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Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808835.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 19 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.9808835.v1","ieee":"O. M. Sigalova et al., “Additional file 19 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 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808835.v1"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808835.v1"}],"oa":1},{"article_processing_charge":"No","month":"09","day":"02","doi":"10.6084/m9.figshare.9808841.v1","date_published":"2019-09-02T00:00:00Z","citation":{"apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 1 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.9808841.v1","ieee":"O. M. Sigalova et al., “Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808841.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808841.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 1 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.9808841.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 1 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808841.v1."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808841.v1","open_access":"1"}],"abstract":[{"lang":"eng","text":"Summary of the analysed genomes. (CSV 24 kb)"}],"type":"research_data_reference","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"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."},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"full_name":"Shelyakin, Pavel V.","first_name":"Pavel V.","last_name":"Shelyakin"},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"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."}],"oa_version":"Published Version","date_updated":"2023-08-30T06:20:21Z","date_created":"2021-08-12T07:50:53Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9896","year":"2019","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","status":"public","title":"Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction"},{"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,"external_id":{"isi":["000485216800009"],"pmid":["31511517"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-019-12068-x","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["20411723"]},"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","author":[{"last_name":"Bornhorst","first_name":"Dorothee","full_name":"Bornhorst, Dorothee"},{"orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xia","first_name":"Peng","full_name":"Xia, Peng"},{"first_name":"Hiroyuki","last_name":"Nakajima","full_name":"Nakajima, Hiroyuki"},{"last_name":"Dingare","first_name":"Chaitanya","full_name":"Dingare, Chaitanya"},{"full_name":"Herzog, Wiebke","last_name":"Herzog","first_name":"Wiebke"},{"first_name":"Virginie","last_name":"Lecaudey","full_name":"Lecaudey, Virginie"},{"full_name":"Mochizuki, Naoki","first_name":"Naoki","last_name":"Mochizuki"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"first_name":"Deborah","last_name":"Yelon","full_name":"Yelon, Deborah"},{"first_name":"Salim","last_name":"Abdelilah-Seyfried","full_name":"Abdelilah-Seyfried, Salim"}],"date_created":"2019-09-22T22:00:37Z","date_updated":"2023-08-30T06:21:23Z","volume":10,"file_date_updated":"2020-07-14T12:47:44Z","license":"https://creativecommons.org/licenses/by/4.0/","publication":"Nature communications","citation":{"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.","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.","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.","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.","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","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.","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"},"page":"4113","date_published":"2019-09-11T00:00:00Z","scopus_import":"1","day":"11","has_accepted_license":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6899","ddc":["570"],"title":"Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions","status":"public","intvolume":" 10","oa_version":"Published Version","file":[{"file_id":"6926","relation":"main_file","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-01T11:18:50Z","checksum":"62c2512712e16d27c1797d318d14ba9f","file_name":"2019_Nature_Bornhorst.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":3905793}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"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":{"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","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.","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.","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."},"abstract":[{"lang":"eng","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."}],"issue":"1","type":"journal_article","file":[{"creator":"kschuh","file_size":4157175,"content_type":"application/pdf","file_name":"2019_BioMed_Sigalova.pdf","access_level":"open_access","date_created":"2019-10-01T10:33:17Z","date_updated":"2020-07-14T12:47:44Z","checksum":"b798773c5823012d31c812c9f7975da2","file_id":"6924","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6898","ddc":["570"],"title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","intvolume":" 20","month":"09","publication_identifier":{"eissn":["14712164"]},"doi":"10.1186/s12864-019-6059-5","language":[{"iso":"eng"}],"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":["000485256100001"]},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:47:44Z","article_number":"710","author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"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"},{"first_name":"Evgeny E.","last_name":"Akkuratov","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."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9731"},{"id":"9783","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9890"},{"id":"9892","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","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"},{"id":"9899","status":"public","relation":"research_data"},{"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","publisher":"BioMed Central","department":[{"_id":"FyKo"}]},{"day":"07","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-07T00:00:00Z","publication":"Molecular Plant","citation":{"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.","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.","short":"C. Artner, E. Benková, Molecular Plant 12 (2019) 1312–1314.","ista":"Artner C, Benková E. 2019. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 12(10), 1312–1314.","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.","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"},"article_type":"original","page":"1312-1314","issue":"10","type":"journal_article","oa_version":"None","_id":"6920","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Ethylene and cytokinin - partners in root growth regulation","intvolume":" 12","month":"10","publication_identifier":{"issn":["1674-2052","1752-9867"]},"doi":"10.1016/j.molp.2019.09.003","language":[{"iso":"eng"}],"external_id":{"pmid":["31541740"],"isi":["000489132500002"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"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"}],"date_updated":"2023-08-30T06:55:02Z","date_created":"2019-09-30T10:00:40Z","volume":12,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Cell Press"},{"type":"research_data_reference","abstract":[{"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)","lang":"eng"}],"publisher":"Springer Nature","department":[{"_id":"FyKo"}],"title":"Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","year":"2019","_id":"9898","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-08-30T06:20:22Z","date_created":"2021-08-12T08:10:23Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"full_name":"Chaplin, Andrei V.","last_name":"Chaplin","first_name":"Andrei V."},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"article_processing_charge":"No","month":"09","day":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/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.","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.","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","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,"doi":"10.6084/m9.figshare.9808859.v1","date_published":"2019-09-12T00:00:00Z"},{"day":"12","month":"09","article_processing_charge":"No","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.","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.","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","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,"date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808907.v1","type":"research_data_reference","abstract":[{"text":"Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)","lang":"eng"}],"title":"Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"_id":"9901","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","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."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","first_name":"Olga","last_name":"Bochkareva","full_name":"Bochkareva, Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]}},{"related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Sigalova, Olga M.","first_name":"Olga M.","last_name":"Sigalova"},{"full_name":"Chaplin, Andrei V.","first_name":"Andrei V.","last_name":"Chaplin"},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"oa_version":"Published Version","date_updated":"2023-08-30T06:20:22Z","date_created":"2021-08-12T08:18:09Z","_id":"9899","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"status":"public","title":"Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","abstract":[{"text":"Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)","lang":"eng"}],"type":"research_data_reference","doi":"10.6084/m9.figshare.9808865.v1","date_published":"2019-09-12T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808865.v1","open_access":"1"}],"citation":{"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","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.","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","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.","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 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."},"oa":1,"article_processing_charge":"No","month":"09","day":"12"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Pan-genome statistics by species. (CSV 3 kb)"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9900","year":"2019","status":"public","title":"Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","author":[{"first_name":"Olga M.","last_name":"Sigalova","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"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"date_updated":"2023-08-30T06:20:22Z","date_created":"2021-08-12T08:44:49Z","oa_version":"Published Version","month":"09","day":"12","article_processing_charge":"No","citation":{"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.","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","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.","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","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.","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.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808886.v1"}],"oa":1,"date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808886.v1"},{"publisher":"Wiley","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2019","volume":42,"date_updated":"2023-08-30T06:57:25Z","date_created":"2019-10-08T13:01:24Z","author":[{"last_name":"Ovaskainen","first_name":"Otso","full_name":"Ovaskainen, Otso"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki","full_name":"Rybicki, Joel"},{"full_name":"Abrego, Nerea","first_name":"Nerea","last_name":"Abrego"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:47:45Z","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"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":["000486348700001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/ecog.04444","publication_identifier":{"issn":["0906-7590"],"eissn":["1600-0587"]},"month":"11","intvolume":" 42","ddc":["577"],"status":"public","title":"What can observational data reveal about metacommunity processes?","_id":"6936","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"6937","relation":"main_file","checksum":"6c9fbbd5ea8ce10ae93e55ad560a7bf9","date_updated":"2020-07-14T12:47:45Z","date_created":"2019-10-08T13:07:44Z","access_level":"open_access","file_name":"ecog.04444.pdf","creator":"jrybicki","file_size":1682718,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"11","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"}],"page":"1877-1886","article_type":"original","citation":{"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","ista":"Ovaskainen O, Rybicki J, Abrego N. 2019. What can observational data reveal about metacommunity processes? Ecography. 