volume":105,"publication_status":"published","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2206.03924","open_access":"1"}],"oa":1,"article_number":"063329","_id":"11592","date_published":"2022-06-30T00:00:00Z","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."}],"arxiv":1,"article_processing_charge":"No","issue":"6","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.105.063329","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).","day":"30","type":"journal_article","author":[{"last_name":"Bighin","full_name":"Bighin, Giacomo","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777"},{"last_name":"Cappellaro","full_name":"Cappellaro, Alberto","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359"},{"last_name":"Salasnich","full_name":"Salasnich, L.","first_name":"L."}],"citation":{"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>.","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.","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.","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).","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>","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>"},"title":"Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations","publication":"Physical Review A","department":[{"_id":"MiLe"}],"quality_controlled":"1","status":"public","intvolume":"       105","publisher":"American Physical Society","isi":1,"month":"06","date_created":"2022-07-17T22:01:55Z"},{"abstract":[{"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.","lang":"eng"}],"_id":"11593","date_published":"2022-09-01T00:00:00Z","article_processing_charge":"No","arxiv":1,"volume":68,"main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"oa":1,"publication_status":"published","year":"2022","oa_version":"Preprint","article_type":"original","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"external_id":{"isi":["000825014500001"],"arxiv":["1803.05085"]},"scopus_import":"1","date_updated":"2023-08-14T12:43:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-07-17T22:01:56Z","month":"09","page":"425-447","intvolume":"        68","status":"public","publication":"Discrete and Computational Geometry","department":[{"_id":"UlWa"}],"quality_controlled":"1","isi":1,"publisher":"Springer Nature","type":"journal_article","author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"}],"day":"01","title":"The Z2-Genus of Kuratowski minors","citation":{"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>.","ista":"Fulek R, Kynčl J. 2022. The Z2-Genus of Kuratowski minors. Discrete and Computational Geometry. 68, 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.","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>.","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>","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>","short":"R. Fulek, J. Kynčl, Discrete and Computational Geometry 68 (2022) 425–447."},"doi":"10.1007/s00454-022-00412-w","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"186","relation":"earlier_version"}]},"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"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."},{"abstract":[{"text":"The Sun’s surface hosts varying magnetic activities and rotation rates (from equator to pole), and unique solar weather. Now, a combination of ground and space observations has unveiled a previously undetected magnetized plasma current.","lang":"eng"}],"_id":"11600","date_published":"2022-05-18T00:00:00Z","date_created":"2022-07-18T09:34:37Z","extern":"1","month":"05","article_processing_charge":"No","page":"631-632","volume":6,"intvolume":"         6","status":"public","quality_controlled":"1","publication":"Nature Astronomy","publication_status":"published","publisher":"Springer Nature","year":"2022","oa_version":"None","author":[{"last_name":"Bugnet","first_name":"Lisa Annabelle","full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501"}],"type":"journal_article","day":"18","article_type":"letter_note","title":"Hidden currents at the Sun’s surface","citation":{"ama":"Bugnet LA. Hidden currents at the Sun’s surface. <i>Nature Astronomy</i>. 2022;6:631-632. doi:<a href=\"https://doi.org/10.1038/s41550-022-01683-2\">10.1038/s41550-022-01683-2</a>","apa":"Bugnet, L. A. (2022). Hidden currents at the Sun’s surface. <i>Nature Astronomy</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41550-022-01683-2\">https://doi.org/10.1038/s41550-022-01683-2</a>","short":"L.A. Bugnet, Nature Astronomy 6 (2022) 631–632.","mla":"Bugnet, Lisa Annabelle. “Hidden Currents at the Sun’s Surface.” <i>Nature Astronomy</i>, vol. 6, Springer Nature, 2022, pp. 631–32, doi:<a href=\"https://doi.org/10.1038/s41550-022-01683-2\">10.1038/s41550-022-01683-2</a>.","chicago":"Bugnet, Lisa Annabelle. “Hidden Currents at the Sun’s Surface.” <i>Nature Astronomy</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41550-022-01683-2\">https://doi.org/10.1038/s41550-022-01683-2</a>.","ieee":"L. A. Bugnet, “Hidden currents at the Sun’s surface,” <i>Nature Astronomy</i>, vol. 6. Springer Nature, pp. 631–632, 2022.","ista":"Bugnet LA. 2022. Hidden currents at the Sun’s surface. Nature Astronomy. 6, 631–632."},"doi":"10.1038/s41550-022-01683-2","publication_identifier":{"eissn":["2397-3366"]},"date_updated":"2022-08-19T09:52:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"keyword":["Astronomy and Astrophysics"],"scopus_import":"1"},{"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.05455"}],"volume":926,"arxiv":1,"article_processing_charge":"No","issue":"2","article_number":"191","_id":"11601","date_published":"2022-02-24T00:00:00Z","abstract":[{"lang":"eng","text":"We present the third and final data release of the K2 Galactic Archaeology Program (K2 GAP) for Campaigns C1–C8 and C10–C18. We provide asteroseismic radius and mass coefficients, κR and κM, for ∼19,000 red giant stars, which translate directly to radius and mass given a temperature. As such, K2 GAP DR3 represents the largest asteroseismic sample in the literature to date. K2 GAP DR3 stellar parameters are calibrated to be on an absolute parallactic scale based on Gaia DR2, with red giant branch and red clump evolutionary state classifications provided via a machine-learning approach. Combining these stellar parameters with GALAH DR3 spectroscopy, we determine asteroseismic ages with precisions of ∼20%–30% and compare