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Gelfand, (2019)."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808841.v1","open_access":"1"}],"oa":1,"doi":"10.6084/m9.figshare.9808841.v1","date_published":"2019-09-02T00:00:00Z","article_processing_charge":"No","day":"02","month":"09","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9896","year":"2019","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","title":"Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"author":[{"full_name":"Sigalova, Olga M.","first_name":"Olga M.","last_name":"Sigalova"},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"last_name":"Filaretov","first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A."},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"oa_version":"Published Version","date_created":"2021-08-12T07:50:53Z","date_updated":"2023-08-30T06:20:21Z","type":"research_data_reference","abstract":[{"text":"Summary of the analysed genomes. (CSV 24 kb)","lang":"eng"}]},{"date_updated":"2023-08-30T06:21:23Z","date_created":"2019-09-22T22:00:37Z","volume":10,"author":[{"full_name":"Bornhorst, Dorothee","last_name":"Bornhorst","first_name":"Dorothee"},{"full_name":"Xia, Peng","last_name":"Xia","first_name":"Peng","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nakajima","first_name":"Hiroyuki","full_name":"Nakajima, Hiroyuki"},{"full_name":"Dingare, Chaitanya","first_name":"Chaitanya","last_name":"Dingare"},{"full_name":"Herzog, Wiebke","last_name":"Herzog","first_name":"Wiebke"},{"full_name":"Lecaudey, Virginie","first_name":"Virginie","last_name":"Lecaudey"},{"full_name":"Mochizuki, Naoki","last_name":"Mochizuki","first_name":"Naoki"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yelon","first_name":"Deborah","full_name":"Yelon, Deborah"},{"first_name":"Salim","last_name":"Abdelilah-Seyfried","full_name":"Abdelilah-Seyfried, Salim"}],"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:44Z","language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-12068-x","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000485216800009"],"pmid":["31511517"]},"oa":1,"month":"09","publication_identifier":{"eissn":["20411723"]},"file":[{"access_level":"open_access","file_name":"2019_Nature_Bornhorst.pdf","creator":"kschuh","content_type":"application/pdf","file_size":3905793,"file_id":"6926","relation":"main_file","checksum":"62c2512712e16d27c1797d318d14ba9f","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-01T11:18:50Z"}],"oa_version":"Published Version","ddc":["570"],"title":"Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions","status":"public","intvolume":" 10","_id":"6899","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed."}],"issue":"1","type":"journal_article","date_published":"2019-09-11T00:00:00Z","page":"4113","publication":"Nature communications","citation":{"ista":"Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 10(1), 4113.","apa":"Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V., … Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-019-12068-x","ieee":"D. Bornhorst et al., “Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions,” Nature communications, vol. 10, no. 1. Nature Publishing Group, p. 4113, 2019.","ama":"Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 2019;10(1):4113. doi:10.1038/s41467-019-12068-x","chicago":"Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications. Nature Publishing Group, 2019. https://doi.org/10.1038/s41467-019-12068-x.","mla":"Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications, vol. 10, no. 1, Nature Publishing Group, 2019, p. 4113, doi:10.1038/s41467-019-12068-x.","short":"D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N. Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications 10 (2019) 4113."},"day":"11","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-09-12T00:00:00Z","publication":"BMC Genomics","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics. BioMed Central, 2019. https://doi.org/10.1186/s12864-019-6059-5.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).","mla":"Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics, vol. 20, no. 1, 710, BioMed Central, 2019, doi:10.1186/s12864-019-6059-5.","ieee":"O. M. Sigalova et al., “Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction,” BMC Genomics, vol. 20, no. 1. BioMed Central, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-019-6059-5","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 20(1), 710.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 2019;20(1). doi:10.1186/s12864-019-6059-5"},"abstract":[{"text":"Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"file_size":4157175,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2019_BioMed_Sigalova.pdf","checksum":"b798773c5823012d31c812c9f7975da2","date_created":"2019-10-01T10:33:17Z","date_updated":"2020-07-14T12:47:44Z","relation":"main_file","file_id":"6924"}],"oa_version":"Published Version","_id":"6898","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","ddc":["570"],"intvolume":" 20","month":"09","publication_identifier":{"eissn":["14712164"]},"doi":"10.1186/s12864-019-6059-5","language":[{"iso":"eng"}],"external_id":{"isi":["000485256100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:44Z","article_number":"710","author":[{"full_name":"Sigalova, Olga