42(11), 1877–1886.","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.","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","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.","short":"O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886.","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."},"publication":"Ecography","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"file":[{"file_name":"2019_BioEssays_Giese.pdf","access_level":"open_access","content_type":"application/pdf","file_size":193248,"creator":"dernst","relation":"main_file","file_id":"6939","date_created":"2019-10-11T06:59:26Z","date_updated":"2020-07-14T12:47:42Z","checksum":"8cc7551bff70b2658f8d5630f228ee12"}],"oa_version":"Published Version","_id":"6857","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 41","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","status":"public","ddc":["570"],"issue":"11","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."}],"type":"journal_article","date_published":"2019-11-01T00:00:00Z","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","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","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.","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."},"publication":"BioEssays","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"full_name":"Giese, B","first_name":"B","last_name":"Giese"},{"full_name":"Friess, J L","first_name":"J L","last_name":"Friess"},{"full_name":"Schetelig, M F ","last_name":"Schetelig","first_name":"M F "},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Messer, Philip","last_name":"Messer","first_name":"Philip"},{"first_name":"Florence","last_name":"Debarre","full_name":"Debarre, Florence"},{"full_name":"Meimberg, H","first_name":"H","last_name":"Meimberg"},{"full_name":"Windbichler, N","last_name":"Windbichler","first_name":"N"},{"last_name":"Boete","first_name":"C","full_name":"Boete, C"}],"volume":41,"date_created":"2019-09-07T14:40:03Z","date_updated":"2023-08-30T06:56:26Z","year":"2019","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","file_date_updated":"2020-07-14T12:47:42Z","article_number":"1900151","doi":"10.1002/bies.201900151","language":[{"iso":"eng"}],"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":["000489502000001"]},"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1521-1878"]},"month":"11"},{"publication_identifier":{"issn":["0065-3527"],"isbn":["9780128184561"]},"month":"08","external_id":{"pmid":[" 31522703"],"isi":["000501594500006"]},"quality_controlled":"1","isi":1,"doi":"10.1016/bs.aivir.2019.07.008","language":[{"iso":"eng"}],"pmid":1,"year":"2019","department":[{"_id":"FlSc"}],"publisher":"Elsevier","editor":[{"first_name":"Félix A.","last_name":"Rey","full_name":"Rey, Félix A."}],"publication_status":"published","author":[{"full_name":"Obr, Martin","first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"volume":105,"date_created":"2019-09-18T08:15:37Z","date_updated":"2023-08-30T06:56:00Z","scopus_import":"1","series_title":"Advances in Virus Research","article_processing_charge":"No","day":"27","citation":{"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","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.","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.","short":"M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159.","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.","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."},"publication":"Complementary Strategies to Study Virus Structure and Function","page":"117-159","date_published":"2019-08-27T00:00:00Z","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."}],"_id":"6890","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 105","status":"public","title":"Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging","oa_version":"None"},{"volume":123,"date_updated":"2023-08-30T06:57:53Z","date_created":"2019-10-14T06:31:13Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-form-of-magnetism-found/","description":"News auf IST Website","relation":"press_release"}]},"author":[{"full_name":"Bighin, Giacomo","first_name":"Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777"},{"full_name":"Defenu, Nicolò","last_name":"Defenu","first_name":"Nicolò"},{"first_name":"István","last_name":"Nándori","full_name":"Nándori, István"},{"first_name":"Luca","last_name":"Salasnich","full_name":"Salasnich, Luca"},{"last_name":"Trombettoni","first_name":"Andrea","full_name":"Trombettoni, Andrea"}],"department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","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","article_number":"100601","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.123.100601","project":[{"grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425","name":"A path-integral approach to composite impurities","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000483587200004"],"arxiv":["1907.06253"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.06253","open_access":"1"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"09","oa_version":"Preprint","intvolume":" 123","title":"Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6940","issue":"10","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."}],"type":"journal_article","date_published":"2019-09-06T00:00:00Z","article_type":"original","citation":{"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.","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","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.","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","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.","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.","short":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical Review Letters 123 (2019)."},"publication":"Physical Review Letters","article_processing_charge":"No","day":"06","scopus_import":"1"},{"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"LeSa"}],"year":"2019","date_updated":"2023-08-30T06:55:31Z","date_created":"2019-09-29T22:00:45Z","volume":5,"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","first_name":"Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449"},{"full_name":"Wutz, Anton","last_name":"Wutz","first_name":"Anton"},{"last_name":"Korkhov","first_name":"Volodymyr M.","full_name":"Korkhov, Volodymyr M."}],"article_number":"eaaw6490","license":"https://creativecommons.org/licenses/by-nc/4.0/","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","month":"09","publication_identifier":{"eissn":["23752548"]},"ddc":["570"],"status":"public","title":"Structural basis of sterol recognition by human hedgehog receptor PTCH1","intvolume":" 5","_id":"6919","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_size":1236101,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2019_AAAS_Qi.pdf","checksum":"b2256c9117655bc15f621ba0babf219f","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-02T11:13:54Z","relation":"main_file","file_id":"6928"}],"type":"journal_article","issue":"9","publication":"Science Advances","citation":{"short":"C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances 5 (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.","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.","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","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.","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","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."},"date_published":"2019-09-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"No","has_accepted_license":"1"},{"publication_identifier":{"issn":["1664-3224"]},"month":"09","doi":"10.3389/fimmu.2019.02153","language":[{"iso":"eng"}],"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":["000487187000001"],"pmid":["31616407"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:46Z","article_number":"2153","author":[{"full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","first_name":"Réka K"},{"last_name":"Rajakaruna","first_name":"H","full_name":"Rajakaruna, H"},{"full_name":"Cockburn, IA","last_name":"Cockburn","first_name":"IA"},{"first_name":"VV","last_name":"Ganusov","full_name":"Ganusov, VV"}],"volume":10,"date_created":"2019-11-04T15:50:06Z","date_updated":"2023-08-30T07:18:23Z","pmid":1,"year":"2019","publisher":"Frontiers","department":[{"_id":"BeVi"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"20","scopus_import":"1","date_published":"2019-09-20T00:00:00Z","citation":{"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.","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).","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.","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.","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","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"},"publication":"Frontiers in Immunology","article_type":"original","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"6984","relation":"main_file","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-11-04T15:54:00Z","checksum":"68d1708f7aa412544159b498ef17a6b9","file_name":"2019_FrontiersImmonology_Kelemen.pdf","access_level":"open_access","creator":"dernst","file_size":2083061,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"6983","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 10","ddc":["570"],"title":"Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells","status":"public"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:46Z","article_number":"32","volume":66,"date_created":"2019-10-24T17:12:48Z","date_updated":"2023-08-30T07:07:23Z","author":[{"last_name":"Lenzen","first_name":"Christoph","full_name":"Lenzen, Christoph"},{"first_name":"Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel"}],"department":[{"_id":"DaAl"}],"publisher":"ACM","publication_status":"published","year":"2019","publication_identifier":{"issn":["0004-5411"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1145/3339471","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"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":{"arxiv":["1705.06173"],"isi":["000496514100001"]},"issue":"5","abstract":[{"text":"We give fault-tolerant algorithms for establishing synchrony in distributed systems in which each of thennodes has its own clock. Our algorithms operate in a very strong fault model: we require self-stabilisation, i.e.,the initial state of the system may be arbitrary, and there can be up to fJournal of the ACM. 2019;66(5). doi:10.1145/3339471","ieee":"C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation is almost as easy as consensus,” Journal of the ACM, vol. 66, no. 5. ACM, 2019.","apa":"Lenzen, C., & Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. ACM. https://doi.org/10.1145/3339471","ista":"Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 66(5), 32.","short":"C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019).","mla":"Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM, vol. 66, no. 5, 32, ACM, 2019, doi:10.1145/3339471.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3339471."},"publication":"Journal of the ACM"},{"month":"09","publication_identifier":{"isbn":["9783030302801"],"eisbn":["9783030302818"],"issn":["0302-9743"]},"external_id":{"arxiv":["1906.08178"],"isi":["000679281300007"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.08178"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"conference":{"location":"Glasgow, United Kingdom","start_date":"2019-09-10","end_date":"2019-09-12","name":"QEST: Quantitative Evaluation of Systems"},"doi":"10.1007/978-3-030-30281-8_7","language":[{"iso":"eng"}],"year":"2019","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ChLa"}],"publisher":"Springer Nature","author":[{"full_name":"Ashok, Pranav","first_name":"Pranav","last_name":"Ashok"},{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Křetínský, Jan","first_name":"Jan","last_name":"Křetínský"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","full_name":"Toman, Viktor"}],"date_updated":"2023-08-30T06:59:36Z","date_created":"2019-10-14T06:57:49Z","volume":11785,"scopus_import":"1","day":"04","article_processing_charge":"No","publication":"16th International Conference on Quantitative Evaluation of Systems","citation":{"ama":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. Strategy representation by decision trees with linear classifiers. In: 16th International Conference on Quantitative Evaluation of Systems. Vol 11785. Springer Nature; 2019:109-128. doi:10.1007/978-3-030-30281-8_7","ista":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. 2019. Strategy representation by decision trees with linear classifiers. 16th International Conference on Quantitative Evaluation of Systems. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11785, 109–128.","ieee":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, and V. Toman, “Strategy representation by decision trees with linear classifiers,” in 16th International Conference on Quantitative Evaluation of Systems, Glasgow, United Kingdom, 2019, vol. 11785, pp. 109–128.","apa":"Ashok, P., Brázdil, T., Chatterjee, K., Křetínský, J., Lampert, C., & Toman, V. (2019). Strategy representation by decision trees with linear classifiers. In 16th International Conference on Quantitative Evaluation of Systems (Vol. 11785, pp. 109–128). Glasgow, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-30281-8_7","mla":"Ashok, Pranav, et al. “Strategy Representation by Decision Trees with Linear Classifiers.” 16th International Conference on Quantitative Evaluation of Systems, vol. 11785, Springer Nature, 2019, pp. 109–28, doi:10.1007/978-3-030-30281-8_7.","short":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, V. Toman, in:, 16th International Conference on Quantitative Evaluation of Systems, Springer Nature, 2019, pp. 109–128.","chicago":"Ashok, Pranav, Tomáš Brázdil, Krishnendu Chatterjee, Jan Křetínský, Christoph Lampert, and Viktor Toman. “Strategy Representation by Decision Trees with Linear Classifiers.” In 16th International Conference on Quantitative Evaluation of Systems, 11785:109–28. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-30281-8_7."},"page":"109-128","date_published":"2019-09-04T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Graph games and Markov decision processes (MDPs) are standard models in reactive synthesis and verification of probabilistic systems with nondeterminism. The class of 𝜔 -regular winning conditions; e.g., safety, reachability, liveness, parity conditions; provides a robust and expressive specification formalism for properties that arise in analysis of reactive systems. The resolutions of nondeterminism in games and MDPs are represented as strategies, and we consider succinct representation of such strategies. The decision-tree data structure from machine learning retains the flavor of decisions of strategies and allows entropy-based minimization to obtain succinct trees. However, in contrast to traditional machine-learning problems where small errors are allowed, for winning strategies in graph games and MDPs no error is allowed, and the decision tree must represent the entire strategy. In this work we propose decision trees with linear classifiers for representation of strategies in graph games and MDPs. We have implemented strategy representation using this data structure and we present experimental results for problems on graph games and MDPs, which show that this new data structure presents a much more efficient strategy representation as compared to standard decision trees."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6942","status":"public","title":"Strategy representation by decision trees with linear classifiers","intvolume":" 11785","oa_version":"Preprint"},{"doi":"10.1016/j.physletb.2019.135016","language":[{"iso":"eng"}],"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":{"isi":["000494939000086"],"arxiv":["1904.00913"]},"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"issn":["0370-2693"]},"author":[{"first_name":"C.H.","last_name":"Schmickler","full_name":"Schmickler, C.H."},{"first_name":"H.-W.","last_name":"Hammer","full_name":"Hammer, H.-W."},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"}],"date_created":"2019-10-18T18:33:32Z","date_updated":"2023-08-30T07:06:42Z","volume":798,"year":"2019","publication_status":"published","publisher":"Elsevier","department":[{"_id":"MiLe"}],"file_date_updated":"2020-07-14T12:47:46Z","article_number":"135016","date_published":"2019-11-10T00:00:00Z","publication":"Physics Letters B","citation":{"chicago":"Schmickler, C.H., H.-W. Hammer, and Artem Volosniev. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B. Elsevier, 2019. https://doi.org/10.1016/j.physletb.2019.135016.","mla":"Schmickler, C. H., et al. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B, vol. 798, 135016, Elsevier, 2019, doi:10.1016/j.physletb.2019.135016.","short":"C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019).","ista":"Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states of a few charged particles. Physics Letters B. 798, 135016.","ieee":"C. H. Schmickler, H.-W. Hammer, and A. Volosniev, “Universal physics of bound states of a few charged particles,” Physics Letters B, vol. 798. Elsevier, 2019.","apa":"Schmickler, C. H., Hammer, H.-W., & Volosniev, A. (2019). Universal physics of bound states of a few charged particles. Physics Letters B. Elsevier. https://doi.org/10.1016/j.physletb.2019.135016","ama":"Schmickler CH, Hammer H-W, Volosniev A. Universal physics of bound states of a few charged particles. Physics Letters B. 2019;798. doi:10.1016/j.physletb.2019.135016"},"article_type":"original","day":"10","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2019_PhysicsLettersB_Schmickler.pdf","creator":"dernst","file_size":528362,"content_type":"application/pdf","file_id":"6974","relation":"main_file","checksum":"d27f983b34ea7dafdf356afbf9472fbf","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-10-25T12:47:04Z"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6955","status":"public","title":"Universal physics of bound states of a few charged particles","ddc":["530"],"intvolume":" 798","abstract":[{"text":"We study few-body bound states of charged particles subject to attractive zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic length scales of the system at zero energy are set by the Coulomb length scale D and the Coulomb-modified effective range r eff. We study shallow bound states of charged particles with D >> r eff and show that these systems obey universal scaling laws different from neutral particles. An accurate description of these states requires both the Coulomb-modified scattering length and the effective range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant for bound states whose spatial extent is significantly larger than the range of the attractive potential. These states enjoy universality – their character is independent of the shape of the short-range potential.","lang":"eng"}],"type":"journal_article"},{"month":"12","publication_identifier":{"eissn":["1471-4159"],"issn":["0022-3042"]},"isi":1,"quality_controlled":"1","external_id":{"isi":["000490703100001"],"pmid":["31479508"]},"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,"language":[{"iso":"eng"}],"doi":"10.1111/jnc.14862","file_date_updated":"2020-07-14T12:47:47Z","publication_status":"published","publisher":"Wiley","department":[{"_id":"SiHi"}],"year":"2019","pmid":1,"date_created":"2019-11-12T14:37:08Z","date_updated":"2023-08-30T07:21:50Z","volume":151,"author":[{"first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"full_name":"Cousin, Michael A.","first_name":"Michael A.","last_name":"Cousin"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"570-583","publication":"Journal of Neurochemistry","citation":{"ista":"Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 151(5), 570–583.","apa":"Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862","ieee":"G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,” Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019.","ama":"Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862","chicago":"Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14862.","mla":"Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi:10.1111/jnc.14862.","short":"G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583."},"date_published":"2019-12-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes.","lang":"eng"}],"issue":"5","ddc":["570"],"status":"public","title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","intvolume":" 151","_id":"7005","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7452","checksum":"ec1fb2aebb874009bc309adaada6e1d7","date_created":"2020-02-05T10:30:02Z","date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","file_name":"2019_JournNeurochemistry_Cheung.pdf","file_size":4334962,"content_type":"application/pdf","creator":"dernst"}]},{"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["2101.09081"],"isi":["000488973100005"]},"main_file_link":[{"url":"https://doi.org/10.1007/s40314-019-0955-9","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/s40314-019-0955-9","publication_identifier":{"issn":["2238-3603"],"eissn":["1807-0302"]},"month":"12","publisher":"Springer Nature","department":[{"_id":"VlKo"}],"publication_status":"published","year":"2019","volume":38,"date_updated":"2023-08-30T07:20:32Z","date_created":"2019-11-12T12:41:44Z","author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","first_name":"Yekini"},{"last_name":"Iyiola","first_name":"Olaniyi S.","full_name":"Iyiola, Olaniyi S."},{"full_name":"Li, Xiao-Huan","first_name":"Xiao-Huan","last_name":"Li"},{"first_name":"Qiao-Li","last_name":"Dong","full_name":"Dong, Qiao-Li"}],"article_number":"161","ec_funded":1,"article_type":"original","citation":{"mla":"Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics, vol. 38, no. 4, 161, Springer Nature, 2019, doi:10.1007/s40314-019-0955-9.","short":"Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019).","chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9.","ama":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 2019;38(4). doi:10.1007/s40314-019-0955-9","ista":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 38(4), 161.","apa":"Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9","ieee":"Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of projection method for variational inequalities,” Computational and Applied Mathematics, vol. 38, no. 4. Springer Nature, 2019."},"publication":"Computational and Applied Mathematics","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","intvolume":" 38","ddc":["510","515","518"],"status":"public","title":"Convergence analysis of projection method for variational inequalities","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7000","oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"text":"The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps.","lang":"eng"}]},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","citation":{"chicago":"Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41580-019-0172-9.","short":"K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752.","mla":"Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology, vol. 20, no. 12, Springer Nature, 2019, pp. 738–752, doi:10.1038/s41580-019-0172-9.","apa":"Yamada, K., & Sixt, M. K. (2019). Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-019-0172-9","ieee":"K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” Nature Reviews Molecular Cell Biology, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019.","ista":"Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 20(12), 738–752.","ama":"Yamada K, Sixt MK. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 2019;20(12):738–752. doi:10.1038/s41580-019-0172-9"},"publication":"Nature Reviews Molecular Cell Biology","page":"738–752","article_type":"review","issue":"12","abstract":[{"text":"Cell migration is essential for physiological processes as diverse as development, immune defence and wound healing. It is also a hallmark of cancer malignancy. Thousands of publications have elucidated detailed molecular and biophysical mechanisms of cultured cells migrating on flat, 2D substrates of glass and plastic. However, much less is known about how cells successfully navigate the complex 3D environments of living tissues. In these more complex, native environments, cells use multiple modes of migration, including mesenchymal, amoeboid, lobopodial and collective, and these are governed by the local extracellular microenvironment, specific modalities of Rho GTPase signalling and non- muscle myosin contractility. Migration through 3D environments is challenging because it requires the cell to squeeze through complex or dense extracellular structures. Doing so requires specific cellular adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling. In addition, besides navigating through diverse ECM environments and overcoming extracellular barriers, cells often interact with neighbouring cells and tissues through physical and signalling interactions. Accordingly, cells need to call on an impressively wide diversity of mechanisms to meet these challenges. This Review examines how cells use both classical and novel mechanisms of locomotion as they traverse challenging 3D matrices and cellular environments. It focuses on principles rather than details of migratory mechanisms and draws comparisons between 1D, 2D and 3D migration.","lang":"eng"}],"type":"journal_article","oa_version":"None","_id":"7009","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 20","title":"Mechanisms of 3D cell