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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."},"main_file_link":[{"open_access":"1","url":"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","day":"12","month":"09","article_processing_charge":"No","title":"Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","year":"2019","_id":"9901","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":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"last_name":"Shelyakin","first_name":"Pavel V.","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."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"type":"research_data_reference","abstract":[{"text":"Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)","lang":"eng"}]},{"abstract":[{"lang":"eng","text":"Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)"}],"type":"research_data_reference","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"full_name":"Chaplin, Andrei V.","first_name":"Andrei V.","last_name":"Chaplin"},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"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_created":"2021-08-12T08:18:09Z","date_updated":"2023-08-30T06:20:22Z","year":"2019","_id":"9899","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","title":"Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","article_processing_charge":"No","month":"09","day":"12","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808865.v1","oa":1,"citation":{"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.","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.","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","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."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808865.v1","open_access":"1"}]},{"article_processing_charge":"No","month":"09","day":"12","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808886.v1","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 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.","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.","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.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808886.v1."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808886.v1","open_access":"1"}],"oa":1,"abstract":[{"text":"Pan-genome statistics by species. (CSV 3 kb)","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-12T08:44:49Z","date_updated":"2023-08-30T06:20:22Z","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.","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"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","status":"public","title":"Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","year":"2019","_id":"9900","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"month":"11","publication_identifier":{"issn":["0906-7590"],"eissn":["1600-0587"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000486348700001"]},"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/ecog.04444","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:45Z","ec_funded":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"DaAl"}],"year":"2019","date_updated":"2023-08-30T06:57:25Z","date_created":"2019-10-08T13:01:24Z","volume":42,"author":[{"full_name":"Ovaskainen, Otso","first_name":"Otso","last_name":"Ovaskainen"},{"full_name":"Rybicki, Joel","last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nerea","last_name":"Abrego","full_name":"Abrego, Nerea"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"1877-1886","publication":"Ecography","citation":{"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","ama":"Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about metacommunity processes? Ecography. 2019;42(11):1877-1886. doi:10.1111/ecog.04444","chicago":"Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography. Wiley, 2019. https://doi.org/10.1111/ecog.04444.","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."},"date_published":"2019-11-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.\r\n"}],"issue":"11","ddc":["577"],"status":"public","title":"What can observational data reveal about metacommunity processes?","intvolume":" 42","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6936","oa_version":"Published Version","file":[{"date_created":"2019-10-08T13:07:44Z","date_updated":"2020-07-14T12:47:45Z","checksum":"6c9fbbd5ea8ce10ae93e55ad560a7bf9","file_id":"6937","relation":"main_file","creator":"jrybicki","file_size":1682718,"content_type":"application/pdf","file_name":"ecog.04444.pdf","access_level":"open_access"}]},{"doi":"10.1002/bies.201900151","language":[{"iso":"eng"}],"external_id":{"isi":["000489502000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"eissn":["1521-1878"]},"author":[{"full_name":"Giese, B","first_name":"B","last_name":"Giese"},{"full_name":"Friess, J L","last_name":"Friess","first_name":"J L"},{"first_name":"M F ","last_name":"Schetelig","full_name":"Schetelig, 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"},{"first_name":"Philip","last_name":"Messer","full_name":"Messer, Philip"},{"full_name":"Debarre, Florence","first_name":"Florence","last_name":"Debarre"},{"full_name":"Meimberg, H","last_name":"Meimberg","first_name":"H"},{"last_name":"Windbichler","first_name":"N","full_name":"Windbichler, N"},{"first_name":"C","last_name":"Boete","full_name":"Boete, C"}],"date_created":"2019-09-07T14:40:03Z","date_updated":"2023-08-30T06:56:26Z","volume":41,"year":"2019","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:42Z","article_number":"1900151","date_published":"2019-11-01T00:00:00Z","publication":"BioEssays","citation":{"ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151","ieee":"B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.","short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.","chicago":"Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151."},"article_type":"original","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"file_id":"6939","relation":"main_file","checksum":"8cc7551bff70b2658f8d5630f228ee12","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-10-11T06:59:26Z","access_level":"open_access","file_name":"2019_BioEssays_Giese.pdf","creator":"dernst","file_size":193248,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6857","status":"public","title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","ddc":["570"],"intvolume":" 41","abstract":[{"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.","lang":"eng"}],"issue":"11","type":"journal_article"},{"quality_controlled":"1","isi":1,"project":[{"grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"A path-integral approach to composite impurities"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.06253"}],"oa":1,"external_id":{"arxiv":["1907.06253"],"isi":["000483587200004"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.123.100601","month":"09","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","acknowledgement":"We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1 - 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021 Joint Project “Strongly interacting systems in confined geometries” is gratefully acknowledged.","year":"2019","date_created":"2019-10-14T06:31:13Z","date_updated":"2023-08-30T06:57:53Z","volume":123,"author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","last_name":"Bighin","full_name":"Bighin, Giacomo"},{"first_name":"Nicolò","last_name":"Defenu","full_name":"Defenu, Nicolò"},{"full_name":"Nándori, István","last_name":"Nándori","first_name":"István"},{"full_name":"Salasnich, Luca","first_name":"Luca","last_name":"Salasnich"},{"full_name":"Trombettoni, Andrea","last_name":"Trombettoni","first_name":"Andrea"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-form-of-magnetism-found/","relation":"press_release","description":"News auf IST Website"}]},"article_number":"100601","article_type":"original","publication":"Physical Review Letters","citation":{"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.","short":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical Review Letters 123 (2019).","mla":"Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters, vol. 123, no. 10, 100601, American Physical Society, 2019, doi:10.1103/physrevlett.123.100601.","ieee":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models,” Physical Review Letters, vol. 123, no. 10. American Physical Society, 2019.","apa":"Bighin, G., Defenu, N., Nándori, I., Salasnich, L., & Trombettoni, A. (2019). Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.100601","ista":"Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 123(10), 100601.","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"},"date_published":"2019-09-06T00:00:00Z","scopus_import":"1","day":"06","article_processing_charge":"No","status":"public","title":"Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models","intvolume":" 123","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6940","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We study the effect of a linear tunneling coupling between two-dimensional systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless (BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the one-body correlation functions are algebraically decaying and the other with\r\nexponential decay. When the linear coupling is turned on, a third BKT-paired phase emerges, in which one-body correlations are exponentially decaying, while two-body correlation functions exhibit power-law\r\ndecay. We perform numerical simulations in the paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent. We provide a picture of the phase diagram using a renormalization group approach."