age-abundance relations to Galactic chemical evolution models among both low- and high-α populations for α, light, iron-peak, and neutron-capture elements. We confirm recent indications in the literature of both increased Ba production at late Galactic times as well as significant contributions to r-process enrichment from prompt sources associated with, e.g., core-collapse supernovae. With an eye toward other Galactic archeology applications, we characterize K2 GAP DR3 uncertainties and completeness using injection tests, suggesting that K2 GAP DR3 is largely unbiased in mass/age, with uncertainties of 2.9% (stat.) ± 0.1% (syst.) and 6.7% (stat.) ± 0.3% (syst.) in κR and κM for red giant branch stars and 4.7% (stat.) ± 0.3% (syst.) and 11% (stat.) ± 0.9% (syst.) for red clump stars. We also identify percent-level asteroseismic systematics, which are likely related to the time baseline of the underlying data, and which therefore should be considered in TESS asteroseismic analysis."}],"scopus_import":"1","external_id":{"arxiv":["2108.05455"]},"date_updated":"2022-08-19T09:52:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"article_type":"original","oa_version":"Preprint","year":"2022","publisher":"IOP Publishing","publication":"The Astrophysical Journal","quality_controlled":"1","intvolume":"       926","status":"public","month":"02","extern":"1","date_created":"2022-07-18T10:57:30Z","acknowledgement":"We would like to thank the anonymous referee whose comments significantly improved the manuscript. J.C.Z. is supported by an NSF Astronomy and Astrophysics Postdoctoral Fellowship under award AST-2001869. J.C.Z. and M.H.P. acknowledge support from NASA grants 80NSSC18K0391 and NNX17AJ40G. Y.E. and C.J. acknowledge the support of the UK Science and Technology Facilities Council (STFC). S.M. acknowledges support from the Spanish Ministry of Science and Innovation with the Ramon y Cajal fellowship number RYC-2015-17697 and the grant number PID2019-107187GB-I00. R.A.G. acknowledges funding received from the PLATO CNES grant. C.K. acknowledges funding from the UK Science and Technology Facilities Council (STFC) through grants ST/M000958/1, ST/R000905/1, and ST/V000632/1.\r\n\r\nFunding for the Stellar Astrophysics Centre (SAC) is provided by the Danish National Research Foundation (grant agreement No. DNRF106).\r\n\r\nThe K2 Galactic Archaeology Program is supported by the National Aeronautics and Space Administration under grant NNX16AJ17G issued through the K2 Guest Observer Program. This publication makes use of data products from the Two Micron All Sky Survey, which is a joint project of the University of Massachusetts and the Infrared Processing and Analysis Center/California Institute of Technology, funded by the National Aeronautics and Space Administration and the National Science Foundation.\r\n\r\nThis paper includes data collected by the Kepler mission. Funding for the Kepler mission is provided by the NASA Science Mission directorate.\r\n\r\nParts of this research were supported by the Australian Research Council Centre of Excellence for All Sky Astrophysics in 3 Dimensions (ASTRO 3D), through project number CE170100013.\r\n\r\nThis research was partially conducted during the Exostar19 program at the Kavli Institute for Theoretical Physics at UC Santa Barbara, which was supported in part by the National Science Foundation under grant No. NSF PHY-1748958.\r\n\r\nBased in part on data obtained at Siding Spring Observatory via GALAH. We acknowledge the traditional owners of the land on which the AAT stands, the Gamilaraay people, and pay our respects to elders past and present.\r\n\r\nThis work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement.\r\n\r\nFunding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. SDSS-IV acknowledges support and resources from the Center for High-Performance Computing at the University of Utah (www.sdss.org).\r\n\r\nSoftware: asfgrid (Sharma & Stello 2016), corner (Foreman-Mackey 2016), emcee (Foreman-Mackey et al. 2013), NumPy (Walt 2011), pandas (McKinney 2010), Matplotlib (Hunter 2007), IPython (Pérez & Granger 2007), SciPy (Virtanen et al.2020).","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"language":[{"iso":"eng"}],"doi":"10.3847/1538-4357/ac2c83","citation":{"mla":"Zinn, Joel C., et al. “The K2 Galactic Archaeology Program Data Release 3: Age-Abundance Patterns in C1–C8 and C10–C18.” <i>The Astrophysical Journal</i>, vol. 926, no. 2, 191, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.3847/1538-4357/ac2c83\">10.3847/1538-4357/ac2c83</a>.","ieee":"J. C. Zinn <i>et al.</i>, “The K2 Galactic Archaeology Program data release 3: Age-abundance patterns in C1–C8 and C10–C18,” <i>The Astrophysical Journal</i>, vol. 926, no. 2. IOP Publishing, 2022.","ista":"Zinn JC, Stello D, Elsworth Y, García RA, Kallinger T, Mathur S, Mosser B, Hon M, Bugnet LA, Jones C, Reyes C, Sharma S, Schönrich R, Warfield JT, Luger R, Vanderburg A, Kobayashi C, Pinsonneault MH, Johnson JA, Huber D, Buder S, Joyce M, Bland-Hawthorn J, Casagrande L, Lewis GF, Miglio A, Nordlander T, Davies GR, Silva GD, Chaplin WJ, Silva Aguirre V. 2022. The K2 Galactic Archaeology Program data release 3: Age-abundance patterns in C1–C8 and C10–C18. The Astrophysical Journal. 926(2), 191.","chicago":"Zinn, Joel C., Dennis Stello, Yvonne Elsworth, Rafael A. García, Thomas Kallinger, Savita Mathur, Benoît Mosser, et al. “The K2 Galactic Archaeology Program Data Release 3: Age-Abundance Patterns in C1–C8 and C10–C18.” <i>The Astrophysical Journal</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.3847/1538-4357/ac2c83\">https://doi.org/10.3847/1538-4357/ac2c83</a>.","apa":"Zinn, J. C., Stello, D., Elsworth, Y., García, R. A., Kallinger, T., Mathur, S., … Silva Aguirre, V. (2022). The K2 Galactic Archaeology Program data release 3: Age-abundance patterns in C1–C8 and C10–C18. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ac2c83\">https://doi.org/10.3847/1538-4357/ac2c83</a>","ama":"Zinn JC, Stello D, Elsworth Y, et al. The K2 Galactic Archaeology Program data release 3: Age-abundance patterns in C1–C8 and C10–C18. <i>The Astrophysical Journal</i>. 