migration","status":"public","publication_identifier":{"eissn":["1471-0080"],"issn":["1471-0072"]},"month":"12","doi":"10.1038/s41580-019-0172-9","language":[{"iso":"eng"}],"external_id":{"pmid":["31582855"],"isi":["000497966900007"]},"quality_controlled":"1","isi":1,"author":[{"full_name":"Yamada, KM","first_name":"KM","last_name":"Yamada"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"volume":20,"date_updated":"2023-08-30T07:22:20Z","date_created":"2019-11-12T14:54:42Z","pmid":1,"year":"2019","publisher":"Springer Nature","department":[{"_id":"MiSi"}],"publication_status":"published"},{"title":"Platelets in host defense: Experimental and clinical insights","status":"public","intvolume":" 40","_id":"6988","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","type":"journal_article","abstract":[{"text":"Platelets are central players in thrombosis and hemostasis but are increasingly recognized as key components of the immune system. They shape ensuing immune responses by recruiting leukocytes, and support the development of adaptive immunity. Recent data shed new light on the complex role of platelets in immunity. Here, we summarize experimental and clinical data on the role of platelets in host defense against bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet proinflammatory effector functions and cross-talk with the coagulation system, can also result in damage to the host (e.g., acute lung injury and sepsis). Novel clinical insights support this dichotomy: platelet inhibition/thrombocytopenia can be either harmful or protective, depending on pathophysiological context. Clinical studies are currently addressing this aspect in greater depth.","lang":"eng"}],"issue":"10","article_type":"review","page":"922-938","publication":"Trends in Immunology","citation":{"ama":"Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 2019;40(10):922-938. doi:10.1016/j.it.2019.08.004","ieee":"L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental and clinical insights,” Trends in Immunology, vol. 40, no. 10. Cell Press, pp. 922–938, 2019.","apa":"Nicolai, L., Gärtner, F. R., & Massberg, S. (2019). Platelets in host defense: Experimental and clinical insights. Trends in Immunology. Cell Press. https://doi.org/10.1016/j.it.2019.08.004","ista":"Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 40(10), 922–938.","short":"L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938.","mla":"Nicolai, Leo, et al. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology, vol. 40, no. 10, Cell Press, 2019, pp. 922–38, doi:10.1016/j.it.2019.08.004.","chicago":"Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology. Cell Press, 2019. https://doi.org/10.1016/j.it.2019.08.004."},"date_published":"2019-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Cell Press","year":"2019","pmid":1,"date_created":"2019-11-04T16:27:36Z","date_updated":"2023-08-30T07:19:23Z","volume":40,"author":[{"full_name":"Nicolai, Leo","first_name":"Leo","last_name":"Nicolai"},{"last_name":"Gärtner","first_name":"Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R"},{"full_name":"Massberg, Steffen","first_name":"Steffen","last_name":"Massberg"}],"ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["31601520"],"isi":["000493292100005"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.it.2019.08.004","month":"10","publication_identifier":{"issn":["1471-4906"]}},{"date_published":"2019-07-01T00:00:00Z","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"ista":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. 2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4), 37.","ieee":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J. Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","apa":"Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., & Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323009","ama":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal multiple importance sampling. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323009","chicago":"Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009.","mla":"Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009.","short":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (2019)."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"None","title":"Optimal multiple importance sampling","status":"public","intvolume":" 38","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7002","abstract":[{"text":"Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem.","lang":"eng"}],"issue":"4","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1145/3306346.3323009","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Distributed 3D Object Design","grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000475740600011"]},"month":"07","publication_identifier":{"issn":["0730-0301"]},"date_created":"2019-11-12T13:05:40Z","date_updated":"2023-08-30T07:21:25Z","volume":38,"author":[{"full_name":"Kondapaneni, Ivo","last_name":"Kondapaneni","first_name":"Ivo"},{"last_name":"Vevoda","first_name":"Petr","full_name":"Vevoda, Petr"},{"last_name":"Grittmann","first_name":"Pascal","full_name":"Grittmann, Pascal"},{"full_name":"Skrivan, Tomas","first_name":"Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Slusallek, Philipp","last_name":"Slusallek","first_name":"Philipp"},{"full_name":"Křivánek, Jaroslav","first_name":"Jaroslav","last_name":"Křivánek"}],"publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","year":"2019","ec_funded":1,"article_number":"37"},{"date_created":"2019-11-04T10:04:01Z","date_updated":"2023-08-30T07:20:03Z","volume":4,"author":[{"full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dogra, Akshunna","first_name":"Akshunna","last_name":"Dogra"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"year":"2019","month":"10","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevFluids.4.102401","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.02211"}],"external_id":{"arxiv":["1810.02211"],"isi":["000493510400001"]},"abstract":[{"text":"In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence.","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"Preprint","status":"public","title":"Geometry of transient chaos in streamwise-localized pipe flow turbulence","intvolume":" 4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6978","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","article_type":"original","page":"102401","publication":"Physical Review Fluids","citation":{"ista":"Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 102401.","ieee":"N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized pipe flow turbulence,” Physical Review Fluids, vol. 4, no. 10. American Physical Society, p. 102401, 2019.","apa":"Budanur, N. B., Dogra, A., & Hof, B. (2019). Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.4.102401","ama":"Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 2019;4(10):102401. doi:10.1103/PhysRevFluids.4.102401","chicago":"Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids. American Physical Society, 2019. https://doi.org/10.1103/PhysRevFluids.4.102401.","mla":"Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids, vol. 4, no. 10, American Physical Society, 2019, p. 102401, doi:10.1103/PhysRevFluids.4.102401.","short":"N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401."}},{"intvolume":" 9","title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7026","oa_version":"Published Version","file":[{"checksum":"7a11d6c2f9523d65b049512d61733178","date_updated":"2020-07-14T12:47:48Z","date_created":"2019-11-15T10:57:42Z","relation":"main_file","file_id":"7027","content_type":"application/pdf","file_size":4238460,"creator":"dernst","access_level":"open_access","file_name":"2019_CellSystems_Lukacisin.pdf"}],"type":"journal_article","issue":"5","abstract":[{"text":"Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway. We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations. A record of this paper’s transparent peer review process is included in the Supplemental Information.","lang":"eng"}],"page":"423-433.e1-e3","article_type":"original","citation":{"short":"M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3.","mla":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems, vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:10.1016/j.cels.2019.10.004.","chicago":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems. Cell Press, 2019. https://doi.org/10.1016/j.cels.2019.10.004.","ama":"Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 2019;9(5):423-433.e1-e3. doi:10.1016/j.cels.2019.10.004","apa":"Lukacisin, M., & Bollenbach, M. T. (2019). Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2019.10.004","ieee":"M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to drug combinations predict higher-order drug interactions,” Cell Systems, vol. 9, no. 5. Cell Press, pp. 423-433.e1-e3, 2019.","ista":"Lukacisin M, Bollenbach MT. 2019. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 9(5), 423-433.e1-e3."},"publication":"Cell Systems","date_published":"2019-11-27T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","department":[{"_id":"ToBo"}],"publisher":"Cell Press","publication_status":"published","year":"2019","volume":9,"date_updated":"2023-08-30T07:24:58Z","date_created":"2019-11-15T10:51:42Z","author":[{"full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin","first_name":"Martin"},{"full_name":"Bollenbach, Tobias","last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:48Z","project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"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":{"isi":["000499495400003"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.1016/j.cels.2019.10.004","publication_identifier":{"issn":["2405-4712"]},"month":"11"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7034","title":"Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4","status":"public","intvolume":" 39","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We find a graph of genus 5 and its drawing on the orientable surface of genus 4 with every pair of independent edges crossing an even number of times. This shows that the strong Hanani–Tutte theorem cannot be extended to the orientable surface of genus 4. As a base step in the construction we use a counterexample to an extension of the unified Hanani–Tutte theorem on the torus.","lang":"eng"}],"issue":"6","publication":"Combinatorica","citation":{"chicago":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica. Springer Nature, 2019. https://doi.org/10.1007/s00493-019-3905-7.","short":"R. Fulek, J. Kynčl, Combinatorica 39 (2019) 1267–1279.","mla":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica, vol. 39, no. 6, Springer Nature, 2019, pp. 1267–79, doi:10.1007/s00493-019-3905-7.","ieee":"R. Fulek and J. Kynčl, “Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4,” Combinatorica, vol. 39, no. 6. Springer Nature, pp. 1267–1279, 2019.","apa":"Fulek, R., & Kynčl, J. (2019). Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-019-3905-7","ista":"Fulek R, Kynčl J. 2019. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 39(6), 1267–1279.","ama":"Fulek R, Kynčl J. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 2019;39(6):1267-1279. doi:10.1007/s00493-019-3905-7"},"article_type":"original","page":"1267-1279","date_published":"2019-10-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"No","year":"2019","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","author":[{"first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"}],"date_updated":"2023-08-30T07:26:25Z","date_created":"2019-11-18T14:29:50Z","volume":39,"ec_funded":1,"external_id":{"arxiv":["1709.00508"],"isi":["000493267200003"]},"main_file_link":[{"url":"https://arxiv.org/abs/1709.00508","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"doi":"10.1007/s00493-019-3905-7","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["1439-6912"],"issn":["0209-9683"]}},{"month":"10","day":"17","article_processing_charge":"No","publication_identifier":{"isbn":["9781728104690"]},"scopus_import":"1","conference":{"name":"CLEO: Conference on Lasers and Electro-Optics Europe","end_date":"2019-06-27","start_date":"2019-06-23","location":"Munich, Germany"},"doi":"10.1109/cleoe-eqec.2019.8873300","date_published":"2019-10-17T00:00:00Z","language":[{"iso":"eng"}],"publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","external_id":{"isi":["000630002701617"]},"citation":{"ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. In: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. IEEE; 2019. doi:10.1109/cleoe-eqec.2019.8873300","ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. 2019. Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. CLEO: Conference on Lasers and Electro-Optics Europe, 8873300.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, and H. G. L. Schwefel, “Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators,” in 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Munich, Germany, 2019.