}],"issue":"10"},{"file_date_updated":"2020-07-14T12:47:44Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","article_number":"eaaw6490","author":[{"full_name":"Qi, Chao","last_name":"Qi","first_name":"Chao"},{"full_name":"Minin, Giulio Di","first_name":"Giulio Di","last_name":"Minin"},{"full_name":"Vercellino, Irene","last_name":"Vercellino","first_name":"Irene","orcid":"0000-0001-5618-3449","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anton","last_name":"Wutz","full_name":"Wutz, Anton"},{"full_name":"Korkhov, Volodymyr M.","last_name":"Korkhov","first_name":"Volodymyr M."}],"volume":5,"date_created":"2019-09-29T22:00:45Z","date_updated":"2023-08-30T06:55:31Z","year":"2019","publisher":"American Association for the Advancement of Science","department":[{"_id":"LeSa"}],"publication_status":"published","publication_identifier":{"eissn":["23752548"]},"month":"09","doi":"10.1126/sciadv.aaw6490","language":[{"iso":"eng"}],"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,"isi":1,"quality_controlled":"1","issue":"9","type":"journal_article","file":[{"creator":"kschuh","file_size":1236101,"content_type":"application/pdf","file_name":"2019_AAAS_Qi.pdf","access_level":"open_access","date_created":"2019-10-02T11:13:54Z","date_updated":"2020-07-14T12:47:44Z","checksum":"b2256c9117655bc15f621ba0babf219f","file_id":"6928","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6919","intvolume":" 5","status":"public","ddc":["570"],"title":"Structural basis of sterol recognition by human hedgehog receptor PTCH1","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1","date_published":"2019-09-18T00:00:00Z","citation":{"ama":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw6490","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.","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."},"publication":"Science Advances"},{"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,"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:47:46Z","article_number":"2153","author":[{"full_name":"Kelemen, Réka K","last_name":"Kelemen","first_name":"Réka K","orcid":"0000-0002-8489-9281","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"H","last_name":"Rajakaruna","full_name":"Rajakaruna, H"},{"first_name":"IA","last_name":"Cockburn","full_name":"Cockburn, IA"},{"last_name":"Ganusov","first_name":"VV","full_name":"Ganusov, VV"}],"volume":10,"date_created":"2019-11-04T15:50:06Z","date_updated":"2023-08-30T07:18:23Z","pmid":1,"year":"2019","department":[{"_id":"BeVi"}],"publisher":"Frontiers","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","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2083061,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_FrontiersImmonology_Kelemen.pdf","checksum":"68d1708f7aa412544159b498ef17a6b9","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-11-04T15:54:00Z","file_id":"6984","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6983","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"},{"scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","publication":"Journal of the ACM","citation":{"ista":"Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 66(5), 32.","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","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.","ama":"Lenzen C, Rybicki J. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 2019;66(5). 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.","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.","short":"C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019)."},"article_type":"original","date_published":"2019-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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 f16th International Conference on Quantitative Evaluation of Systems, 11785:109–28. Springer Nature, 2019. 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.","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","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"},"publication":"16th International Conference on Quantitative Evaluation of Systems","abstract":[{"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.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 11785","status":"public","title":"Strategy representation by decision trees with linear classifiers","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6942"},{"year":"2019","publisher":"Elsevier","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"last_name":"Schmickler","first_name":"C.H.","full_name":"Schmickler, C.H."},{"first_name":"H.-W.","last_name":"Hammer","full_name":"Hammer, H.-W."},{"last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"volume":798,"date_updated":"2023-08-30T07:06:42Z","date_created":"2019-10-18T18:33:32Z","article_number":"135016","file_date_updated":"2020-07-14T12:47:46Z","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,"doi":"10.1016/j.physletb.2019.135016","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0370-2693"]},"month":"11","_id":"6955","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 798","status":"public","title":"Universal physics of bound states of a few charged particles","ddc":["530"],"file":[{"checksum":"d27f983b34ea7dafdf356afbf9472fbf","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-10-25T12:47:04Z","file_id":"6974","relation":"main_file","creator":"dernst","file_size":528362,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_PhysicsLettersB_Schmickler.pdf"}],"oa_version":"Published Version","type":"journal_article","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"}],"citation":{"ista":"Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states of a few charged particles. Physics Letters B. 798, 135016.","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","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.","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","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)."},"publication":"Physics Letters B","article_type":"original","date_published":"2019-11-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"10"},{"publication_identifier":{"issn":["0022-3042"],"eissn":["1471-4159"]},"month":"12","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":{"isi":["000490703100001"],"pmid":["31479508"]},"language":[{"iso":"eng"}],"doi":"10.1111/jnc.14862","file_date_updated":"2020-07-14T12:47:47Z","publisher":"Wiley","department":[{"_id":"SiHi"}],"publication_status":"published","pmid":1,"year":"2019","volume":151,"date_updated":"2023-08-30T07:21:50Z","date_created":"2019-11-12T14:37:08Z","author":[{"first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"last_name":"Cousin","first_name":"Michael A.","full_name":"Cousin, Michael A."}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"570-583","article_type":"original","citation":{"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.","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.","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.","short":"G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583.","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."},"publication":"Journal of Neurochemistry","date_published":"2019-12-01T00:00:00Z","type":"journal_article","issue":"5","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"}],"intvolume":" 151","status":"public","ddc":["570"],"title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","_id":"7005","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4334962,"file_name":"2019_JournNeurochemistry_Cheung.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:47Z","date_created":"2020-02-05T10:30:02Z","checksum":"ec1fb2aebb874009bc309adaada6e1d7","file_id":"7452","relation":"main_file"}],"oa_version":"Published Version"},{"article_type":"original","publication":"Computational and Applied Mathematics","citation":{"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.","short":"Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019).","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.","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.","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","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.","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"},"date_published":"2019-12-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","ddc":["510","515","518"],"title":"Convergence analysis of projection method for variational inequalities","status":"public","intvolume":" 38","_id":"7000","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","type":"journal_article","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"}],"issue":"4","quality_controlled":"1","isi":1,"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s40314-019-0955-9","open_access":"1"}],"external_id":{"arxiv":["2101.09081"],"isi":["000488973100005"]},"language":[{"iso":"eng"}],"doi":"10.1007/s40314-019-0955-9","month":"12","publication_identifier":{"eissn":["1807-0302"],"issn":["2238-3603"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"VlKo"}],"year":"2019","date_created":"2019-11-12T12:41:44Z","date_updated":"2023-08-30T07:20:32Z","volume":38,"author":[{"full_name":"Shehu, Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","first_name":"Yekini","last_name":"Shehu"},{"last_name":"Iyiola","first_name":"Olaniyi S.","full_name":"Iyiola, Olaniyi S."