2022;926(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ac2c83\">10.3847/1538-4357/ac2c83</a>","short":"J.C. Zinn, D. Stello, Y. Elsworth, R.A. García, T. Kallinger, S. Mathur, B. Mosser, M. Hon, L.A. Bugnet, C. Jones, C. Reyes, S. Sharma, R. Schönrich, J.T. Warfield, R. Luger, A. Vanderburg, C. Kobayashi, M.H. Pinsonneault, J.A. Johnson, D. Huber, S. Buder, M. Joyce, J. Bland-Hawthorn, L. Casagrande, G.F. Lewis, A. Miglio, T. Nordlander, G.R. Davies, G.D. Silva, W.J. Chaplin, V. Silva Aguirre, The Astrophysical Journal 926 (2022)."},"title":"The K2 Galactic Archaeology Program data release 3: Age-abundance patterns in C1–C8 and C10–C18","day":"24","author":[{"first_name":"Joel C.","full_name":"Zinn, Joel C.","last_name":"Zinn"},{"first_name":"Dennis","full_name":"Stello, Dennis","last_name":"Stello"},{"last_name":"Elsworth","full_name":"Elsworth, Yvonne","first_name":"Yvonne"},{"last_name":"García","first_name":"Rafael A.","full_name":"García, Rafael A."},{"last_name":"Kallinger","full_name":"Kallinger, Thomas","first_name":"Thomas"},{"full_name":"Mathur, Savita","first_name":"Savita","last_name":"Mathur"},{"last_name":"Mosser","full_name":"Mosser, Benoît","first_name":"Benoît"},{"first_name":"Marc","full_name":"Hon, Marc","last_name":"Hon"},{"full_name":"Bugnet, Lisa Annabelle","first_name":"Lisa Annabelle","last_name":"Bugnet","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000"},{"full_name":"Jones, Caitlin","first_name":"Caitlin","last_name":"Jones"},{"last_name":"Reyes","first_name":"Claudia","full_name":"Reyes, Claudia"},{"first_name":"Sanjib","full_name":"Sharma, Sanjib","last_name":"Sharma"},{"first_name":"Ralph","full_name":"Schönrich, Ralph","last_name":"Schönrich"},{"first_name":"Jack T.","full_name":"Warfield, Jack T.","last_name":"Warfield"},{"first_name":"Rodrigo","full_name":"Luger, Rodrigo","last_name":"Luger"},{"first_name":"Andrew","full_name":"Vanderburg, Andrew","last_name":"Vanderburg"},{"first_name":"Chiaki","full_name":"Kobayashi, Chiaki","last_name":"Kobayashi"},{"last_name":"Pinsonneault","first_name":"Marc H.","full_name":"Pinsonneault, Marc H."},{"last_name":"Johnson","full_name":"Johnson, Jennifer A.","first_name":"Jennifer A."},{"last_name":"Huber","first_name":"Daniel","full_name":"Huber, Daniel"},{"last_name":"Buder","full_name":"Buder, Sven","first_name":"Sven"},{"last_name":"Joyce","first_name":"Meridith","full_name":"Joyce, Meridith"},{"last_name":"Bland-Hawthorn","full_name":"Bland-Hawthorn, Joss","first_name":"Joss"},{"last_name":"Casagrande","full_name":"Casagrande, Luca","first_name":"Luca"},{"first_name":"Geraint F.","full_name":"Lewis, Geraint F.","last_name":"Lewis"},{"first_name":"Andrea","full_name":"Miglio, Andrea","last_name":"Miglio"},{"last_name":"Nordlander","full_name":"Nordlander, Thomas","first_name":"Thomas"},{"last_name":"Davies","full_name":"Davies, Guy R.","first_name":"Guy R."},{"first_name":"Gayandhi De","full_name":"Silva, Gayandhi De","last_name":"Silva"},{"last_name":"Chaplin","full_name":"Chaplin, William J.","first_name":"William J."},{"last_name":"Silva Aguirre","first_name":"Victor","full_name":"Silva Aguirre, Victor"}],"type":"journal_article"},{"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"external_id":{"arxiv":["2109.14058"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-08-19T09:56:58Z","oa_version":"Preprint","year":"2022","article_type":"original","volume":657,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2109.14058"}],"oa":1,"publication_status":"published","_id":"11602","abstract":[{"lang":"eng","text":"During the survey phase of the Kepler mission, several thousand stars were observed in short cadence, allowing for the detection of solar-like oscillations in more than 500 main-sequence and subgiant stars. These detections showed the power of asteroseismology in determining fundamental stellar parameters. However, the Kepler Science Office discovered an issue in the calibration that affected half of the store of short-cadence data, leading to a new data release (DR25) with corrections on the light curves. In this work, we re-analyzed the one-month time series of the Kepler survey phase to search for solar-like oscillations that might have been missed when using the previous data release. We studied the seismic parameters of 99 stars, among which there are 46 targets with new reported solar-like oscillations, increasing, by around 8%, the known sample of solar-like stars with an asteroseismic analysis of the short-cadence data from this mission. The majority of these stars have mid- to high-resolution spectroscopy publicly available with the LAMOST and APOGEE surveys, respectively, as well as precise Gaia parallaxes. We computed the masses and radii using seismic scaling relations and we find that this new sample features massive stars (above 1.2 M⊙ and up to 2 M⊙) and subgiants. We determined the granulation parameters and amplitude of the modes, which agree with the scaling relations derived for dwarfs and subgiants. The stars studied here are slightly fainter than the previously known sample of main-sequence and subgiants with asteroseismic detections. We also studied the surface rotation and magnetic activity levels of those stars. Our sample of 99 stars has similar levels of activity compared to the previously known sample and is in the same range as the Sun between the minimum and maximum of its activity cycle. We find that for seven stars, a possible blend could be the reason for the non-detection with the early data release. Finally, we compared the radii obtained from the scaling relations with the Gaia ones and we find that the Gaia radii are overestimated by 4.4%, on average, compared to the seismic radii, with a scatter of 12.3% and a decreasing trend according to the evolutionary stage. In addition, for homogeneity purposes, we re-analyzed the DR25 of the main-sequence and subgiant stars with solar-like oscillations that were previously detected and, as a result, we provide the global seismic parameters for a total of 525 stars."