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kuamri, M., & Schwefel, H. G. L. (2019). Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Munich, Germany: IEEE. https://doi.org/10.1109/cleoe-eqec.2019.8873300","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Frequency Comb Generation in Lithium Niobate Whispering Gallery Mode Resonators.” 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, 8873300, IEEE, 2019, doi:10.1109/cleoe-eqec.2019.8873300.","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, H.G.L. Schwefel, in:, 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, IEEE, 2019.","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kuamri, and Harald G. L. Schwefel. “Electro-Optic Frequency Comb Generation in Lithium Niobate Whispering Gallery Mode Resonators.” In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. IEEE, 2019. https://doi.org/10.1109/cleoe-eqec.2019.8873300."},"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Optical frequency combs (OFCs) are light sources whose spectra consists of equally spaced frequency lines in the optical domain [1]. They have great potential for improving high-capacity data transfer, all-optical atomic clocks, spectroscopy, and high-precision measurements [2]."}],"article_number":"8873300","type":"conference","author":[{"first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Sedlmeir, Florian","first_name":"Florian","last_name":"Sedlmeir"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"first_name":"Madhuri","last_name":"Kuamri","full_name":"Kuamri, Madhuri"},{"last_name":"Schwefel","first_name":"Harald G. L.","full_name":"Schwefel, Harald G. L."}],"date_updated":"2023-08-30T07:26:01Z","date_created":"2019-11-18T13:58:22Z","oa_version":"None","_id":"7032","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","title":"Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators","status":"public","publisher":"IEEE","department":[{"_id":"JoFi"}]},{"date_published":"2019-11-12T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"chicago":"Maes, Margaret E, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-53049-w.","short":"M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific Reports 9 (2019).","mla":"Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” Scientific Reports, vol. 9, 16565, Springer Nature, 2019, doi:10.1038/s41598-019-53049-w.","ieee":"M. E. Maes, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells, “Completion of BAX recruitment correlates with mitochondrial fission during apoptosis,” Scientific Reports, vol. 9. Springer Nature, 2019.","apa":"Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., & Nickells, R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-53049-w","ista":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. 2019. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 9, 16565.","ama":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 2019;9. doi:10.1038/s41598-019-53049-w"},"day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":6467393,"creator":"dernst","access_level":"open_access","file_name":"2019_ScientificReports_Maes.pdf","checksum":"9ab397ed9c1c454b34bffb8cc863d734","date_created":"2019-11-25T07:49:52Z","date_updated":"2020-07-14T12:47:49Z","relation":"main_file","file_id":"7096"}],"oa_version":"Published Version","status":"public","title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","ddc":["570"],"intvolume":" 9","_id":"7095","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"BAX, a member of the BCL2 gene family, controls the committed step of the intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed feature of apoptosis, which occurs through the process of mitochondrial fission. BAX has consistently been associated with mitochondrial fission, yet how BAX participates in the process of mitochondrial fragmentation during apoptosis remains to be tested. Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates that rapid mitochondrial fragmentation during apoptosis occurs after the complete recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement of a fully functioning BAX protein for the fission process was demonstrated further in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant performed fusion to restore the mitochondrial network. but was not demonstrably recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial fragmentation was blocked. Additionally, we show that loss of the fission protein, dynamin-like protein 1 (DRP1), does not temporally affect the initiation time or rate of BAX recruitment, but does reduce the final level of BAX recruited to the MOM during the late phase of BAX recruitment. These correlative observations suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial fragmentation machinery in apoptotic cells.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41598-019-53049-w","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"},"oa":1,"external_id":{"pmid":["31719602"],"isi":["000495857600019"]},"month":"11","publication_identifier":{"eissn":["2045-2322"]},"date_updated":"2023-08-30T07:26:54Z","date_created":"2019-11-25T07:45:17Z","volume":9,"author":[{"full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","first_name":"Margaret E"},{"first_name":"J. A.","last_name":"Grosser","full_name":"Grosser, J. A."},{"full_name":"Fehrman, R. L.","first_name":"R. L.","last_name":"Fehrman"},{"last_name":"Schlamp","first_name":"C. L.","full_name":"Schlamp, C. L."},{"first_name":"R. W.","last_name":"Nickells","full_name":"Nickells, R. W."}],"publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Springer Nature","year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:49Z","article_number":"16565"},{"type":"journal_article","abstract":[{"text":"Early endosomes, also called sorting endosomes, are known to mature into late endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early endosome existence isthought to be maintained by the continual fusion of transport vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial for the formation of endosomes andthe subsequent endolysosomal traffic regulated by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide exchange on Vps21p arefirst recruited to theTGN before transport to the endosome, namely the GEF Vps9p and the epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation and identify the TGN as a critical location forregulating progress through the endolysosomal trafficking pathway.","lang":"eng"}],"issue":"1","title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","status":"public","ddc":["570"],"intvolume":" 2","_id":"7097","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"7098","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T07:58:05Z","checksum":"c63c69a264fc8a0e52f2b0d482f3bdae","file_name":"2019_CommunicBiology_Nagano.pdf","access_level":"open_access","file_size":2626069,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Communications Biology","citation":{"chicago":"Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0670-5.","short":"M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019).","mla":"Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology, vol. 2, no. 1, 419, Springer Nature, 2019, doi:10.1038/s42003-019-0670-5.","apa":"Nagano, M., Toshima, J. Y., Siekhaus, D. E., & Toshima, J. (2019). Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0670-5","ieee":"M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome formation is regulated at the trans-Golgi network,” Communications Biology, vol. 2, no. 1. Springer Nature, 2019.","ista":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. 2019. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2(1), 419.","ama":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2019;2(1). doi:10.1038/s42003-019-0670-5"},"date_published":"2019-11-15T00:00:00Z","article_number":"419","file_date_updated":"2020-07-14T12:47:49Z","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaSi"}],"year":"2019","date_updated":"2023-08-30T07:27:55Z","date_created":"2019-11-25T07:55:01Z","volume":2,"author":[{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"last_name":"Toshima","first_name":"Junko Y.","full_name":"Toshima, Junko Y."},{"first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"month":"11","publication_identifier":{"issn":["2399-3642"]},"quality_controlled":"1","isi":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":["000496767800005"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s42003-019-0670-5"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2019.08.013","quality_controlled":"1","isi":1,"external_id":{"isi":["000497963500017"],"pmid":["31543297"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.013"}],"publication_identifier":{"issn":["0896-6273"]},"month":"11","volume":104,"date_updated":"2023-08-30T07:28:22Z","date_created":"2019-11-25T08:02:39Z","author":[{"first_name":"Yu","last_name":"Kasugai","full_name":"Kasugai, Yu"},{"first_name":"Elisabeth","last_name":"Vogel","full_name":"Vogel, Elisabeth"},{"first_name":"Heide","last_name":"Hörtnagl","full_name":"Hörtnagl, Heide"},{"first_name":"Sabine","last_name":"Schönherr","full_name":"Schönherr, Sabine"},{"full_name":"Paradiso, Enrica","first_name":"Enrica","last_name":"Paradiso"},{"first_name":"Markus","last_name":"Hauschild","full_name":"Hauschild, Markus"},{"last_name":"Göbel","first_name":"Georg","full_name":"Göbel, Georg"},{"last_name":"Milenkovic","first_name":"Ivan","full_name":"Milenkovic, Ivan"},{"full_name":"Peterschmitt, Yvan","first_name":"Yvan","last_name":"Peterschmitt"},{"full_name":"Tasan, Ramon","last_name":"Tasan","first_name":"Ramon"},{"first_name":"Günther","last_name":"Sperk","full_name":"Sperk, Günther"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Sieghart, Werner","last_name":"Sieghart","first_name":"Werner"},{"first_name":"Nicolas","last_name":"Singewald","full_name":"Singewald, Nicolas"},{"full_name":"Lüthi, Andreas","last_name":"Lüthi","first_name":"Andreas"},{"full_name":"Ferraguti, Francesco","first_name":"Francesco","last_name":"Ferraguti"}],"department":[{"_id":"RySh"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"The authors thank Gabi Schmid for excellent technical support. We also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the specificity\r\nof some of the antibodies used in this study on replicas. Funding was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung) Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.), and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous version of the manuscript.","year":"2019","date_published":"2019-11-20T00:00:00Z","page":"781-794.e4","article_type":"original","citation":{"apa":"Kasugai, Y., Vogel, E., Hörtnagl, H., Schönherr, S., Paradiso, E., Hauschild, M., … Ferraguti, F. (2019). Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.013","ieee":"Y. Kasugai et al., “Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning,” Neuron, vol. 104, no. 4. Elsevier, p. 781–794.e4, 2019.","ista":"Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4.","ama":"Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 2019;104(4):781-794.e4. doi:10.1016/j.neuron.2019.08.013","chicago":"Kasugai, Yu, Elisabeth Vogel, Heide Hörtnagl, Sabine Schönherr, Enrica Paradiso, Markus Hauschild, Georg Göbel, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.013.","short":"Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild, G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W. Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4.","mla":"Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron, vol. 104, no. 4, Elsevier, 2019, p. 781–794.e4, doi:10.1016/j.neuron.2019.08.013."