},{"last_name":"Li","first_name":"Xiao-Huan","full_name":"Li, Xiao-Huan"},{"last_name":"Dong","first_name":"Qiao-Li","full_name":"Dong, Qiao-Li"}],"article_number":"161","ec_funded":1},{"oa_version":"Preprint","intvolume":" 4","title":"Geometry of transient chaos in streamwise-localized pipe flow turbulence","status":"public","_id":"6978","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"10","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"}],"type":"journal_article","date_published":"2019-10-01T00:00:00Z","page":"102401","article_type":"original","citation":{"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","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","ista":"Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 102401.","short":"N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 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.","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."},"publication":"Physical Review Fluids","article_processing_charge":"No","day":"01","scopus_import":"1","volume":4,"date_created":"2019-11-04T10:04:01Z","date_updated":"2023-08-30T07:20:03Z","author":[{"full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dogra","first_name":"Akshunna","full_name":"Dogra, Akshunna"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","year":"2019","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1103/PhysRevFluids.4.102401","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1810.02211","open_access":"1"}],"oa":1,"external_id":{"isi":["000493510400001"],"arxiv":["1810.02211"]},"month":"10"},{"file_date_updated":"2020-07-14T12:47:48Z","year":"2019","publisher":"Cell Press","department":[{"_id":"ToBo"}],"publication_status":"published","author":[{"full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177","first_name":"Martin","last_name":"Lukacisin"},{"first_name":"Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias"}],"volume":9,"date_updated":"2023-08-30T07:24:58Z","date_created":"2019-11-15T10:51:42Z","publication_identifier":{"issn":["2405-4712"]},"month":"11","external_id":{"isi":["000499495400003"]},"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,"project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.cels.2019.10.004","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"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"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7026","intvolume":" 9","ddc":["570"],"status":"public","title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","file":[{"file_name":"2019_CellSystems_Lukacisin.pdf","access_level":"open_access","file_size":4238460,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7027","date_created":"2019-11-15T10:57:42Z","date_updated":"2020-07-14T12:47:48Z","checksum":"7a11d6c2f9523d65b049512d61733178"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","citation":{"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.","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.","short":"M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3.","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.","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.","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","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"},"publication":"Cell Systems","page":"423-433.e1-e3","article_type":"original","date_published":"2019-11-27T00:00:00Z"},{"ec_funded":1,"author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"}],"volume":39,"date_created":"2019-11-18T14:29:50Z","date_updated":"2023-08-30T07:26:25Z","year":"2019","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["0209-9683"],"eissn":["1439-6912"]},"month":"10","doi":"10.1007/s00493-019-3905-7","language":[{"iso":"eng"}],"external_id":{"isi":["000493267200003"],"arxiv":["1709.00508"]},"main_file_link":[{"url":"https://arxiv.org/abs/1709.00508","open_access":"1"}],"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}],"quality_controlled":"1","isi":1,"issue":"6","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7034","intvolume":" 39","title":"Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4","status":"public","article_processing_charge":"No","day":"29","scopus_import":"1","date_published":"2019-10-29T00:00:00Z","citation":{"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","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.","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.","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."},"publication":"Combinatorica","page":"1267-1279","article_type":"original"},{"publication_identifier":{"eissn":["2045-2322"]},"month":"11","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":["000495857600019"],"pmid":["31719602"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41598-019-53049-w","language":[{"iso":"eng"}],"article_number":"16565","file_date_updated":"2020-07-14T12:47:49Z","pmid":1,"year":"2019","publisher":"Springer Nature","department":[{"_id":"SaSi"}],"publication_status":"published","author":[{"orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","first_name":"Margaret E","full_name":"Maes, Margaret E"},{"full_name":"Grosser, J. A.","last_name":"Grosser","first_name":"J. A."},{"full_name":"Fehrman, R. L.","last_name":"Fehrman","first_name":"R. L."},{"first_name":"C. L.","last_name":"Schlamp","full_name":"Schlamp, C. L."},{"last_name":"Nickells","first_name":"R. W.","full_name":"Nickells, R. W."}],"volume":9,"date_updated":"2023-08-30T07:26:54Z","date_created":"2019-11-25T07:45:17Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"12","citation":{"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.","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.","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","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."},"publication":"Scientific Reports","article_type":"original","date_published":"2019-11-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7095","intvolume":" 9","title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_ScientificReports_Maes.pdf","creator":"dernst","file_size":6467393,"content_type":"application/pdf","file_id":"7096","relation":"main_file","checksum":"9ab397ed9c1c454b34bffb8cc863d734","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T07:49:52Z"}]},{"article_type":"original","publication":"Communications Biology","citation":{"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","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.","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","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.","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.","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."},"date_published":"2019-11-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1","title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","ddc":["570"],"status":"public","intvolume":" 2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7097","oa_version":"Published Version","file":[{"file_name":"2019_CommunicBiology_Nagano.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2626069,"creator":"dernst","relation":"main_file","file_id":"7098","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T07:58:05Z","checksum":"c63c69a264fc8a0e52f2b0d482f3bdae"}],"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","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":["000496767800005"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42003-019-0670-5","month":"11","publication_identifier":{"issn":["2399-3642"]},"publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Springer Nature","year":"2019","date_updated":"2023-08-30T07:27:55Z","date_created":"2019-11-25T07:55:01Z","volume":2,"author":[{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"full_name":"Toshima, Junko Y.","last_name":"Toshima","first_name":"Junko Y."},{"full_name":"Siekhaus, Daria E","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"article_number":"419","file_date_updated":"2020-07-14T12:47:49Z"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","citation":{"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.","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","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","page":"781-794.e4","article_type":"original","date_published":"2019-11-20T00:00:00Z","type":"journal_article","issue":"4","_id":"7099","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 104","status":"public","title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","ddc":["571","599"],"oa_version":"Published