M.","first_name":"Olga M.","last_name":"Sigalova"},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"related_material":{"record":[{"id":"9731","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9783"},{"id":"9890","status":"public","relation":"research_data"},{"id":"9892","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9893"},{"relation":"research_data","status":"public","id":"9894"},{"id":"9895","status":"public","relation":"research_data"},{"id":"9896","relation":"research_data","status":"public"},{"id":"9897","relation":"research_data","status":"public"},{"id":"9898","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9899"},{"id":"9900","relation":"research_data","status":"public"},{"id":"9901","relation":"research_data","status":"public"}]},"date_created":"2019-09-22T22:00:36Z","date_updated":"2023-08-30T06:20:22Z","volume":20,"year":"2019","publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"BioMed Central"},{"scopus_import":"1","day":"07","article_processing_charge":"No","article_type":"original","page":"1312-1314","publication":"Molecular Plant","citation":{"apa":"Artner, C., & Benková, E. (2019). Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2019.09.003","ieee":"C. Artner and E. Benková, “Ethylene and cytokinin - partners in root growth regulation,” Molecular Plant, vol. 12, no. 10. Cell Press, pp. 1312–1314, 2019.","ista":"Artner C, Benková E. 2019. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 12(10), 1312–1314.","ama":"Artner C, Benková E. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 2019;12(10):1312-1314. doi:10.1016/j.molp.2019.09.003","chicago":"Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant. Cell Press, 2019. https://doi.org/10.1016/j.molp.2019.09.003.","short":"C. Artner, E. Benková, Molecular Plant 12 (2019) 1312–1314.","mla":"Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant, vol. 12, no. 10, Cell Press, 2019, pp. 1312–14, doi:10.1016/j.molp.2019.09.003."},"date_published":"2019-10-07T00:00:00Z","type":"journal_article","issue":"10","title":"Ethylene and cytokinin - partners in root growth regulation","status":"public","intvolume":" 12","_id":"6920","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","month":"10","publication_identifier":{"issn":["1674-2052","1752-9867"]},"quality_controlled":"1","isi":1,"project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"external_id":{"pmid":["31541740"],"isi":["000489132500002"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2019.09.003","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Cell Press","year":"2019","pmid":1,"date_created":"2019-09-30T10:00:40Z","date_updated":"2023-08-30T06:55:02Z","volume":12,"author":[{"full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner","first_name":"Christina"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}]},{"oa_version":"Published Version","date_created":"2021-08-12T08:10:23Z","date_updated":"2023-08-30T06:20:22Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga","full_name":"Bochkareva, Olga"},{"full_name":"Shelyakin, Pavel V.","first_name":"Pavel V.","last_name":"Shelyakin"},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","title":"Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","_id":"9898","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb)"}],"type":"research_data_reference","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808859.v1","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808859.v1.","mla":"Sigalova, Olga M., et al. Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808859.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808859.v1.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808859.v1","ieee":"O. M. Sigalova et al., “Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808859.v1"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808859.v1"}],"article_processing_charge":"No","day":"12","month":"09"},{"day":"12","month":"09","article_processing_charge":"No","doi":"10.6084/m9.figshare.9808907.v1","date_published":"2019-09-12T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808907.v1"}],"citation":{"ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808907.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808907.v1.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808907.v1","ieee":"O. M. Sigalova et al., “Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","mla":"Sigalova, Olga M., et al. Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808907.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808907.v1."},"oa":1,"abstract":[{"lang":"eng","text":"Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)"}],"type":"research_data_reference","date_updated":"2023-08-30T06:20:22Z","date_created":"2021-08-12T10:54:03Z","oa_version":"Published Version","author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"full_name":"Chaplin, Andrei V.","last_name":"Chaplin","first_name":"Andrei V."