}],"date_published":"2022-01-01T00:00:00Z","article_number":"A31","article_processing_charge":"No","arxiv":1,"doi":"10.1051/0004-6361/202141168","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"language":[{"iso":"eng"}],"acknowledgement":"This paper includes data collected by the Kepler mission. Funding for the Kepler mission is provided by the NASA Science Mission directorate. Some of the data presented in this paper were obtained from the Mikulski Archive for Space Telescopes (MAST). STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. S. M. acknowledges support by the Spanish Ministry of Science and Innovation with the Ramon y Cajal fellowship number RYC-2015-17697 and the grant number PID2019-107187GB-I00. R. A. G. and S. N. B acknowledge the support from PLATO and GOLF CNES grants. A. R. G. S. acknowledges the support from National Aeronautics and Space Administration under Grant NNX17AF27G and STFC consolidated grant ST/T000252/1. D.H. acknowledges support from the Alfred P. Sloan Foundation, the National Aeronautics and Space Administration (80NSSC19K0597), and the National Science Foundation (AST-1717000). M.S. is supported by the Research Corporation for Science Advancement through Scialog award #26080. Guoshoujing Telescope (the Large Sky Area Multi-Object Fiber Spectroscopic Telescope LAMOST) is a National Major Scientific Project built by the Chinese Academy of Sciences. Funding for the project has been provided by the National Development and Reform Commission. LAMOST is operated and managed by the National Astronomical Observatories, Chinese Academy of Sciences.","type":"journal_article","author":[{"first_name":"S.","full_name":"Mathur, S.","last_name":"Mathur"},{"last_name":"García","full_name":"García, R. A.","first_name":"R. A."},{"last_name":"Breton","first_name":"S.","full_name":"Breton, S."},{"last_name":"Santos","full_name":"Santos, A. R. G.","first_name":"A. R. G."},{"full_name":"Mosser, B.","first_name":"B.","last_name":"Mosser"},{"last_name":"Huber","first_name":"D.","full_name":"Huber, D."},{"last_name":"Sayeed","full_name":"Sayeed, M.","first_name":"M."},{"last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000"},{"last_name":"Chontos","first_name":"A.","full_name":"Chontos, A."}],"day":"01","title":"Detections of solar-like oscillations in dwarfs and subgiants with Kepler DR25 short-cadence data","citation":{"chicago":"Mathur, S., R. A. García, S. Breton, A. R. G. Santos, B. Mosser, D. Huber, M. Sayeed, Lisa Annabelle Bugnet, and A. Chontos. “Detections of Solar-like Oscillations in Dwarfs and Subgiants with Kepler DR25 Short-Cadence Data.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202141168\">https://doi.org/10.1051/0004-6361/202141168</a>.","ista":"Mathur S, García RA, Breton S, Santos ARG, Mosser B, Huber D, Sayeed M, Bugnet LA, Chontos A. 2022. Detections of solar-like oscillations in dwarfs and subgiants with Kepler DR25 short-cadence data. Astronomy &#38; Astrophysics. 657, A31.","ieee":"S. Mathur <i>et al.</i>, “Detections of solar-like oscillations in dwarfs and subgiants with Kepler DR25 short-cadence data,” <i>Astronomy &#38; Astrophysics</i>, vol. 657. EDP Sciences, 2022.","mla":"Mathur, S., et al. “Detections of Solar-like Oscillations in Dwarfs and Subgiants with Kepler DR25 Short-Cadence Data.” <i>Astronomy &#38; Astrophysics</i>, vol. 657, A31, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202141168\">10.1051/0004-6361/202141168</a>.","short":"S. Mathur, R.A. García, S. Breton, A.R.G. Santos, B. Mosser, D. Huber, M. Sayeed, L.A. Bugnet, A. Chontos, Astronomy &#38; Astrophysics 657 (2022).","ama":"Mathur S, García RA, Breton S, et al. Detections of solar-like oscillations in dwarfs and subgiants with Kepler DR25 short-cadence data. <i>Astronomy &#38; Astrophysics</i>. 2022;657. doi:<a href=\"https://doi.org/10.1051/0004-6361/202141168\">10.1051/0004-6361/202141168</a>","apa":"Mathur, S., García, R. A., Breton, S., Santos, A. R. G., Mosser, B., Huber, D., … Chontos, A. (2022). Detections of solar-like oscillations in dwarfs and subgiants with Kepler DR25 short-cadence data. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202141168\">https://doi.org/10.1051/0004-6361/202141168</a>"},"status":"public","intvolume":"       657","publication":"Astronomy & Astrophysics","quality_controlled":"1","publisher":"EDP Sciences","date_created":"2022-07-18T11:41:59Z","month":"01","extern":"1"},{"date_updated":"2022-08-22T07:58:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","external_id":{"arxiv":["2202.10026"]},"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"article_type":"original","year":"2022","oa_version":"Preprint","volume":661,"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2202.10026"}],"article_number":"A133","date_published":"2022-05-19T00:00:00Z","_id":"11621","abstract":[{"lang":"eng","text":"Context. Asteroseismology has revealed small core-to-surface rotation contrasts in stars in the whole Hertzsprung–Russell diagram. This is the signature of strong transport of angular momentum (AM) in stellar interiors. One of the plausible candidates to efficiently carry AM is magnetic fields with various topologies that could be present in stellar radiative zones. Among them, strong axisymmetric azimuthal (toroidal) magnetic fields have received a lot of interest. Indeed, if they are subject to the so-called Tayler instability, the accompanying triggered Maxwell stresses can transport AM efficiently. In addition, the electromotive force induced by the fluctuations of magnetic and velocity fields could potentially sustain a dynamo action that leads to the regeneration of the initial strong axisymmetric azimuthal magnetic field.\r\n\r\nAims. The key question we aim to answer is whether we can detect signatures of these deep strong azimuthal magnetic fields. The only way to answer this question is asteroseismology, and the best laboratories of study are intermediate-mass and massive stars with external radiative envelopes. Most of these are rapid rotators during their main sequence. Therefore, we have to study stellar pulsations propagating in stably stratified, rotating, and potentially strongly magnetised radiative zones, namely magneto-gravito-inertial (MGI) waves.\r\n\r\nMethods. We generalise the traditional approximation of rotation (TAR) by simultaneously taking general axisymmetric differential rotation and azimuthal magnetic fields into account. Both the Coriolis acceleration and the Lorentz force are therefore treated in a non-perturbative way. Using this new formalism, we derive the asymptotic properties of MGI waves and their period spacings.\r\n\r\nResults. We find that toroidal magnetic fields induce a shift in the period spacings of gravity (g) and Rossby (r) modes. An equatorial azimuthal magnetic field with an amplitude of the order of 105 G leads to signatures that are detectable in period spacings for high-radial-order g and r modes in γ Doradus (γ Dor) and slowly pulsating B (SPB) stars. More complex hemispheric configurations are more difficult to observe, particularly when they are localised out of the propagation region of MGI modes, which can be localised in an equatorial belt.