Version","publication_identifier":{"issn":["0896-6273"]},"month":"11","external_id":{"isi":["000497963500017"],"pmid":["31543297"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.013","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1016/j.neuron.2019.08.013","language":[{"iso":"eng"}],"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","publisher":"Elsevier","department":[{"_id":"RySh"}],"publication_status":"published","author":[{"full_name":"Kasugai, Yu","last_name":"Kasugai","first_name":"Yu"},{"first_name":"Elisabeth","last_name":"Vogel","full_name":"Vogel, Elisabeth"},{"full_name":"Hörtnagl, Heide","last_name":"Hörtnagl","first_name":"Heide"},{"first_name":"Sabine","last_name":"Schönherr","full_name":"Schönherr, Sabine"},{"last_name":"Paradiso","first_name":"Enrica","full_name":"Paradiso, Enrica"},{"full_name":"Hauschild, Markus","last_name":"Hauschild","first_name":"Markus"},{"full_name":"Göbel, Georg","first_name":"Georg","last_name":"Göbel"},{"full_name":"Milenkovic, Ivan","last_name":"Milenkovic","first_name":"Ivan"},{"last_name":"Peterschmitt","first_name":"Yvan","full_name":"Peterschmitt, Yvan"},{"last_name":"Tasan","first_name":"Ramon","full_name":"Tasan, Ramon"},{"last_name":"Sperk","first_name":"Günther","full_name":"Sperk, Günther"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"first_name":"Werner","last_name":"Sieghart","full_name":"Sieghart, Werner"},{"first_name":"Nicolas","last_name":"Singewald","full_name":"Singewald, Nicolas"},{"full_name":"Lüthi, Andreas","first_name":"Andreas","last_name":"Lüthi"},{"full_name":"Ferraguti, Francesco","first_name":"Francesco","last_name":"Ferraguti"}],"volume":104,"date_updated":"2023-08-30T07:28:22Z","date_created":"2019-11-25T08:02:39Z"},{"main_file_link":[{"open_access":"1","url":"https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf"}],"oa":1,"external_id":{"pmid":["31073041"],"isi":["000467631800034"]},"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"},{"name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031"}],"isi":1,"quality_controlled":"1","doi":"10.1126/science.aav2522","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"05","pmid":1,"year":"2019","publisher":"AAAS","department":[{"_id":"SiHi"}],"publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"full_name":"Telley, L","first_name":"L","last_name":"Telley"},{"full_name":"Agirman, G","last_name":"Agirman","first_name":"G"},{"first_name":"J","last_name":"Prados","full_name":"Prados, J"},{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole"},{"full_name":"Fièvre, S","first_name":"S","last_name":"Fièvre"},{"full_name":"Oberst, P","first_name":"P","last_name":"Oberst"},{"last_name":"Bartolini","first_name":"G","full_name":"Bartolini, G"},{"full_name":"Vitali, I","last_name":"Vitali","first_name":"I"},{"full_name":"Cadilhac, C","last_name":"Cadilhac","first_name":"C"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"L","last_name":"Nguyen","full_name":"Nguyen, L"},{"last_name":"Dayer","first_name":"A","full_name":"Dayer, A"},{"full_name":"Jabaudon, D","first_name":"D","last_name":"Jabaudon"}],"volume":364,"date_created":"2019-05-14T13:07:47Z","date_updated":"2023-09-05T11:51:09Z","article_number":"eaav2522","ec_funded":1,"citation":{"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","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.","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.","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","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.","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).","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."},"publication":"Science","article_type":"original","date_published":"2019-05-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6455","intvolume":" 364","status":"public","title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","oa_version":"Published Version","type":"journal_article","issue":"6440","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"}]},{"volume":141,"date_created":"2019-06-25T11:53:35Z","date_updated":"2023-09-05T12:03:45Z","author":[{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"full_name":"Genç, Aziz","last_name":"Genç","first_name":"Aziz"},{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"last_name":"Kuster","first_name":"Beatrice","full_name":"Kuster, Beatrice"},{"full_name":"Schuster, Maximilian","last_name":"Schuster","first_name":"Maximilian"},{"first_name":"Oleksandr","last_name":"Dobrozhan","full_name":"Dobrozhan, Oleksandr"},{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"},{"first_name":"Maksym V.","last_name":"Kovalenko","full_name":"Kovalenko, Maksym V."}],"department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:34Z","language":[{"iso":"eng"}],"doi":"10.1021/jacs.9b01394","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000469292300004"],"pmid":["31017419 "]},"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"month":"04","file":[{"file_id":"6587","relation":"main_file","checksum":"34d7ec837869cc6a07996b54f75696b7","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-06-25T11:59:00Z","access_level":"open_access","file_name":"JACS_April2019.pdf","creator":"cpetz","file_size":6234004,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 141","ddc":["540"],"title":"Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6586","issue":"20","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."}],"type":"journal_article","date_published":"2019-04-19T00:00:00Z","page":"8025-8029","article_type":"original","citation":{"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.","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.","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.","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","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"},"publication":"Journal of the American Chemical Society","article_processing_charge":"No","has_accepted_license":"1","day":"19","scopus_import":"1"},{"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.99.094205","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000462883200001"],"arxiv":["1811.03103"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.03103"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"03","volume":99,"date_updated":"2023-09-05T12:11:13Z","date_created":"2019-03-25T07:32:08Z","author":[{"last_name":"Dumitrescu","first_name":"Philipp T.","full_name":"Dumitrescu, Philipp T."},{"full_name":"Goremykina, Anna","first_name":"Anna","last_name":"Goremykina"},{"last_name":"Parameswaran","first_name":"Siddharth A.","full_name":"Parameswaran, Siddharth A."},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"last_name":"Vasseur","first_name":"Romain","full_name":"Vasseur, Romain"}],"publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","year":"2019","article_number":"094205","date_published":"2019-03-22T00:00:00Z","article_type":"original","citation":{"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","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.","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","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.","short":"P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur, Physical Review B 99 (2019).","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.","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."},"publication":"Physical Review B","article_processing_charge":"No","day":"22","scopus_import":"1","oa_version":"Preprint","intvolume":" 99","title":"Kosterlitz-Thouless scaling at many-body localization phase transitions","status":"public","_id":"6174","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"9","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."}],"type":"journal_article"},{"month":"06","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"doi":"10.1104/pp.18.01377","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"www.doi.org/10.1104/pp.18.01377"}],"external_id":{"isi":["000470086100019"],"pmid":["31000634"]},"isi":1,"quality_controlled":"1","author":[{"full_name":"Bellstaedt, Julia","last_name":"Bellstaedt","first_name":"Julia"},{"full_name":"Trenner, Jana","last_name":"Trenner","first_name":"Jana"},{"first_name":"Rebecca","last_name":"Lippmann","full_name":"Lippmann, Rebecca"},{"first_name":"Yvonne","last_name":"Poeschl","full_name":"Poeschl, 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","last_name":"Quint","first_name":"Marcel"},{"full_name":"Delker, Carolin","first_name":"Carolin","last_name":"Delker"}],"date_updated":"2023-09-05T12:25:19Z","date_created":"2019-04-30T15:24:22Z","volume":180,"year":"2019","pmid":1,"publication_status":"published","publisher":"ASPB","department":[{"_id":"JiFr"}],"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","publication":"Plant Physiology","citation":{"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.","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","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.","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","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.","short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","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."},"article_type":"original","page":"757-766","abstract":[{"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.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6366","status":"public","title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","intvolume":" 180"},{"month":"11","publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1810.07039","open_access":"1"}],"external_id":{"arxiv":["1810.07039"],"isi":["000488621700004"]},"language":[{"iso":"eng"}],"doi":"10.1090/proc/14586","ec_funded":1,"publication_status":"published","publisher":"AMS","department":[{"_id":"TaHa"}],"year":"2019","date_updated":"2023-09-05T12:22:21Z","date_created":"2019-11-04T16:10:50Z","volume":147,"author":[{"id":"42A24CCC-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Penghui","full_name":"Li, Penghui"}],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"4597-4604","publication":"Proceedings of the American Mathematical Society","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."