},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"status":"public","title":"Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","_id":"9901","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"date_created":"2021-08-12T08:18:09Z","date_updated":"2023-08-30T06:20:22Z","oa_version":"Published Version","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"full_name":"Chaplin, Andrei V.","first_name":"Andrei V.","last_name":"Chaplin"},{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"title":"Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"year":"2019","_id":"9899","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)","lang":"eng"}],"type":"research_data_reference","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808865.v1","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808865.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808865.v1.","ieee":"O. M. Sigalova et al., “Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808865.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808865.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808865.v1"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808865.v1","open_access":"1"}],"day":"12","month":"09","article_processing_charge":"No"},{"article_processing_charge":"No","day":"12","month":"09","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808886.v1","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808886.v1","open_access":"1"}],"citation":{"ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808886.v1","ieee":"O. M. Sigalova et al., “Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808886.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808886.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808886.v1.","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808886.v1."},"abstract":[{"text":"Pan-genome statistics by species. (CSV 3 kb)","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-08-30T06:20:22Z","date_created":"2021-08-12T08:44:49Z","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Olga M.","last_name":"Sigalova","full_name":"Sigalova, Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"last_name":"Filaretov","first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","status":"public","title":"Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","year":"2019","_id":"9900","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000486348700001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"doi":"10.1111/ecog.04444","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"eissn":["1600-0587"],"issn":["0906-7590"]},"year":"2019","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Wiley","author":[{"full_name":"Ovaskainen, Otso","first_name":"Otso","last_name":"Ovaskainen"},{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki"},{"first_name":"Nerea","last_name":"Abrego","full_name":"Abrego, Nerea"}],"date_created":"2019-10-08T13:01:24Z","date_updated":"2023-08-30T06:57:25Z","volume":42,"file_date_updated":"2020-07-14T12:47:45Z","ec_funded":1,"publication":"Ecography","citation":{"apa":"Ovaskainen, O., Rybicki, J., & Abrego, N. (2019). What can observational data reveal about metacommunity processes? Ecography. Wiley. https://doi.org/10.1111/ecog.04444","ieee":"O. Ovaskainen, J. Rybicki, and N. Abrego, “What can observational data reveal about metacommunity processes?,” Ecography, vol. 42, no. 11. Wiley, pp. 1877–1886, 2019.","ista":"Ovaskainen O, Rybicki J, Abrego N. 2019. What can observational data reveal about metacommunity processes? Ecography. 42(11), 1877–1886.","ama":"Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about metacommunity processes? Ecography. 2019;42(11):1877-1886. doi:10.1111/ecog.04444","chicago":"Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography. Wiley, 2019. https://doi.org/10.1111/ecog.04444.","short":"O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886.","mla":"Ovaskainen, Otso, et al. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography, vol. 42, no. 11, Wiley, 2019, pp. 1877–86, doi:10.1111/ecog.04444."},"article_type":"original","page":"1877-1886","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","_id":"6936","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["577"],"status":"public","title":"What can observational data reveal about metacommunity processes?","intvolume":" 42","oa_version":"Published Version","file":[{"checksum":"6c9fbbd5ea8ce10ae93e55ad560a7bf9","date_created":"2019-10-08T13:07:44Z","date_updated":"2020-07-14T12:47:45Z","file_id":"6937","relation":"main_file","creator":"jrybicki","file_size":1682718,"content_type":"application/pdf","access_level":"open_access","file_name":"ecog.04444.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.\r\n"}],"issue":"11"},{"file_date_updated":"2020-07-14T12:47:42Z","article_number":"1900151","date_updated":"2023-08-30T06:56:26Z","date_created":"2019-09-07T14:40:03Z","volume":41,"author":[{"full_name":"Giese, B","first_name":"B","last_name":"Giese"},{"first_name":"J L","last_name":"Friess","full_name":"Friess, J L"},{"full_name":"Schetelig, M F ","last_name":"Schetelig","first_name":"M F "},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Philip","last_name":"Messer","full_name":"Messer, Philip"},{"full_name":"Debarre, Florence","last_name":"Debarre","first_name":"Florence"},{"full_name":"Meimberg, H","last_name":"Meimberg","first_name":"H"},{"full_name":"Windbichler, N","last_name":"Windbichler","first_name":"N"},{"last_name":"Boete","first_name":"C","full_name":"Boete, C"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","month":"11","publication_identifier":{"eissn":["1521-1878"]},"language":[{"iso":"eng"}],"doi":"10.1002/bies.201900151","quality_controlled":"1","isi":1,"external_id":{"isi":["000489502000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"lang":"eng","text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop."}],"issue":"11","type":"journal_article","file":[{"file_name":"2019_BioEssays_Giese.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":193248,"file_id":"6939","relation":"main_file","date_created":"2019-10-11T06:59:26Z","date_updated":"2020-07-14T12:47:42Z","checksum":"8cc7551bff70b2658f8d5630f228ee12"}],"oa_version":"Published Version","title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","ddc":["570"],"status":"public","intvolume":" 41","_id":"6857","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","article_type":"original","publication":"BioEssays","citation":{"ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151","ieee":"B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.","short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.","chicago":"Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151."}},{"isi":1,"quality_controlled":"1","external_id":{"pmid":[" 31522703"],"isi":["000501594500006"]},"language":[{"iso":"eng"}],"doi":"10.1016/bs.aivir.2019.07.008","month":"08","publication_identifier":{"isbn":["9780128184561"],"issn":["0065-3527"]},"publication_status":"published","editor":[{"last_name":"Rey","first_name":"Félix A.","full_name":"Rey, Félix A."}],"department":[{"_id":"FlSc"}],"publisher":"Elsevier","year":"2019","pmid":1,"date_created":"2019-09-18T08:15:37Z","date_updated":"2023-08-30T06:56:00Z","volume":105,"author":[{"last_name":"Obr","first_name":"Martin","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"page":"117-159","publication":"Complementary Strategies to Study Virus Structure and Function","citation":{"mla":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008.","short":"M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159.","chicago":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” In Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008.","ama":"Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008","ista":"Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies to Study Virus Structure and Function. vol. 105, 117–159.","apa":"Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function (Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008","ieee":"M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging,” in Complementary Strategies to Study Virus Structure and Function, vol. 105, F. A. Rey, Ed. Elsevier, 2019, pp. 117–159."},"date_published":"2019-08-27T00:00:00Z","series_title":"Advances in Virus Research","scopus_import":"1","day":"27","article_processing_charge":"No","status":"public","title":"Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging","intvolume":" 105","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6890","oa_version":"None","type":"book_chapter","abstract":[{"lang":"eng","text":"Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods."}]},{"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"acknowledgement":"We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1 - 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021 Joint Project “Strongly interacting systems in confined geometries” is gratefully acknowledged.","year":"2019","date_updated":"2023-08-30T06:57:53Z","date_created":"2019-10-14T06:31:13Z","volume":123,"author":[{"first_name":"Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"first_name":"Nicolò","last_name":"Defenu","full_name":"Defenu, Nicolò"},{"full_name":"Nándori, István","last_name":"Nándori","first_name":"István"},{"last_name":"Salasnich","first_name":"Luca","full_name":"Salasnich, Luca"},{"first_name":"Andrea","last_name":"Trombettoni","full_name":"Trombettoni, Andrea"}],"related_material":{"link":[{"description":"News auf IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/new-form-of-magnetism-found/"}]},"article_number":"100601","quality_controlled":"1","isi":1,"project":[{"_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641","call_identifier":"FWF","name":"A path-integral approach to composite impurities"}],"oa":1,"external_id":{"isi":["000483587200004"],"arxiv":["1907.06253"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.06253"}],"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.123.100601","month":"09","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"title":"Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models","status":"public","intvolume":" 123","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6940","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We study the effect of a linear tunneling coupling between two-dimensional systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless (BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the one-body correlation functions are algebraically decaying and the other with\r\nexponential decay. When the linear coupling is turned on, a third BKT-paired phase emerges, in which one-body correlations are exponentially decaying, while two-body correlation functions exhibit power-law\r\ndecay. We perform numerical simulations in the paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent. We provide a picture of the phase diagram using a renormalization group approach."