\r\n\r\nConclusions. The magnetic TAR, which takes into account toroidal magnetic fields in a non-perturbative way, is derived. This new formalism allows us to assess the effects of the magnetic field in γ Dor and SPB stars on g and r modes. We find that these effects should be detectable for equatorial fields thanks to modern space photometry using observations from Kepler, TESS CVZ, and PLATO."}],"arxiv":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"keyword":["Space and Planetary Science","Astronomy and Astrophysics","magnetohydrodynamics (MHD) / waves / stars","rotation / stars: magnetic field / stars","oscillations / methods"],"doi":"10.1051/0004-6361/202142956","acknowledgement":"We thank the referee for her/his positive and constructive report, which has allowed us to improve the quality of our article. H.D. and S.M. acknowledge support from the CNES PLATO grant at CEA/DAp. T.V.R. gratefully acknowledges support from the Research Foundation Flanders (FWO) under grant agreement No. 12ZB620N and V414021N. This research was supported in part by the National Science Foundation under Grant No. NSF PHY-1748958. C.A. is supported by the KU Leuven Research Council (grant C16/18/005: PARADISE) as well as from the BELgian federal Science Policy Office (BELSPO) through a PLATO PRODEX grant.","day":"19","type":"journal_article","author":[{"first_name":"H.","full_name":"Dhouib, H.","last_name":"Dhouib"},{"last_name":"Mathis","first_name":"S.","full_name":"Mathis, S."},{"id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet"},{"last_name":"Van Reeth","first_name":"T.","full_name":"Van Reeth, T."},{"last_name":"Aerts","first_name":"C.","full_name":"Aerts, C."}],"citation":{"short":"H. Dhouib, S. Mathis, L.A. Bugnet, T. Van Reeth, C. Aerts, Astronomy &#38; Astrophysics 661 (2022).","ama":"Dhouib H, Mathis S, Bugnet LA, Van Reeth T, Aerts C. Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field. <i>Astronomy &#38; Astrophysics</i>. 2022;661. doi:<a href=\"https://doi.org/10.1051/0004-6361/202142956\">10.1051/0004-6361/202142956</a>","apa":"Dhouib, H., Mathis, S., Bugnet, L. A., Van Reeth, T., &#38; Aerts, C. (2022). Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202142956\">https://doi.org/10.1051/0004-6361/202142956</a>","chicago":"Dhouib, H., S. Mathis, Lisa Annabelle Bugnet, T. Van Reeth, and C. Aerts. “Detecting Deep Axisymmetric Toroidal Magnetic Fields in Stars: The Traditional Approximation of Rotation for Differentially Rotating Deep Spherical Shells with a General Azimuthal Magnetic Field.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202142956\">https://doi.org/10.1051/0004-6361/202142956</a>.","ieee":"H. Dhouib, S. Mathis, L. A. Bugnet, T. Van Reeth, and C. Aerts, “Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field,” <i>Astronomy &#38; Astrophysics</i>, vol. 661. EDP Sciences, 2022.","ista":"Dhouib H, Mathis S, Bugnet LA, Van Reeth T, Aerts C. 2022. Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field. Astronomy &#38; Astrophysics. 661, A133.","mla":"Dhouib, H., et al. “Detecting Deep Axisymmetric Toroidal Magnetic Fields in Stars: The Traditional Approximation of Rotation for Differentially Rotating Deep Spherical Shells with a General Azimuthal Magnetic Field.” <i>Astronomy &#38; Astrophysics</i>, vol. 661, A133, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202142956\">10.1051/0004-6361/202142956</a>."},"title":"Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field","quality_controlled":"1","publication":"Astronomy & Astrophysics","intvolume":"       661","status":"public","publisher":"EDP Sciences","extern":"1","month":"05","date_created":"2022-07-19T08:04:15Z"},{"file_date_updated":"2022-07-25T11:48:45Z","publication_status":"published","oa":1,"file":[{"file_name":"Thesis_Gallei.pdf","file_size":9730864,"creator":"mgallei","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","date_updated":"2022-07-25T09:08:47Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"11645","date_created":"2022-07-25T09:08:47Z"},{"file_id":"11646","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2022-07-25T09:09:09Z","file_size":19560720,"creator":"mgallei","file_name":"Thesis_Gallei_source.docx","access_level":"closed","date_updated":"2022-07-25T09:39:58Z","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb"},{"content_type":"application/pdf","relation":"source_file","file_id":"11647","date_created":"2022-07-25T09:09:32Z","file_name":"Thesis_Gallei_to_print.pdf","creator":"mgallei","file_size":24542837,"date_updated":"2022-07-25T09:39:58Z","access_level":"closed","description":"This is the print version of the thesis including the full appendix","checksum":"3994f7f20058941b5bb8a16886b21e71"},{"file_name":"Thesis_Gallei_Appendix.pdf","file_size":15435966,"creator":"mgallei","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","date_updated":"2022-07-25T11:48:45Z","access_level":"open_access","content_type":"application/pdf","file_id":"11650","relation":"main_file","date_created":"2022-07-25T11:48:45Z"}],"_id":"11626","date_published":"2022-07-20T00:00:00Z","abstract":[{"lang":"eng","text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth."}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-10-29T10:22:45Z","publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"year":"2022","has_accepted_license":"1","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"status":"public","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","month":"07","date_created":"2022-07-20T11:21:53Z","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"last_name":"Shani","first_name":"Eilon","full_name":"Shani, Eilon"}],"page":"248","language":[{"iso":"eng"}],"ddc":["575"],"doi":"10.15479/at:ista:11626","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9287"},{"status":"public","id":"7142","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7465"},{"relation":"part_of_dissertation","id":"8138","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6260"},{"status":"public","id":"8931","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10411"}]},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"day":"20","alternative_title":["ISTA Thesis"],"author":[{"last_name":"Gallei","full_name":"Gallei, Michelle C","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"}],"type":"dissertation","ec_funded":1,"citation":{"ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>.","mla":"Gallei, Michelle C. <i>Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","apa":"Gallei, M. C. (2022). <i>Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>"},"title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana"},{"publication_status":"published","oa":1,"file_date_updated":"2023-02-02T07:56:34Z","volume":83,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"arxiv":1,"issue":"10","article_processing_charge":"Yes (via OA deal)","article_number":"102085","file":[{"checksum":"3ca88decb1011180dc6de7e0862153e1","access_level":"open_access","date_updated":"2023-02-02T07:56:34Z","file_size":247615,"creator":"dernst","file_name":"2022_FiniteFields_Kmentt.pdf","date_created":"2023-02-02T07:56:34Z","success":1,"relation":"main_file","file_id":"12475","content_type":"application/pdf"}],"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"}],"_id":"11636","date_published":"2022-10-01T00:00:00Z","date_updated":"2023-08-03T12:12:57Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"arxiv":["2111.06697"],"isi":["000835490600001"]},"publication_identifier":{"issn":["10715797"],"eissn":["10902465"]},"article_type":"original","year":"2022","has_accepted_license":"1","oa_version":"Published Version","publisher":"Elsevier","isi":1,"quality_controlled":"1","department":[{"_id":"TiBr"}],"publication":"Finite Fields and their Applications","intvolume":"        83","status":"public","month":"10","date_created":"2022-07-24T22:01:41Z","language":[{"iso":"eng"}],"ddc":["510"],"doi":"10.1016/j.ffa.2022.102085","citation":{"short":"P. Kmentt, A.L. Shute, Finite Fields and Their Applications 83 (2022).","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>","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>","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>.","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.","ista":"Kmentt P, Shute AL. 2022. The Bertini irreducibility theorem for higher codimensional slices. Finite Fields and their Applications. 83(10), 102085.","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>."},"title":"The Bertini irreducibility theorem for higher codimensional slices","day":"01","type":"journal_article","author":[{"last_name":"Kmentt","full_name":"Kmentt, Philip","first_name":"Philip","id":"c90670c9-0bf0-11ed-86f5-ed522ece2fac"},{"id":"440EB050-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1812-2810","first_name":"Alec L","full_name":"Shute, Alec L","last_name":"Shute"}]},{"date_created":"2022-07-24T22:01:42Z","month":"06","intvolume":"        20","status":"public","publication":"PLoS Biology","department":[{"_id":"MaDe"}],"quality_controlled":"1","isi":1,"publisher":"Public Library of Science","type":"journal_article","author":[{"last_name":"Zhao","full_name":"Zhao, Lina","first_name":"Lina"},{"last_name":"Fenk","full_name":"Fenk, Lorenz A.","first_name":"Lorenz A."},{"first_name":"Lars","full_name":"Nilsson, Lars","last_name":"Nilsson"},{"id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","last_name":"Amin-Wetzel","full_name":"Amin-Wetzel, Niko Paresh","first_name":"Niko Paresh"},{"last_name":"Ramirez","full_name":"Ramirez, Nelson","first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"last_name":"De Bono","full_name":"De Bono, Mario","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","full_name":"Chen, Changchun","first_name":"Changchun"}],"day":"21","title":"ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans","citation":{"short":"L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono, C. Chen, PLoS Biology 20 (2022).","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>","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>","ieee":"L. Zhao <i>et al.</i>, “ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans,” <i>PLoS Biology</i>, vol. 20, no. 6. Public Library of Science, 2022.","ista":"Zhao L, Fenk LA, Nilsson L, Amin-Wetzel NP, Ramirez N, de Bono M, Chen C. 2022. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. PLoS Biology. 20(6), e3001684.","chicago":"Zhao, Lina, Lorenz A. Fenk, Lars Nilsson, Niko Paresh Amin-Wetzel, Nelson Ramirez, Mario de Bono, and Changchun Chen. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>.","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>."},"ddc":["570"],"doi":"10.1371/journal.pbio.3001684","language":[{"iso":"eng"}],"pmid":1,"project":[{"name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"}],"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.","_id":"11637","date_published":"2022-06-21T00:00:00Z","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."}],"file":[{"file_name":"2022_PLoSBiology_Zhao.pdf","creator":"dernst","file_size":3721585,"checksum":"df4902f854ad76769d3203bfdc69f16c","date_updated":"2022-07-25T07:38:49Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"11643","date_created":"2022-07-25T07:38:49Z","success":1}],"article_number":"e3001684","article_processing_charge":"No","issue":"6","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":20,"file_date_updated":"2022-07-25T07:38:49Z","oa":1,"publication_status":"published","oa_version":"Published Version","year":"2022","has_accepted_license":"1","article_type":"original","publication_identifier":{"eissn":["1545-7885"]},"external_id":{"isi":["000828679600001"],"pmid":["35727855"]},"scopus_import":"1","date_updated":"2023-08-03T12:11:44Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"doi":"10.1103/PhysRevResearch.4.023240","ddc":["530"],"language":[{"iso":"eng"}],"acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030).","author":[{"first_name":"Vudtiwat","full_name":"Ngampruetikorn, Vudtiwat","last_name":"Ngampruetikorn"},{"full_name":"Sachdeva, Vedant","first_name":"Vedant","last_name":"Sachdeva"},{"first_name":"Johanna","full_name":"Torrence, Johanna","last_name":"Torrence"},{"id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","last_name":"Humplik","full_name":"Humplik, Jan","first_name":"Jan"},{"full_name":"Schwab, David J.","first_name":"David J.","last_name":"Schwab"},{"last_name":"Palmer","full_name":"Palmer, Stephanie E.","first_name":"Stephanie E."