},"publication":"Neuron","article_processing_charge":"No","has_accepted_license":"1","day":"20","scopus_import":"1","oa_version":"Published Version","intvolume":" 104","ddc":["571","599"],"title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","status":"public","_id":"7099","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"4","type":"journal_article"},{"isi":1,"quality_controlled":"1","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression"}],"oa":1,"main_file_link":[{"url":"https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf","open_access":"1"}],"external_id":{"isi":["000467631800034"],"pmid":["31073041"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.aav2522","month":"05","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","publisher":"AAAS","department":[{"_id":"SiHi"}],"year":"2019","pmid":1,"date_updated":"2023-09-05T11:51:09Z","date_created":"2019-05-14T13:07:47Z","volume":364,"author":[{"last_name":"Telley","first_name":"L","full_name":"Telley, L"},{"full_name":"Agirman, G","last_name":"Agirman","first_name":"G"},{"first_name":"J","last_name":"Prados","full_name":"Prados, J"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole","last_name":"Amberg","full_name":"Amberg, Nicole"},{"full_name":"Fièvre, S","last_name":"Fièvre","first_name":"S"},{"full_name":"Oberst, P","first_name":"P","last_name":"Oberst"},{"last_name":"Bartolini","first_name":"G","full_name":"Bartolini, G"},{"first_name":"I","last_name":"Vitali","full_name":"Vitali, I"},{"full_name":"Cadilhac, C","first_name":"C","last_name":"Cadilhac"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"first_name":"L","last_name":"Nguyen","full_name":"Nguyen, L"},{"full_name":"Dayer, A","first_name":"A","last_name":"Dayer"},{"full_name":"Jabaudon, D","first_name":"D","last_name":"Jabaudon"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/","relation":"press_release","description":"News on IST Homepage"}]},"article_number":"eaav2522","ec_funded":1,"article_type":"original","publication":"Science","citation":{"short":"L. Telley, G. Agirman, J. Prados, N. Amberg, S. Fièvre, P. Oberst, G. Bartolini, I. Vitali, C. Cadilhac, S. Hippenmeyer, L. Nguyen, A. Dayer, D. Jabaudon, Science 364 (2019).","mla":"Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” Science, vol. 364, no. 6440, eaav2522, AAAS, 2019, doi:10.1126/science.aav2522.","chicago":"Telley, L, G Agirman, J Prados, Nicole Amberg, S Fièvre, P Oberst, G Bartolini, et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” Science. AAAS, 2019. https://doi.org/10.1126/science.aav2522.","ama":"Telley L, Agirman G, Prados J, et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 2019;364(6440). doi:10.1126/science.aav2522","apa":"Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., … Jabaudon, D. (2019). Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. AAAS. https://doi.org/10.1126/science.aav2522","ieee":"L. Telley et al., “Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex,” Science, vol. 364, no. 6440. AAAS, 2019.","ista":"Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G, Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. 2019. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 364(6440), eaav2522."},"date_published":"2019-05-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"No","status":"public","title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","intvolume":" 364","_id":"6455","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"During corticogenesis, distinct subtypes of neurons are sequentially born from ventricular zone progenitors. How these cells are molecularly temporally patterned is poorly understood. We used single-cell RNA sequencing at high temporal resolution to trace the lineage of the molecular identities of successive generations of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified a core set of evolutionarily conserved, temporally patterned genes that drive APs from internally driven to more exteroceptive states. We found that the Polycomb repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic age–dependent AP molecular states are transmitted to their progeny as successive ground states, onto which essentially conserved early postmitotic differentiation programs are applied, and are complemented by later-occurring environment-dependent signals. Thus, epigenetically regulated temporal molecular birthmarks present in progenitors act in their postmitotic progeny to seed adult neuronal diversity.","lang":"eng"}],"issue":"6440"},{"file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"date_updated":"2023-09-05T12:03:45Z","date_created":"2019-06-25T11:53:35Z","volume":141,"author":[{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"full_name":"Genç, Aziz","first_name":"Aziz","last_name":"Genç"},{"orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu","full_name":"Liu, Yu"},{"last_name":"Kuster","first_name":"Beatrice","full_name":"Kuster, Beatrice"},{"full_name":"Schuster, Maximilian","last_name":"Schuster","first_name":"Maximilian"},{"full_name":"Dobrozhan, Oleksandr","first_name":"Oleksandr","last_name":"Dobrozhan"},{"full_name":"Cadavid, Doris","last_name":"Cadavid","first_name":"Doris"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"},{"first_name":"Maksym V.","last_name":"Kovalenko","full_name":"Kovalenko, Maksym V."}],"publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","year":"2019","pmid":1,"month":"04","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"language":[{"iso":"eng"}],"doi":"10.1021/jacs.9b01394","isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"oa":1,"external_id":{"isi":["000469292300004"],"pmid":["31017419 "]},"abstract":[{"lang":"eng","text":"The bottom-up assembly of colloidal nanocrystals is a versatile methodology to produce composite nanomaterials with precisely tuned electronic properties. Beyond the synthetic control over crystal domain size, shape, crystal phase, and composition, solution-processed nanocrystals allow exquisite surface engineering. This provides additional means to modulate the nanomaterial characteristics and particularly its electronic transport properties. For instance, inorganic surface ligands can be used to tune the type and concentration of majority carriers or to modify the electronic band structure. Herein, we report the thermoelectric properties of SnTe nanocomposites obtained from the consolidation of surface-engineered SnTe nanocrystals into macroscopic pellets. A CdSe-based ligand is selected to (i) converge the light and heavy bands through partial Cd alloying and (ii) generate CdSe nanoinclusions as a secondary phase within the SnTe matrix, thereby reducing the thermal conductivity. These SnTe-CdSe nanocomposites possess thermoelectric figures of merit of up to 1.3 at 850 K, which is, to the best of our knowledge, the highest thermoelectric figure of merit reported for solution-processed SnTe."}],"issue":"20","type":"journal_article","file":[{"file_id":"6587","relation":"main_file","date_created":"2019-06-25T11:59:00Z","date_updated":"2020-07-14T12:47:34Z","checksum":"34d7ec837869cc6a07996b54f75696b7","file_name":"JACS_April2019.pdf","access_level":"open_access","creator":"cpetz","content_type":"application/pdf","file_size":6234004}],"oa_version":"Published Version","status":"public","ddc":["540"],"title":"Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion","intvolume":" 141","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6586","day":"19","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-04-19T00:00:00Z","article_type":"original","page":"8025-8029","publication":"Journal of the American Chemical Society","citation":{"ista":"Ibáñez M, Hasler R, Genç A, Liu Y, Kuster B, Schuster M, Dobrozhan O, Cadavid D, Arbiol J, Cabot A, Kovalenko MV. 2019. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. 141(20), 8025–8029.","apa":"Ibáñez, M., Hasler, R., Genç, A., Liu, Y., Kuster, B., Schuster, M., … Kovalenko, M. V. (2019). Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b01394","ieee":"M. Ibáñez et al., “Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion,” Journal of the American Chemical Society, vol. 141, no. 20. American Chemical Society, pp. 8025–8029, 2019.","ama":"Ibáñez M, Hasler R, Genç A, et al. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. 2019;141(20):8025-8029. doi:10.1021/jacs.9b01394","chicago":"Ibáñez, Maria, Roger Hasler, Aziz Genç, Yu Liu, Beatrice Kuster, Maximilian Schuster, Oleksandr Dobrozhan, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b01394.","mla":"Ibáñez, Maria, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal of the American Chemical Society, vol. 141, no. 20, American Chemical Society, 2019, pp. 8025–29, doi:10.1021/jacs.9b01394.","short":"M. Ibáñez, R. Hasler, A. Genç, Y. Liu, B. Kuster, M. Schuster, O. Dobrozhan, D. Cadavid, J. Arbiol, A. Cabot, M.V. Kovalenko, Journal of the American Chemical Society 141 (2019) 8025–8029."}},{"article_number":"094205","year":"2019","publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","author":[{"full_name":"Dumitrescu, Philipp T.","first_name":"Philipp T.","last_name":"Dumitrescu"},{"full_name":"Goremykina, Anna","last_name":"Goremykina","first_name":"Anna"},{"full_name":"Parameswaran, Siddharth A.","first_name":"Siddharth A.","last_name":"Parameswaran"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"last_name":"Vasseur","first_name":"Romain","full_name":"Vasseur, Romain"}],"date_created":"2019-03-25T07:32:08Z","date_updated":"2023-09-05T12:11:13Z","volume":99,"month":"03","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.03103"}],"external_id":{"isi":["000462883200001"],"arxiv":["1811.03103"]},"isi":1,"quality_controlled":"1","doi":"10.1103/physrevb.99.094205","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We propose a scaling theory for the many-body localization (MBL) phase transition in one dimension, building on the idea that it proceeds via a “quantum avalanche.” We argue that the critical properties can be captured at a coarse-grained level by a Kosterlitz-Thouless (KT) renormalization group (RG) flow. On phenomenological grounds, we identify the scaling variables as the density of thermal regions and the length scale that controls the decay of typical matrix elements. Within this KT picture, the MBL phase is a line of fixed points that terminates at the delocalization transition. We discuss two possible scenarios distinguished by the distribution of rare, fractal thermal inclusions within the MBL phase. In the first scenario, these regions have a stretched exponential distribution in the MBL phase. In the second scenario, the near-critical MBL phase hosts rare thermal regions that are power-law-distributed in size. This points to the existence of a second transition within the MBL phase, at which these power laws change to the stretched exponential form expected at strong disorder. We numerically simulate two different phenomenological RGs previously proposed to describe the MBL transition. Both RGs display a universal power-law length distribution of thermal regions at the transition with a critical exponent αc=2, and continuously varying exponents in the MBL phase consistent with the KT picture."}],"issue":"9","_id":"6174","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Kosterlitz-Thouless scaling at many-body localization phase transitions","intvolume":" 99","oa_version":"Preprint","scopus_import":"1","day":"22","article_processing_charge":"No","publication":"Physical Review B","citation":{"mla":"Dumitrescu, Philipp T., et al. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” Physical Review B, vol. 99, no. 9, 094205, American Physical Society, 2019, doi:10.1103/physrevb.99.094205.","short":"P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur, Physical Review B 99 (2019).","chicago":"Dumitrescu, Philipp T., Anna Goremykina, Siddharth A. Parameswaran, Maksym Serbyn, and Romain Vasseur. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.99.094205.","ama":"Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 2019;99(9). doi:10.1103/physrevb.99.094205","ista":"Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. 2019. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 99(9), 094205.","apa":"Dumitrescu, P. T., Goremykina, A., Parameswaran, S. A., Serbyn, M., & Vasseur, R. (2019). Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.99.094205","ieee":"P. T. Dumitrescu, A. Goremykina, S. A. Parameswaran, M. Serbyn, and R. Vasseur, “Kosterlitz-Thouless scaling at many-body localization phase transitions,” Physical Review B, vol. 99, no. 9. American Physical Society, 2019."},"article_type":"original","date_published":"2019-03-22T00:00:00Z"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","article_type":"original","page":"757-766","publication":"Plant Physiology","citation":{"chicago":"Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01377.","mla":"Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:10.1104/pp.18.01377.","short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","ista":"Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766.","apa":"Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01377","ieee":"J. Bellstaedt et al., “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 757–766, 2019.","ama":"Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 2019;180(2):757-766. doi:10.1104/pp.18.01377"},"abstract":[{"lang":"eng","text":"Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl."}],"issue":"2","type":"journal_article","oa_version":"Published Version","status":"public","title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","intvolume":" 180","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6366","month":"06","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"language":[{"iso":"eng"}],"doi":"10.1104/pp.18.01377","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"www.doi.org/10.1104/pp.18.01377"}],"external_id":{"isi":["000470086100019"],"pmid":["31000634"]},"date_updated":"2023-09-05T12:25:19Z","date_created":"2019-04-30T15:24:22Z","volume":180,"author":[{"last_name":"Bellstaedt","first_name":"Julia","full_name":"Bellstaedt, Julia"},{"first_name":"Jana","last_name":"Trenner","full_name":"Trenner, Jana"},{"full_name":"Lippmann, Rebecca","last_name":"Lippmann","first_name":"Rebecca"},{"full_name":"Poeschl, Yvonne","last_name":"Poeschl","first_name":"Yvonne"},{"first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"full_name":"Quint, Marcel","first_name":"Marcel","last_name":"Quint"},{"full_name":"Delker, Carolin","last_name":"Delker","first_name":"Carolin"}],"publication_status":"published","publisher":"ASPB","department":[{"_id":"JiFr"}],"year":"2019","pmid":1},{"date_published":"2019-11-01T00:00:00Z","citation":{"ista":"Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 147(11), 4597–4604.","ieee":"P. Li, “A colimit of traces of reflection groups,” Proceedings of the American Mathematical Society, vol. 147, no. 11. AMS, pp. 4597–4604, 2019.","apa":"Li, P. (2019). A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14586","ama":"Li P. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 2019;147(11):4597-4604. doi:10.1090/proc/14586","chicago":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14586.","mla":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society, vol. 147, no. 11, AMS, 2019, pp. 4597–604, doi:10.1090/proc/14586.","short":"P. Li, Proceedings of the American Mathematical Society 147 (2019) 4597–4604."},"publication":"Proceedings of the American Mathematical Society","page":"4597-4604","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"6986","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 147","title":"A colimit of traces of reflection groups","status":"public","issue":"11","abstract":[{"lang":"eng","text":"Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory. "}],"type":"journal_article","doi":"10.1090/proc/14586","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000488621700004"],"arxiv":["1810.07039"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.07039"}],"project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"month":"11","author":[{"full_name":"Li, Penghui","id":"42A24CCC-F248-11E8-B48F-1D18A9856A87","first_name":"Penghui","last_name":"Li"}],"volume":147,"date_created":"2019-11-04T16:10:50Z","date_updated":"2023-09-05T12:22:21Z","year":"2019","department":[{"_id":"TaHa"}],"publisher":"AMS","publication_status":"published","ec_funded":1},{"type":"journal_article","issue":"1","abstract":[{"text":"Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells.","lang":"eng"}],"intvolume":" 102","status":"public","title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6454","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6457","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-15T09:28:41Z","checksum":"1fb6e195c583eb0c5cabf26f69ff6675","file_name":"2019_Neuron_Ortiz.pdf","access_level":"open_access","file_size":7288572,"content_type":"application/pdf","creator":"dernst"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"03","page":"159-172.e7","citation":{"ista":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 102(1), 159–172.e7.","ieee":"G. Ortiz-Álvarez et al., “Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members,” Neuron, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019.","apa":"Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt, M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.051","ama":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 2019;102(1):159-172.e7. doi:10.1016/j.neuron.2019.01.051","chicago":"Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt, S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.051.","mla":"Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron, vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:10.1016/j.neuron.2019.01.051.","short":"G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt, S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A. Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7."},"publication":"Neuron","date_published":"2019-04-03T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z","department":[{"_id":"SiHi"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","volume":102,"date_created":"2019-05-14T13:06:30Z","date_updated":"2023-09-05T13:02:21Z","author":[{"last_name":"Ortiz-Álvarez","first_name":"G","full_name":"Ortiz-Álvarez, G"},{"first_name":"M","last_name":"Daclin","full_name":"Daclin, M"},{"full_name":"Shihavuddin, A","last_name":"Shihavuddin","first_name":"A"},{"full_name":"Lansade, P","first_name":"P","last_name":"Lansade"},{"last_name":"Fortoul","first_name":"A","full_name":"Fortoul, A"},{"full_name":"Faucourt, M","last_name":"Faucourt","first_name":"M"},{"full_name":"Clavreul, S","first_name":"S","last_name":"Clavreul"},{"full_name":"Lalioti, ME","last_name":"Lalioti","first_name":"ME"},{"first_name":"S","last_name":"Taraviras","full_name":"Taraviras, S"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"Livet, J","last_name":"Livet","first_name":"J"},{"last_name":"Meunier","first_name":"A","full_name":"Meunier, A"},{"full_name":"Genovesio, A","first_name":"A","last_name":"Genovesio"},{"full_name":"Spassky, N","last_name":"Spassky","first_name":"N"}],"publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"month":"04","project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["30824354"],"isi":["000463337900018"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2019.01.051"},{"date_published":"2019-10-21T00:00:00Z","citation":{"short":"A. Kopf, M.K. Sixt, Current Biology 29 (2019) R1091–R1093.","mla":"Kopf, Aglaja, and Michael K. Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology, vol. 29, no. 20, Cell Press, 2019, pp. R1091–93, doi:10.1016/j.cub.2019.08.068.","chicago":"Kopf, Aglaja, and Michael K Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology. Cell Press, 2019. https://doi.org/10.1016/j.cub.2019.08.068.","ama":"Kopf A, Sixt MK. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 2019;29(20):R1091-R1093. doi:10.1016/j.cub.2019.08.068","ieee":"A. Kopf and M. K. Sixt, “Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal,” Current Biology, vol. 29, no. 20. Cell Press, pp. R1091–R1093, 2019.","apa":"Kopf, A., & Sixt, M. K. (2019). Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.08.068","ista":"Kopf A, Sixt MK. 2019. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 29(20), R1091–R1093."},"publication":"Current Biology","page":"R1091-R1093","article_type":"original","article_processing_charge":"No","day":"21","scopus_import":"1","oa_version":"None","_id":"6979","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 29","title":"Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal","status":"public","issue":"20","type":"journal_article","doi":"10.1016/j.cub.2019.08.068","language":[{"iso":"eng"}],"external_id":{"pmid":["31639357"],"isi":["000491286200016"]},"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"month":"10","author":[{"full_name":"Kopf, Aglaja","first_name":"Aglaja","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"volume":29,"date_updated":"2023-09-05T12:43:43Z","date_created":"2019-11-04T15:18:29Z","pmid":1,"year":"2019","publisher":"Cell Press","department":[{"_id":"MiSi"}],"publication_status":"published"},{"date_updated":"2023-09-05T13:04:13Z","date_created":"2019-11-04T15:24:29Z","volume":38,"author":[{"full_name":"Petridou, Nicoletta","last_name":"Petridou","first_name":"Nicoletta","orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"publication_status":"published","publisher":"EMBO","department":[{"_id":"CaHe"}],"year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:46Z","ec_funded":1,"article_number":"e102497","language":[{"iso":"eng"}],"doi":"10.15252/embj.2019102497","isi":1,"quality_controlled":"1","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"call_identifier":"FWF","name":"Tissue material properties in embryonic development","grant_number":"V00736","_id":"2693FD8C-B435-11E9-9278-68D0E5697425"}],"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,"external_id":{"isi":["000485561900001"],"pmid":["31512749"]},"month":"10","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"file":[{"creator":"dernst","content_type":"application/pdf","file_size":847356,"access_level":"open_access","file_name":"2019_Embo_Petridou.pdf","checksum":"76f7f4e79ab6d850c30017a69726fd85","date_created":"2019-11-04T15:30:08Z","date_updated":"2020-07-14T12:47:46Z","file_id":"6981","relation":"main_file"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Tissue rheology in embryonic organization","intvolume":" 38","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6980","abstract":[{"text":"Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development.","lang":"eng"}],"issue":"20","type":"journal_article","date_published":"2019-10-15T00:00:00Z","article_type":"review","publication":"The EMBO Journal","citation":{"chicago":"Petridou, Nicoletta, and Carl-Philipp J Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal. EMBO, 2019. https://doi.org/10.15252/embj.2019102497.","mla":"Petridou, Nicoletta, and Carl-Philipp J. Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal, vol. 38, no. 20, e102497, EMBO, 2019, doi:10.15252/embj.2019102497.","short":"N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (2019).","ista":"Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization. The EMBO Journal. 38(20), e102497.","ieee":"N. Petridou and C.-P. J. Heisenberg, “Tissue rheology in embryonic organization,” The EMBO Journal, vol. 38, no. 20. EMBO, 2019.","apa":"Petridou, N., & Heisenberg, C.-P. J. (2019). Tissue rheology in embryonic organization. The EMBO Journal. EMBO. https://doi.org/10.15252/embj.2019102497","ama":"Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. The EMBO Journal. 2019;38(20). doi:10.15252/embj.2019102497"},"day":"15","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1"},{"issue":"9","abstract":[{"lang":"eng","text":"Due to the importance of zero-shot learning, i.e. classifying images where there is a lack of labeled training data, the number of proposed approaches has recently increased steadily. We argue that it is time to take a step back and to analyze the status quo of the area. The purpose of this paper is three-fold. First, given the fact that there is no agreed upon zero-shot learning benchmark, we first define a new benchmark by unifying both the evaluation protocols and data splits of publicly available datasets used for this task. This is an important contribution as published results are often not comparable and sometimes even flawed due to, e.g. pre-training on zero-shot test classes. Moreover, we propose a new zero-shot learning dataset, the Animals with Attributes 2 (AWA2) dataset which we make publicly available both in terms of image features and the images themselves. Second, we compare and analyze a significant number of the state-of-the-art methods in depth, both in the classic zero-shot setting but also in the more realistic generalized zero-shot setting. Finally, we discuss in detail the limitations of the current status of the area which can be taken as a basis for advancing it."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 41","title":"Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly","status":"public","_id":"6554","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-09-01T00:00:00Z","page":"2251 - 2265","article_type":"original","citation":{"ama":"Xian Y, Lampert C, Schiele B, Akata Z. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2019;41(9):2251-2265. doi:10.1109/tpami.2018.2857768","ista":"Xian Y, Lampert C, Schiele B, Akata Z. 2019. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 41(9), 2251–2265.","apa":"Xian, Y., Lampert, C., Schiele, B., & Akata, Z. (2019). Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE). https://doi.org/10.1109/tpami.2018.2857768","ieee":"Y. Xian, C. Lampert, B. Schiele, and Z. Akata, “Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9. Institute of Electrical and Electronics Engineers (IEEE), pp. 2251–2265, 2019.","mla":"Xian, Yongqin, et al. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9, Institute of Electrical and Electronics Engineers (IEEE), 2019, pp. 2251–65, doi:10.1109/tpami.2018.2857768.","short":"Y. Xian, C. Lampert, B. Schiele, Z. Akata, IEEE Transactions on Pattern Analysis and Machine Intelligence 41 (2019) 2251–2265.","chicago":"Xian, Yongqin, Christoph Lampert, Bernt Schiele, and Zeynep Akata. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE), 2019. https://doi.org/10.1109/tpami.2018.2857768."