}],"issue":"10","article_type":"original","publication":"Physical Review Letters","citation":{"short":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical Review Letters 123 (2019).","mla":"Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters, vol. 123, no. 10, 100601, American Physical Society, 2019, doi:10.1103/physrevlett.123.100601.","chicago":"Bighin, Giacomo, Nicolò Defenu, István Nándori, Luca Salasnich, and Andrea Trombettoni. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.100601.","ama":"Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 2019;123(10). doi:10.1103/physrevlett.123.100601","ieee":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models,” Physical Review Letters, vol. 123, no. 10. American Physical Society, 2019.","apa":"Bighin, G., Defenu, N., Nándori, I., Salasnich, L., & Trombettoni, A. (2019). Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.100601","ista":"Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 123(10), 100601."},"date_published":"2019-09-06T00:00:00Z","scopus_import":"1","day":"06","article_processing_charge":"No"},{"intvolume":" 5","ddc":["570"],"status":"public","title":"Structural basis of sterol recognition by human hedgehog receptor PTCH1","_id":"6919","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"6928","relation":"main_file","checksum":"b2256c9117655bc15f621ba0babf219f","date_created":"2019-10-02T11:13:54Z","date_updated":"2020-07-14T12:47:44Z","access_level":"open_access","file_name":"2019_AAAS_Qi.pdf","creator":"kschuh","file_size":1236101,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"9","citation":{"ama":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw6490","ista":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490.","apa":"Qi, C., Minin, G. D., Vercellino, I., Wutz, A., & Korkhov, V. M. (2019). Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw6490","ieee":"C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural basis of sterol recognition by human hedgehog receptor PTCH1,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","mla":"Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances, vol. 5, no. 9, eaaw6490, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw6490.","short":"C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances 5 (2019).","chicago":"Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw6490."},"publication":"Science Advances","date_published":"2019-09-18T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"18","department":[{"_id":"LeSa"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","year":"2019","volume":5,"date_updated":"2023-08-30T06:55:31Z","date_created":"2019-09-29T22:00:45Z","author":[{"first_name":"Chao","last_name":"Qi","full_name":"Qi, Chao"},{"last_name":"Minin","first_name":"Giulio Di","full_name":"Minin, Giulio Di"},{"full_name":"Vercellino, Irene","last_name":"Vercellino","first_name":"Irene","orcid":"0000-0001-5618-3449","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anton","last_name":"Wutz","full_name":"Wutz, Anton"},{"full_name":"Korkhov, Volodymyr M.","last_name":"Korkhov","first_name":"Volodymyr M."}],"article_number":"eaaw6490","file_date_updated":"2020-07-14T12:47:44Z","isi":1,"quality_controlled":"1","external_id":{"isi":["000491128800062"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.aaw6490","publication_identifier":{"eissn":["23752548"]},"month":"09"},{"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Frontiers","year":"2019","pmid":1,"date_created":"2019-11-04T15:50:06Z","date_updated":"2023-08-30T07:18:23Z","volume":10,"author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","first_name":"Réka K","last_name":"Kelemen","full_name":"Kelemen, Réka K"},{"last_name":"Rajakaruna","first_name":"H","full_name":"Rajakaruna, H"},{"full_name":"Cockburn, IA","last_name":"Cockburn","first_name":"IA"},{"full_name":"Ganusov, VV","last_name":"Ganusov","first_name":"VV"}],"article_number":"2153","file_date_updated":"2020-07-14T12:47:46Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31616407"],"isi":["000487187000001"]},"language":[{"iso":"eng"}],"doi":"10.3389/fimmu.2019.02153","month":"09","publication_identifier":{"issn":["1664-3224"]},"status":"public","title":"Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells","ddc":["570"],"intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6983","file":[{"date_created":"2019-11-04T15:54:00Z","date_updated":"2020-07-14T12:47:46Z","checksum":"68d1708f7aa412544159b498ef17a6b9","file_id":"6984","relation":"main_file","creator":"dernst","file_size":2083061,"content_type":"application/pdf","file_name":"2019_FrontiersImmonology_Kelemen.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver."}],"article_type":"original","publication":"Frontiers in Immunology","citation":{"ama":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153","ista":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153.","apa":"Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153","ieee":"R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers, 2019.","mla":"Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153.","short":"R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019).","chicago":"Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153."},"date_published":"2019-09-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No","has_accepted_license":"1"}]