}],"type":"journal_article","day":"24","title":"Inferring couplings in networks across order-disorder phase transitions","citation":{"ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","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.","chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>.","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., &#38; Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>","ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. 2022;4(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>"},"status":"public","intvolume":"         4","publication":"Physical Review Research","department":[{"_id":"GaTk"}],"quality_controlled":"1","publisher":"American Physical Society","date_created":"2022-07-24T22:01:42Z","month":"06","publication_identifier":{"issn":["2643-1564"]},"external_id":{"arxiv":["2106.02349"]},"scopus_import":"1","date_updated":"2022-07-25T07:52:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","has_accepted_license":"1","oa_version":"Published Version","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":4,"file_date_updated":"2022-07-25T07:47:23Z","oa":1,"funded_apc":"1","publication_status":"published","date_published":"2022-06-24T00:00:00Z","_id":"11638","abstract":[{"lang":"eng","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."}],"file":[{"checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","date_updated":"2022-07-25T07:47:23Z","access_level":"open_access","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","creator":"dernst","file_size":1379683,"date_created":"2022-07-25T07:47:23Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"11644"}],"article_number":"023240","article_processing_charge":"No","issue":"2","arxiv":1},{"author":[{"full_name":"Zhang, Yihan","first_name":"Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c"},{"last_name":"Vatedka","full_name":"Vatedka, Shashank","first_name":"Shashank"}],"type":"journal_article","day":"01","title":"List decoding random Euclidean codes and Infinite constellations","citation":{"short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786.","ama":"Zhang Y, Vatedka S. List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. 2022;68(12):7753-7786. doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>","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>","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>.","ieee":"Y. Zhang and S. Vatedka, “List decoding random Euclidean codes and Infinite constellations,” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12. IEEE, pp. 7753–7786, 2022.","ista":"Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.","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>."},"doi":"10.1109/TIT.2022.3189542","language":[{"iso":"eng"}],"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].","date_created":"2022-07-24T22:01:42Z","month":"12","page":"7753-7786","status":"public","intvolume":"        68","quality_controlled":"1","department":[{"_id":"MaMo"}],"publication":"IEEE Transactions on Information Theory","isi":1,"publisher":"IEEE","year":"2022","oa_version":"Preprint","article_type":"original","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:12:19Z","external_id":{"isi":["000891796100007"],"arxiv":["1901.03790"]},"scopus_import":"1","date_published":"2022-12-01T00:00:00Z","_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"}],"issue":"12","article_processing_charge":"No","arxiv":1,"volume":68,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1901.03790"}],"publication_status":"published"},{"article_type":"original","year":"2022","has_accepted_license":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:11:01Z","external_id":{"isi":["000825873600001"]},"scopus_import":"1","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"issue":"8","article_processing_charge":"Yes (via OA deal)","file":[{"success":1,"date_created":"2023-02-02T08:11:23Z","content_type":"application/pdf","file_id":"12477","relation":"main_file","date_updated":"2023-02-02T08:11:23Z","access_level":"open_access","checksum":"3102e203e77b884bffffdbe8e548da88","file_name":"2022_MolecularEcologyRes_Szep.pdf","creator":"dernst","file_size":6431779}],"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"}],"_id":"11640","date_published":"2022-11-01T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2023-02-02T08:11:23Z","volume":22,"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"ec_funded":1,"citation":{"short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","apa":"Szep, E., Trubenova, B., &#38; Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>","ama":"Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. 2022;22(8):2941-2955. doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>","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.","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.","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>.","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>."},"title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","day":"01","type":"journal_article","author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","full_name":"Szep, Eniko","first_name":"Eniko"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova"},{"last_name":"Csilléry","full_name":"Csilléry, Katalin","first_name":"Katalin"}],"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.","project":[{"grant_number":"704172","name":"Rate of Adaptation in Changing Environment","call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1111/1755-0998.13676","page":"2941-2955","month":"11","date_created":"2022-07-24T22:01:43Z","publisher":"Wiley","isi":1,"quality_controlled":"1","department":[{"_id":"NiBa"}],"publication":"Molecular Ecology Resources","status":"public","intvolume":"        22"},{"month":"10","date_created":"2022-07-25T10:04:58Z","page":"249-261","publication":"Microscopy","quality_controlled":"1","department":[{"_id":"LeSa"}],"intvolume":"        71","status":"public","publisher":"Oxford University Press","isi":1,"day":"01","type":"journal_article","author":[{"last_name":"Gerle","full_name":"Gerle, Christoph","first_name":"Christoph"},{"last_name":"Kishikawa","full_name":"Kishikawa, Jun-ichi","first_name":"Jun-ichi"},{"last_name":"Yamaguchi","full_name":"Yamaguchi, Tomoko","first_name":"Tomoko"},{"last_name":"Nakanishi","first_name":"Atsuko","full_name":"Nakanishi, Atsuko"},{"id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","orcid":"0000-0002-3219-2022","last_name":"Çoruh","first_name":"Mehmet Orkun","full_name":"Çoruh, Mehmet Orkun"},{"full_name":"Makino, Fumiaki","first_name":"Fumiaki","last_name":"Makino"},{"last_name":"Miyata","first_name":"Tomoko","full_name":"Miyata, Tomoko"},{"last_name":"Kawamoto","full_name":"Kawamoto, Akihiro","first_name":"Akihiro"},{"first_name":"Ken","full_name":"Yokoyama, Ken","last_name":"Yokoyama"},{"first_name":"Keiichi","full_name":"Namba, Keiichi","last_name":"Namba"},{"full_name":"Kurisu, Genji","first_name":"Genji","last_name":"Kurisu"},{"full_name":"Kato, Takayuki","first_name":"Takayuki","last_name":"Kato"}],"citation":{"ama":"Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. 