},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","volume":41,"date_created":"2019-06-11T14:05:59Z","date_updated":"2023-09-05T13:18:09Z","author":[{"first_name":"Yongqin","last_name":"Xian","full_name":"Xian, Yongqin"},{"orcid":"0000-0002-4561-241X","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"},{"first_name":"Bernt","last_name":"Schiele","full_name":"Schiele, Bernt"},{"full_name":"Akata, Zeynep","first_name":"Zeynep","last_name":"Akata"}],"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","department":[{"_id":"ChLa"}],"publication_status":"published","year":"2019","publication_identifier":{"eissn":["1939-3539"],"issn":["0162-8828"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1109/tpami.2018.2857768","quality_controlled":"1","isi":1,"external_id":{"arxiv":["1707.00600"],"isi":["000480343900015"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1707.00600"}],"oa":1},{"date_published":"2019-04-11T00:00:00Z","citation":{"ista":"Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z, Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 568, 240–243.","apa":"Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1069-7","ieee":"M. Cao et al., “TMK1-mediated auxin signalling regulates differential growth of the apical hook,” Nature, vol. 568. Springer Nature, pp. 240–243, 2019.","ama":"Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 2019;568:240-243. doi:10.1038/s41586-019-1069-7","chicago":"Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1069-7.","mla":"Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature, vol. 568, Springer Nature, 2019, pp. 240–43, doi:10.1038/s41586-019-1069-7.","short":"M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu, Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243."},"publication":"Nature","page":"240-243","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"11","scopus_import":"1","oa_version":"Submitted Version","file":[{"success":1,"checksum":"6b84ab602a34382cf0340a37a1378c75","date_created":"2020-11-13T07:37:41Z","date_updated":"2020-11-13T07:37:41Z","file_id":"8751","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4321328,"access_level":"open_access","file_name":"2019_Nature _Cao_accepted.pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6259","intvolume":" 568","status":"public","ddc":["580"],"title":"TMK1-mediated auxin signalling regulates differential growth of the apical hook","abstract":[{"text":"The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes.","lang":"eng"}],"type":"journal_article","doi":"10.1038/s41586-019-1069-7","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["30944466"],"isi":["000464412700050"]},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"04","related_material":{"link":[{"url":"https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"full_name":"Cao, Min","last_name":"Cao","first_name":"Min"},{"first_name":"Rong","last_name":"Chen","full_name":"Chen, Rong"},{"full_name":"Li, Pan","last_name":"Li","first_name":"Pan"},{"full_name":"Yu, Yongqiang","last_name":"Yu","first_name":"Yongqiang"},{"first_name":"Rui","last_name":"Zheng","full_name":"Zheng, Rui"},{"first_name":"Danfeng","last_name":"Ge","full_name":"Ge, Danfeng"},{"last_name":"Zheng","first_name":"Wei","full_name":"Zheng, Wei"},{"last_name":"Wang","first_name":"Xuhui","full_name":"Wang, Xuhui"},{"full_name":"Gu, Yangtao","last_name":"Gu","first_name":"Yangtao"},{"full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","first_name":"Zuzana"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Zhang, Heng","first_name":"Heng","last_name":"Zhang"},{"last_name":"Liu","first_name":"Renyi","full_name":"Liu, Renyi"},{"full_name":"He, Jun","last_name":"He","first_name":"Jun"},{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"}],"volume":568,"date_created":"2019-04-09T08:37:05Z","date_updated":"2023-09-05T14:58:41Z","pmid":1,"year":"2019","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-11-13T07:37:41Z"},{"publication_identifier":{"issn":["0080-1844"],"eissn":["1861-0412"],"isbn":["9783030234584","9783030234591"]},"month":"10","quality_controlled":"1","oa":1,"external_id":{"pmid":["31598855"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-23459-1_6","file_date_updated":"2020-07-14T12:47:46Z","publisher":"Springer Nature","editor":[{"full_name":"Tworzydlo, Waclaw","first_name":"Waclaw","last_name":"Tworzydlo"},{"full_name":"Bilinski, Szczepan M.","first_name":"Szczepan M.","last_name":"Bilinski"}],"department":[{"_id":"CaHe"}],"publication_status":"published","pmid":1,"year":"2019","volume":68,"date_created":"2019-11-04T16:20:19Z","date_updated":"2023-09-05T15:01:12Z","author":[{"first_name":"Alex","last_name":"McDougall","full_name":"McDougall, Alex"},{"full_name":"Chenevert, Janet","last_name":"Chenevert","first_name":"Janet"},{"first_name":"Benoit G","last_name":"Godard","id":"33280250-F248-11E8-B48F-1D18A9856A87","full_name":"Godard, Benoit G"},{"first_name":"Remi","last_name":"Dumollard","full_name":"Dumollard, Remi"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"10","page":"127-154","citation":{"ama":"McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. Evo-Devo: Non-Model Species in Cell and Developmental Biology. Vol 68. Springer Nature; 2019:127-154. doi:10.1007/978-3-030-23459-1_6","ista":"McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental biology. RESULTS, vol. 68, 127–154.","ieee":"A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of embryo shape during cleavage divisions,” in Evo-Devo: Non-model species in cell and developmental biology, vol. 68, W. Tworzydlo and S. M. Bilinski, Eds. Springer Nature, 2019, pp. 127–154.","apa":"McDougall, A., Chenevert, J., Godard, B. G., & Dumollard, R. (2019). Emergence of embryo shape during cleavage divisions. In W. Tworzydlo & S. M. Bilinski (Eds.), Evo-Devo: Non-model species in cell and developmental biology (Vol. 68, pp. 127–154). Springer Nature. https://doi.org/10.1007/978-3-030-23459-1_6","mla":"McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.” Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp. 127–54, doi:10.1007/978-3-030-23459-1_6.","short":"A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo, S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology, Springer Nature, 2019, pp. 127–154.","chicago":"McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard. “Emergence of Embryo Shape during Cleavage Divisions.” In Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23459-1_6."},"publication":"Evo-Devo: Non-model species in cell and developmental biology","date_published":"2019-10-10T00:00:00Z","alternative_title":["RESULTS"],"type":"book_chapter","abstract":[{"lang":"eng","text":"Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern."}],"intvolume":" 68","status":"public","ddc":["570"],"title":"Emergence of embryo shape during cleavage divisions","_id":"6987","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_updated":"2020-07-14T12:47:46Z","date_created":"2020-05-14T10:09:30Z","checksum":"7f43e1e3706d15061475c5c57efc2786","file_id":"7829","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":19317348,"file_name":"2019_RESULTS_McDougall.pdf","access_level":"open_access"}],"oa_version":"Submitted Version"},{"scopus_import":"1","day":"16","article_processing_charge":"No","page":"926-947","publication":"Multiscale Modeling and Simulation","citation":{"chicago":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation. SIAM, 2019. https://doi.org/10.1137/18M1207272.","mla":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272.","short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.","ista":"Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947.","apa":"Friesecke, G., & Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. SIAM. https://doi.org/10.1137/18M1207272","ieee":"G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” Multiscale Modeling and Simulation, vol. 17, no. 3. SIAM, pp. 926–947, 2019.","ama":"Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947. doi:10.1137/18M1207272"},"date_published":"2019-07-16T00:00:00Z","type":"journal_article","abstract":[{"text":"We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size.","lang":"eng"}],"issue":"3","title":"New optimal control problems in density functional theory motivated by photovoltaics","status":"public","intvolume":" 17","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6762","oa_version":"Preprint","month":"07","publication_identifier":{"eissn":["15403467"],"issn":["15403459"]},"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04200"}],"external_id":{"isi":["000487931800002"],"arxiv":["1808.04200"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1137/18M1207272","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"SIAM","year":"2019","date_created":"2019-08-04T21:59:21Z","date_updated":"2023-09-05T15:05:45Z","volume":17,"author":[{"full_name":"Friesecke, Gero","first_name":"Gero","last_name":"Friesecke"},{"full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","first_name":"Michael"}]},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.08986"}],"oa":1,"external_id":{"arxiv":["1807.08986"]},"quality_controlled":"1","doi":"10.1007/s40993-018-0146-6","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["2363-9555"],"issn":["2522-0160"]},"year":"2019","acknowledgement":"The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. ","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"TiBr"}],"author":[{"full_name":"Ionica, Sorina","first_name":"Sorina","last_name":"Ionica"},{"last_name":"Kılıçer","first_name":"Pınar","full_name":"Kılıçer, Pınar"},{"first_name":"Kristin","last_name":"Lauter","full_name":"Lauter, Kristin"},{"full_name":"Lorenzo García, Elisa","last_name":"Lorenzo García","first_name":"Elisa"},{"id":"be8d652e-a908-11ec-82a4-e2867729459c","last_name":"Manzateanu","first_name":"Maria-Adelina","full_name":"Manzateanu, Maria-Adelina"},{"first_name":"Maike","last_name":"Massierer","full_name":"Massierer, Maike"},{"first_name":"Christelle","last_name":"Vincent","full_name":"Vincent, Christelle"}],"date_updated":"2023-09-05T15:39:31Z","date_created":"2022-03-18T12:09:48Z","volume":5,"article_number":"9","publication":"Research in Number Theory","citation":{"chicago":"Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019. https://doi.org/10.1007/s40993-018-0146-6.","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019).","mla":"Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6.","ieee":"S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 2019.","apa":"Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6","ista":"Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9.","ama":"Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6"},"article_type":"original","date_published":"2019-01-02T00:00:00Z","scopus_import":"1","keyword":["Algebra and Number Theory"],"day":"02","article_processing_charge":"No","_id":"10874","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Modular invariants for genus 3 hyperelliptic curves","status":"public","intvolume":" 5","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM."}]},{"date_created":"2019-11-25T08:08:02Z","date_updated":"2023-09-06T10:47:43Z","volume":372,"author":[{"full_name":"Jeblick, Maximilian","last_name":"Jeblick","first_name":"Maximilian"},{"first_name":"Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","acknowledgement":"OA fund by IST Austria","year":"2019","file_date_updated":"2020-07-14T12:47:49Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00220-019-03599-x","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"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,"external_id":{"isi":["000495193700002"]},"month":"11","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"oa_version":"Published Version","file":[{"checksum":"cd283b475dd739e04655315abd46f528","date_created":"2019-11-25T08:11:11Z","date_updated":"2020-07-14T12:47:49Z","relation":"main_file","file_id":"7101","file_size":884469,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_CommMathPhys_Jeblick.pdf"}],"ddc":["510"],"status":"public","title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","intvolume":" 372","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7100","abstract":[{"lang":"eng","text":"We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics."}],"issue":"1","type":"journal_article","date_published":"2019-11-08T00:00:00Z","article_type":"original","page":"1-69","publication":"Communications in Mathematical Physics","citation":{"mla":"Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics, vol. 372, no. 1, Springer Nature, 2019, pp. 1–69, doi:10.1007/s00220-019-03599-x.","short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69.","chicago":"Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03599-x.","ama":"Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 2019;372(1):1-69. doi:10.1007/s00220-019-03599-x","ista":"Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69.","apa":"Jeblick, M., Leopold, N. K., & Pickl, P. (2019). Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03599-x","ieee":"M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent Gross–Pitaevskii equation in two dimensions,” Communications in Mathematical Physics, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019."},"day":"08","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1"}]