},"date_published":"2019-11-01T00:00:00Z","type":"journal_article","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. "}],"issue":"11","title":"A colimit of traces of reflection groups","status":"public","intvolume":" 147","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6986","oa_version":"Preprint"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2019.01.051","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000463337900018"],"pmid":["30824354"]},"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,"publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"month":"04","volume":102,"date_created":"2019-05-14T13:06:30Z","date_updated":"2023-09-05T13:02:21Z","author":[{"first_name":"G","last_name":"Ortiz-Álvarez","full_name":"Ortiz-Álvarez, G"},{"full_name":"Daclin, M","last_name":"Daclin","first_name":"M"},{"first_name":"A","last_name":"Shihavuddin","full_name":"Shihavuddin, A"},{"first_name":"P","last_name":"Lansade","full_name":"Lansade, P"},{"full_name":"Fortoul, A","last_name":"Fortoul","first_name":"A"},{"first_name":"M","last_name":"Faucourt","full_name":"Faucourt, M"},{"last_name":"Clavreul","first_name":"S","full_name":"Clavreul, S"},{"full_name":"Lalioti, ME","last_name":"Lalioti","first_name":"ME"},{"full_name":"Taraviras, S","last_name":"Taraviras","first_name":"S"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"full_name":"Livet, J","last_name":"Livet","first_name":"J"},{"first_name":"A","last_name":"Meunier","full_name":"Meunier, A"},{"first_name":"A","last_name":"Genovesio","full_name":"Genovesio, A"},{"full_name":"Spassky, N","last_name":"Spassky","first_name":"N"}],"publisher":"Elsevier","department":[{"_id":"SiHi"}],"publication_status":"published","pmid":1,"year":"2019","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z","date_published":"2019-04-03T00:00:00Z","page":"159-172.e7","citation":{"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.","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.","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","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"},"publication":"Neuron","has_accepted_license":"1","article_processing_charge":"No","day":"03","scopus_import":"1","file":[{"relation":"main_file","file_id":"6457","date_created":"2019-05-15T09:28:41Z","date_updated":"2020-07-14T12:47:30Z","checksum":"1fb6e195c583eb0c5cabf26f69ff6675","file_name":"2019_Neuron_Ortiz.pdf","access_level":"open_access","file_size":7288572,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","intvolume":" 102","title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","status":"public","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6454","issue":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"20","_id":"6980","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["570"],"title":"Tissue rheology in embryonic organization","intvolume":" 38","file":[{"file_name":"2019_Embo_Petridou.pdf","access_level":"open_access","content_type":"application/pdf","file_size":847356,"creator":"dernst","relation":"main_file","file_id":"6981","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-11-04T15:30:08Z","checksum":"76f7f4e79ab6d850c30017a69726fd85"}],"oa_version":"Published Version","scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"The EMBO Journal","citation":{"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","ista":"Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization. The EMBO Journal. 38(20), e102497.","ama":"Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. The EMBO Journal. 2019;38(20). doi:10.15252/embj.2019102497","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.","short":"N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (2019).","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."},"article_type":"review","date_published":"2019-10-15T00:00:00Z","article_number":"e102497","file_date_updated":"2020-07-14T12:47:46Z","ec_funded":1,"year":"2019","pmid":1,"publication_status":"published","publisher":"EMBO","department":[{"_id":"CaHe"}],"author":[{"last_name":"Petridou","first_name":"Nicoletta","orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Petridou, Nicoletta"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-05T13:04:13Z","date_created":"2019-11-04T15:24:29Z","volume":38,"month":"10","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"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":["31512749"],"isi":["000485561900001"]},"isi":1,"quality_controlled":"1","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"grant_number":"V00736","_id":"2693FD8C-B435-11E9-9278-68D0E5697425","name":"Tissue material properties in embryonic development","call_identifier":"FWF"}],"doi":"10.15252/embj.2019102497","language":[{"iso":"eng"}]},{"abstract":[{"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.","lang":"eng"}],"issue":"9","type":"journal_article","oa_version":"Preprint","_id":"6554","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly","status":"public","intvolume":" 41","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-09-01T00:00:00Z","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","citation":{"short":"Y. Xian, C. Lampert, B. Schiele, Z. Akata, IEEE Transactions on Pattern Analysis and Machine Intelligence 41 (2019) 2251–2265.","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.","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.","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","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.","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","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."},"article_type":"original","page":"2251 - 2265","author":[{"full_name":"Xian, Yongqin","last_name":"Xian","first_name":"Yongqin"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Christoph","last_name":"Lampert"},{"full_name":"Schiele, Bernt","first_name":"Bernt","last_name":"Schiele"},{"first_name":"Zeynep","last_name":"Akata","full_name":"Akata, Zeynep"}],"date_created":"2019-06-11T14:05:59Z","date_updated":"2023-09-05T13:18:09Z","volume":41,"year":"2019","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","month":"09","publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"doi":"10.1109/tpami.2018.2857768","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000480343900015"],"arxiv":["1707.00600"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1707.00600"}],"isi":1,"quality_controlled":"1"},{"date_published":"2019-04-11T00:00:00Z","citation":{"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.","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","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.","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.","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.","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."},"publication":"Nature","page":"240-243","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"11","scopus_import":"1","file":[{"date_created":"2020-11-13T07:37:41Z","date_updated":"2020-11-13T07:37:41Z","success":1,"checksum":"6b84ab602a34382cf0340a37a1378c75","file_id":"8751","relation":"main_file","creator":"dernst","file_size":4321328,"content_type":"application/pdf","file_name":"2019_Nature _Cao_accepted.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","_id":"6259","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 568","title":"TMK1-mediated auxin signalling regulates differential growth of the apical hook","status":"public","ddc":["580"],"abstract":[{"lang":"eng","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."}],"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","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"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":[{"first_name":"Min","last_name":"Cao","full_name":"Cao, Min"},{"full_name":"Chen, Rong","last_name":"Chen","first_name":"Rong"},{"full_name":"Li, Pan","first_name":"Pan","last_name":"Li"},{"full_name":"Yu, Yongqiang","last_name":"Yu","first_name":"Yongqiang"},{"full_name":"Zheng, Rui","last_name":"Zheng","first_name":"Rui"},{"full_name":"Ge, Danfeng","first_name":"Danfeng","last_name":"Ge"},{"full_name":"Zheng, Wei","first_name":"Wei","last_name":"Zheng"},{"first_name":"Xuhui","last_name":"Wang","full_name":"Wang, Xuhui"},{"full_name":"Gu, Yangtao","last_name":"Gu","first_name":"Yangtao"},{"full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","first_name":"Zuzana","last_name":"Gelová"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"Heng","last_name":"Zhang","full_name":"Zhang, Heng"},{"last_name":"Liu","first_name":"Renyi","full_name":"Liu, Renyi"},{"first_name":"Jun","last_name":"He","full_name":"He, Jun"},{"full_name":"Xu, Tongda","first_name":"Tongda","last_name":"Xu"}],"volume":568,"date_updated":"2023-09-05T14:58:41Z","date_created":"2019-04-09T08:37:05Z","pmid":1,"year":"2019","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-11-13T07:37:41Z"},{"file":[{"creator":"dernst","file_size":19317348,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_RESULTS_McDougall.pdf","checksum":"7f43e1e3706d15061475c5c57efc2786","date_updated":"2020-07-14T12:47:46Z","date_created":"2020-05-14T10:09:30Z","file_id":"7829","relation":"main_file"}],"oa_version":"Submitted Version","status":"public","ddc":["570"],"title":"Emergence of embryo shape during cleavage divisions","intvolume":" 68","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6987","abstract":[{"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.","lang":"eng"}],"alternative_title":["RESULTS"],"type":"book_chapter","date_published":"2019-10-10T00:00:00Z","page":"127-154","publication":"Evo-Devo: Non-model species in cell and developmental biology","citation":{"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.","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.","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","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"},"day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_created":"2019-11-04T16:20:19Z","date_updated":"2023-09-05T15:01:12Z","volume":68,"author":[{"first_name":"Alex","last_name":"McDougall","full_name":"McDougall, Alex"},{"full_name":"Chenevert, Janet","first_name":"Janet","last_name":"Chenevert"},{"last_name":"Godard","first_name":"Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","full_name":"Godard, Benoit G"},{"first_name":"Remi","last_name":"Dumollard","full_name":"Dumollard, Remi"}],"publication_status":"published","editor":[{"first_name":"Waclaw","last_name":"Tworzydlo","full_name":"Tworzydlo, Waclaw"},{"first_name":"Szczepan M.","last_name":"Bilinski","full_name":"Bilinski, Szczepan M."