2022;71(5):249-261. doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>","apa":"Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino, F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>","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.","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>.","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>.","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.","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."},"title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1093/jmicro/dfac037","pmid":1,"acknowledgement":"Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266 to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows (20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer project and also would like to thank Hideki Shigematsu for critical reading of the manuscript. And we are indebted to the two anonymous reviewers who helped us to improve our manuscript.","file":[{"date_created":"2023-02-03T08:34:48Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"12498","checksum":"23b51c163636bf9313f7f0818312e67e","date_updated":"2023-02-03T08:34:48Z","access_level":"open_access","file_name":"2022_Microscopy_Gerle.pdf","file_size":7812696,"creator":"dernst"}],"date_published":"2022-10-01T00:00:00Z","_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."}],"article_processing_charge":"No","issue":"5","file_date_updated":"2023-02-03T08:34:48Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":71,"publication_status":"published","oa":1,"article_type":"original","has_accepted_license":"1","year":"2022","oa_version":"Published Version","scopus_import":"1","external_id":{"pmid":["35861182"],"isi":["000837950900001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:13:37Z","publication_identifier":{"issn":["2050-5698"],"eissn":["2050-5701"]}},{"article_processing_charge":"No","file":[{"title":"Supplementary Datasets","file_id":"11655","relation":"main_file","content_type":"application/x-zip-compressed","date_created":"2022-07-26T12:37:52Z","file_size":2209382998,"creator":"melkrewi","file_name":"Data.zip","embargo":"2022-08-07","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","access_level":"open_access","date_updated":"2022-08-08T22:30:04Z"}],"month":"08","_id":"11653","abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"date_published":"2022-08-05T00:00:00Z","date_created":"2022-07-26T11:01:47Z","publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2022-08-08T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>.","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","short":"M.N. Elkrewi, (2022).","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>"},"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","day":"05","contributor":[{"last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"first_name":"Luca","last_name":"Sax"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K"},{"first_name":"Francisco","last_name":"Hontoria "},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz"}],"year":"2022","oa_version":"Published Version","has_accepted_license":"1","author":[{"full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"}],"type":"research_data","related_material":{"record":[{"status":"public","id":"12248","relation":"used_in_publication"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:35:53Z","ddc":["570"],"doi":"10.15479/AT:ISTA:11653"},{"status":"public","publication":"Leibniz International Proceedings on Mathematics","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","date_created":"2022-07-27T09:27:34Z","month":"07","ddc":["510"],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","last_name":"Biswas","full_name":"Biswas, Ranita","first_name":"Ranita"},{"last_name":"Cultrera di Montesano","first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"first_name":"Morteza","full_name":"Saghafian, Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"type":"journal_article","day":"27","title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","citation":{"apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.).","mla":"Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>, Schloss Dagstuhl - Leibniz Zentrum für Informatik.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings on Mathematics.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth in arrangements: Dehn–Sommerville–Euler relations with applications,” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik, n.d."},"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2022-07-27T09:25:53Z","oa":1,"publication_status":"submitted","date_published":"2022-07-27T00:00:00Z","_id":"11658","abstract":[{"lang":"eng","text":"The depth of a cell in an arrangement of n (non-vertical) great-spheres in Sd is the number of great-spheres that pass above the cell. We prove Euler-type relations, which imply extensions of the classic Dehn–Sommerville relations for convex polytopes to sublevel sets of the depth function, and we use the relations to extend the expressions for the number of faces of neighborly polytopes to the number of cells of levels in neighborly arrangements."}],"file":[{"date_created":"2022-07-27T09:25:53Z","content_type":"application/pdf","file_id":"11659","relation":"main_file","date_updated":"2022-07-27T09:25:53Z","access_level":"open_access","checksum":"b2f511e8b1cae5f1892b0cdec341acac","file_name":"D-S-E.pdf","file_size":639266,"creator":"scultrer"}],"article_processing_charge":"No","date_updated":"2022-07-28T07:57:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","year":"2022","has_accepted_license":"1"}]