}],"publisher":"Springer Nature","department":[{"_id":"CaHe"}],"year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:46Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-23459-1_6","quality_controlled":"1","oa":1,"external_id":{"pmid":["31598855"]},"month":"10","publication_identifier":{"eissn":["1861-0412"],"isbn":["9783030234584","9783030234591"],"issn":["0080-1844"]}},{"month":"07","publication_identifier":{"eissn":["15403467"],"issn":["15403459"]},"external_id":{"isi":["000487931800002"],"arxiv":["1808.04200"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04200"}],"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1137/18M1207272","language":[{"iso":"eng"}],"year":"2019","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"SIAM","author":[{"full_name":"Friesecke, Gero","first_name":"Gero","last_name":"Friesecke"},{"full_name":"Kniely, Michael","first_name":"Michael","last_name":"Kniely","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333"}],"date_created":"2019-08-04T21:59:21Z","date_updated":"2023-09-05T15:05:45Z","volume":17,"scopus_import":"1","day":"16","article_processing_charge":"No","publication":"Multiscale Modeling and Simulation","citation":{"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","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.","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.","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."},"page":"926-947","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","_id":"6762","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"New optimal control problems in density functional theory motivated by photovoltaics","status":"public","intvolume":" 17","oa_version":"Preprint"},{"month":"01","publication_identifier":{"eissn":["2363-9555"],"issn":["2522-0160"]},"doi":"10.1007/s40993-018-0146-6","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.08986"}],"external_id":{"arxiv":["1807.08986"]},"quality_controlled":"1","article_number":"9","author":[{"first_name":"Sorina","last_name":"Ionica","full_name":"Ionica, Sorina"},{"full_name":"Kılıçer, Pınar","first_name":"Pınar","last_name":"Kılıçer"},{"last_name":"Lauter","first_name":"Kristin","full_name":"Lauter, Kristin"},{"full_name":"Lorenzo García, Elisa","last_name":"Lorenzo García","first_name":"Elisa"},{"full_name":"Manzateanu, Maria-Adelina","last_name":"Manzateanu","first_name":"Maria-Adelina","id":"be8d652e-a908-11ec-82a4-e2867729459c"},{"last_name":"Massierer","first_name":"Maike","full_name":"Massierer, Maike"},{"full_name":"Vincent, Christelle","first_name":"Christelle","last_name":"Vincent"}],"date_updated":"2023-09-05T15:39:31Z","date_created":"2022-03-18T12:09:48Z","volume":5,"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"}],"day":"02","article_processing_charge":"No","scopus_import":"1","keyword":["Algebra and Number Theory"],"date_published":"2019-01-02T00:00:00Z","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.","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.","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019).","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.","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","ieee":"S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 2019.","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","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"10874","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Modular invariants for genus 3 hyperelliptic curves","intvolume":" 5"},{"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":884469,"access_level":"open_access","file_name":"2019_CommMathPhys_Jeblick.pdf","checksum":"cd283b475dd739e04655315abd46f528","date_created":"2019-11-25T08:11:11Z","date_updated":"2020-07-14T12:47:49Z","file_id":"7101","relation":"main_file"}],"status":"public","ddc":["510"],"title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","intvolume":" 372","_id":"7100","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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":{"short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69.","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.","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","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.","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."},"day":"08","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_created":"2019-11-25T08:08:02Z","date_updated":"2023-09-06T10:47:43Z","volume":372,"author":[{"full_name":"Jeblick, Maximilian","first_name":"Maximilian","last_name":"Jeblick"},{"orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","last_name":"Leopold","first_name":"Nikolai K","full_name":"Leopold, Nikolai K"},{"last_name":"Pickl","first_name":"Peter","full_name":"Pickl, 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":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"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"]}},{"doi":"10.1038/s41477-019-0542-5","language":[{"iso":"eng"}],"external_id":{"isi":["000496526100010"],"pmid":["31712756"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"month":"11","publication_identifier":{"issn":["2055-0278"]},"author":[{"last_name":"Skokan","first_name":"Roman","full_name":"Skokan, Roman"},{"full_name":"Medvecká, Eva","last_name":"Medvecká","first_name":"Eva"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"first_name":"Stanislav","last_name":"Vosolsobě","full_name":"Vosolsobě, Stanislav"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Müller, Karel","first_name":"Karel","last_name":"Müller"},{"first_name":"Petr","last_name":"Skůpa","full_name":"Skůpa, Petr"},{"first_name":"Michal","last_name":"Karady","full_name":"Karady, Michal"},{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou"},{"full_name":"Janacek, Dorina P.","first_name":"Dorina P.","last_name":"Janacek"},{"first_name":"Ulrich Z.","last_name":"Hammes","full_name":"Hammes, Ulrich Z."},{"full_name":"Ljung, Karin","last_name":"Ljung","first_name":"Karin"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"date_created":"2019-11-25T09:08:04Z","date_updated":"2023-09-06T11:09:49Z","volume":5,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","file_date_updated":"2020-10-14T08:54:49Z","ec_funded":1,"date_published":"2019-11-01T00:00:00Z","publication":"Nature Plants","citation":{"ieee":"R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019.","apa":"Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5","ista":"Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119.","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5","chicago":"Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.","short":"R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.","mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:10.1038/s41477-019-0542-5."},"article_type":"original","page":"1114-1119","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"date_updated":"2020-10-14T08:54:49Z","date_created":"2020-10-14T08:54:49Z","checksum":"94e0426856aad9a9bd0135d5436efbf1","success":1,"relation":"main_file","file_id":"8660","content_type":"application/pdf","file_size":1980851,"creator":"dernst","file_name":"2019_NaturePlants_Skokan_accepted.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7106","ddc":["580"],"status":"public","title":"PIN-driven auxin transport emerged early in streptophyte evolution","intvolume":" 5","abstract":[{"text":"PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.","lang":"eng"}],"issue":"11","type":"journal_article"},{"_id":"7105","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 21","status":"public","title":"Persistent and polarized global actin flow is essential for directionality during cell migration","oa_version":"Submitted Version","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence."}],"citation":{"mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5.","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5.","ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5","ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","ieee":"L. Yolland et al., “Persistent and polarized global actin flow is essential for directionality during cell migration,” Nature Cell Biology, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0411-5"},"publication":"Nature Cell Biology","page":"1370-1381","article_type":"original","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","pmid":1,"year":"2019","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Lawrence","last_name":"Yolland","full_name":"Yolland, Lawrence"},{"full_name":"Burki, Mubarik","last_name":"Burki","first_name":"Mubarik"},{"first_name":"Stefania","last_name":"Marcotti","full_name":"Marcotti, Stefania"},{"last_name":"Luchici","first_name":"Andrei","full_name":"Luchici, Andrei"},{"first_name":"Fiona N.","last_name":"Kenny","full_name":"Kenny, Fiona N."},{"last_name":"Davis","first_name":"John Robert","full_name":"Davis, John Robert"},{"first_name":"Eduardo","last_name":"Serna-Morales","full_name":"Serna-Morales, Eduardo"},{"last_name":"Müller","first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Davidson, Andrew","last_name":"Davidson","first_name":"Andrew"},{"first_name":"Will","last_name":"Wood","full_name":"Wood, Will"},{"full_name":"Schumacher, Linus J.","last_name":"Schumacher","first_name":"Linus J."},{"first_name":"Robert G.","last_name":"Endres","full_name":"Endres, Robert G."},{"full_name":"Miodownik, Mark","first_name":"Mark","last_name":"Miodownik"},{"full_name":"Stramer, Brian M.","first_name":"Brian M.","last_name":"Stramer"}],"volume":21,"date_created":"2019-11-25T08:55:00Z","date_updated":"2023-09-06T11:08:52Z","oa":1,"external_id":{"isi":["000495888300009"],"pmid":["31685997"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41556-019-0411-5","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"month":"11"},{"citation":{"ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. Journal of the ACM. 2019;66(3). doi:10.1145/3314024","chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.","mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM, vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024.","short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019)."},"publication":"Journal of the ACM","article_type":"original","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7108","intvolume":" 66","status":"public","title":"Shellability is NP-complete","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable."}],"main_file_link":[{"url":"https://arxiv.org/pdf/1711.08436.pdf","open_access":"1"}],"external_id":{"arxiv":["1711.08436"],"isi":["000495406300007"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1145/3314024","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-5411"]},"month":"06","year":"2019","department":[{"_id":"UlWa"}],"publisher":"ACM","publication_status":"published","related_material":{"record":[{"id":"184","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Goaoc, Xavier","first_name":"Xavier","last_name":"Goaoc"},{"id":"B593B804-1035-11EA-B4F1-947645A5BB83","last_name":"Patak","first_name":"Pavel","full_name":"Patak, Pavel"},{"last_name":"Patakova","first_name":"Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","full_name":"Patakova, Zuzana"},{"full_name":"Tancer, Martin","first_name":"Martin","last_name":"Tancer"},{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"volume":66,"date_updated":"2023-09-06T11:10:58Z","date_created":"2019-11-26T10:13:59Z","article_number":"21"},{"type":"conference","abstract":[{"lang":"eng","text":"It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X2019 IEEE International Symposium on Information Theory. Paris, France: IEEE. https://doi.org/10.1109/isit.2019.8849240","ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in 2019 IEEE International Symposium on Information Theory, Paris, France, 2019.","ista":"Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240.","ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: 2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In 2019 IEEE International Symposium on Information Theory. IEEE, 2019. https://doi.org/10.1109/isit.2019.8849240.","short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019.","mla":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” 2019 IEEE International Symposium on Information Theory, 8849240, IEEE, 2019, doi:10.1109/isit.2019.8849240."},"date_published":"2019-07-01T00:00:00Z","article_number":"8849240","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"IEEE","year":"2019","date_created":"2019-11-28T10:19:21Z","date_updated":"2023-09-06T11:15:41Z","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","first_name":"Maciej","full_name":"Skórski, Maciej"}],"month":"07","publication_identifier":{"isbn":["9781538692912"]},"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.08476"}],"oa":1,"external_id":{"isi":["000489100301043"],"arxiv":["1702.08476"]},"language":[{"iso":"eng"}],"conference":{"location":"Paris, France","start_date":"2019-07-07","end_date":"2019-07-12","name":"ISIT: International Symposium on Information Theory"},"doi":"10.1109/isit.2019.8849240"},{"month":"12","publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41422-019-0254-4","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41422-019-0254-4"}],"oa":1,"external_id":{"isi":["000500749600001"],"pmid":["31745287"]},"date_created":"2019-12-02T12:30:48Z","date_updated":"2023-09-06T11:20:58Z","volume":29,"author":[{"first_name":"Scott A","last_name":"Sinclair","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"year":"2019","pmid":1,"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","article_type":"original","page":"965-966","publication":"Cell Research","citation":{"ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.","apa":"Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966.","ama":"Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. Cell Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4","chicago":"Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4.","short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.","mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4."},"abstract":[{"text":"Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","status":"public","title":"Defying gravity: a plant's quest for moisture","intvolume":" 29","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7143"},{"date_published":"2019-12-01T00:00:00Z","citation":{"chicago":"Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information. Springer Nature, 2019. https://doi.org/10.1038/s41534-019-0220-5.","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information, vol. 5, 108, Springer Nature, 2019, doi:10.1038/s41534-019-0220-5.","short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019).","ista":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 5, 108.","apa":"Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., & Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-019-0220-5","ieee":"A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic entanglement source for microwave to telecom quantum state transfer,” npj Quantum Information, vol. 5. Springer Nature, 2019.","ama":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 2019;5. doi:10.1038/s41534-019-0220-5"},"publication":"npj Quantum Information","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-09T08:25:06Z","checksum":"13e0ea1d4f9b5f5710780d9473364f58","relation":"main_file","file_id":"7157","content_type":"application/pdf","file_size":1580132,"creator":"dernst","file_name":"2019_NPJ_Rueda.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7156","intvolume":" 5","title":"Electro-optic entanglement source for microwave to telecom quantum state transfer","status":"public","ddc":["530"],"abstract":[{"lang":"eng","text":"We propose an efficient microwave-photonic modulator as a resource for stationary entangled microwave-optical fields and develop the theory for deterministic entanglement generation and quantum state transfer in multi-resonant electro-optic systems. The device is based on a single crystal whispering gallery mode resonator integrated into a 3D-microwave cavity. The specific design relies on a new combination of thin-film technology and conventional machining that is optimized for the lowest dissipation rates in the microwave, optical, and mechanical domains. We extract important device properties from finite-element simulations and predict continuous variable entanglement generation rates on the order of a Mebit/s for optical pump powers of only a few tens of microwatts. We compare the quantum state transfer fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation and direct conversion protocols under realistic conditions. Combining the unique capabilities of circuit quantum electrodynamics with the resilience of fiber optic communication could facilitate long-distance solid-state qubit networks, new methods for quantum signal synthesis, quantum key distribution, and quantum enhanced detection, as well as more power-efficient classical sensing and modulation."}],"type":"journal_article","doi":"10.1038/s41534-019-0220-5","language":[{"iso":"eng"}],"external_id":{"isi":["000502996200003"],"arxiv":["1909.01470"]},"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,"project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438"},{"_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"},{"_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2056-6387"]},"month":"12","author":[{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Hease, William J","first_name":"William J","last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166"},{"orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"volume":5,"date_created":"2019-12-09T08:18:56Z","date_updated":"2023-09-06T11:22:39Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"JoFi"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z","article_number":"108"},{"citation":{"chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297.","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:10.1242/dev.176297.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297.","ieee":"P. Guerrero et al., “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” Development, vol. 146, no. 23. The Company of Biologists, 2019.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. The Company of Biologists. https://doi.org/10.1242/dev.176297","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 2019;146(23). doi:10.1242/dev.176297"},"publication":"Development","article_type":"original","date_published":"2019-12-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"04","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7165","intvolume":" 146","ddc":["570"],"title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","status":"public","oa_version":"Published Version","file":[{"file_name":"2019_Development_Guerrero.pdf","access_level":"open_access","file_size":7797881,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7177","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-13T07:34:06Z","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a"}],"type":"journal_article","issue":"23","abstract":[{"lang":"eng","text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube."}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31784457"],"isi":["000507575700004"]},"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"isi":1,"quality_controlled":"1","doi":"10.1242/dev.176297","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"month":"12","pmid":1,"year":"2019","publisher":"The Company of Biologists","department":[{"_id":"AnKi"}],"publication_status":"published","author":[{"last_name":"Guerrero","first_name":"Pilar","full_name":"Guerrero, Pilar"},{"full_name":"Perez-Carrasco, Ruben","last_name":"Perez-Carrasco","first_name":"Ruben"},{"last_name":"Zagórski","first_name":"Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P"},{"full_name":"Page, David","last_name":"Page","first_name":"David"},{"full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"full_name":"Page, Karen M.","last_name":"Page","first_name":"Karen M."}],"volume":146,"date_updated":"2023-09-06T11:26:36Z","date_created":"2019-12-10T14:39:50Z","article_number":"dev176297","ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z"},{"department":[{"_id":"KrCh"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","volume":11781,"date_created":"2019-12-15T23:00:44Z","date_updated":"2023-09-06T12:40:58Z","author":[{"full_name":"Brázdil, Tomás","first_name":"Tomás","last_name":"Brázdil"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Kucera","first_name":"Antonín","full_name":"Kucera, Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný","first_name":"Petr","full_name":"Novotný, Petr"},{"full_name":"Velan, Dominik","last_name":"Velan","first_name":"Dominik"}],"publication_identifier":{"isbn":["9783030317836"],"eissn":["16113349"],"issn":["03029743"]},"month":"10","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.11010","open_access":"1"}],"external_id":{"isi":["000723515700027"],"arxiv":["1907.11010"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-31784-3_27","conference":{"end_date":"2019-10-31","start_date":"2019-10-28","location":"Taipei, Taiwan","name":"ATVA: Automated TEchnology for Verification and Analysis"},"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2)."}],"intvolume":" 11781","status":"public","title":"Deciding fast termination for probabilistic VASS with nondeterminism","_id":"7183","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"21","page":"462-478","citation":{"chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In International Symposium on Automated Technology for Verification and Analysis, 11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27.","short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” International Symposium on Automated Technology for Verification and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27.","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in International Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In International Symposium on Automated Technology for Verification and Analysis (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478.","ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: International Symposium on Automated Technology for Verification and Analysis. Vol 11781. Springer Nature; 2019:462-478. doi:10.1007/978-3-030-31784-3_27"},"publication":"International Symposium on Automated Technology for Verification and Analysis","date_published":"2019-10-21T00:00:00Z"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"14","article_type":"original","citation":{"ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437","ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437","ieee":"A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019.","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers, 2019, doi:10.3389/fpls.2019.01437.","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019).","chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science. Frontiers, 2019. https://doi.org/10.3389/fpls.2019.01437."},"publication":"Frontiers in Plant Science","date_published":"2019-11-14T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.","lang":"eng"}],"intvolume":" 10","status":"public","title":"Systematic Y2H screening reveals extensive effector-complex formation","ddc":["580"],"_id":"7182","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"open_access","file_name":"2019_FrontiersPlant_Alcantara.pdf","creator":"dernst","content_type":"application/pdf","file_size":1532505,"file_id":"7185","relation":"main_file","checksum":"995aa838aec2064d93550de82b40bbd1","date_created":"2019-12-16T07:58:43Z","date_updated":"2020-07-14T12:47:52Z"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1664462X"]},"month":"11","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":["000499821700001"],"pmid":["31803201"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fpls.2019.01437","article_number":"1437","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"JiFr"}],"publisher":"Frontiers","publication_status":"published","pmid":1,"year":"2019","volume":10,"date_created":"2019-12-15T23:00:43Z","date_updated":"2023-09-06T14:33:46Z","author":[{"first_name":"André","last_name":"Alcântara","full_name":"Alcântara, André"},{"full_name":"Bosch, Jason","last_name":"Bosch","first_name":"Jason"},{"full_name":"Nazari, Fahimeh","last_name":"Nazari","first_name":"Fahimeh"},{"first_name":"Gesa","last_name":"Hoffmann","full_name":"Hoffmann, Gesa"},{"full_name":"Gallei, Michelle C","first_name":"Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"first_name":"Martin A.","last_name":"Darino","full_name":"Darino, Martin A."},{"last_name":"Olukayode","first_name":"Toluwase","full_name":"Olukayode, Toluwase"},{"full_name":"Reumann, Daniel","first_name":"Daniel","last_name":"Reumann"},{"full_name":"Baggaley, Laura","first_name":"Laura","last_name":"Baggaley"},{"full_name":"Djamei, Armin","first_name":"Armin","last_name":"Djamei"}]},{"month":"12","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-13543-1","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Modeling epithelial tissue mechanics during cell invasion","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","grant_number":"M02379"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31797871"],"isi":["000500508100001"]},"oa":1,"file_date_updated":"2020-07-14T12:47:52Z","article_number":"5516","date_created":"2019-12-15T23:00:43Z","date_updated":"2023-09-06T14:08:21Z","volume":10,"author":[{"last_name":"Retzer","first_name":"Katarzyna","full_name":"Retzer, Katarzyna"},{"last_name":"Akhmanova","first_name":"Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","full_name":"Akhmanova, Maria"},{"full_name":"Konstantinova, Nataliia","last_name":"Konstantinova","first_name":"Nataliia"},{"full_name":"Malínská, Kateřina","first_name":"Kateřina","last_name":"Malínská"},{"last_name":"Leitner","first_name":"Johannes","full_name":"Leitner, Johannes"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaSi"}],"year":"2019","pmid":1,"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ieee":"K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., & Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13543-1","ista":"Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516.","ama":"Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 2019;10. doi:10.1038/s41467-019-13543-1","chicago":"Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1.","short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019).","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications, vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1."},"abstract":[{"text":"Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7184","checksum":"77e8720a8e0f3091b98159f85be40893","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-16T07:37:50Z","access_level":"open_access","file_name":"2019_NatureComm_Retzer.pdf","content_type":"application/pdf","file_size":5156533,"creator":"dernst"}],"status":"public","title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","ddc":["570"],"intvolume":" 10","_id":"7180","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"intvolume":" 37","title":"Large multiple sequence alignments with a root-to-leaf regressive method","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7181","oa_version":"Submitted Version","type":"journal_article","issue":"12","abstract":[{"text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6.","lang":"eng"}],"page":"1466-1470","article_type":"original","citation":{"chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.","ieee":"E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6","ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.","ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6"},"publication":"Nature Biotechnology","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2019","volume":37,"date_updated":"2023-09-06T14:32:52Z","date_created":"2019-12-15T23:00:43Z","related_material":{"record":[{"id":"13059","status":"public","relation":"research_data"}]},"author":[{"first_name":"Edgar","last_name":"Garriga","full_name":"Garriga, Edgar"},{"full_name":"Di Tommaso, Paolo","first_name":"Paolo","last_name":"Di Tommaso"},{"full_name":"Magis, Cedrik","last_name":"Magis","first_name":"Cedrik"},{"first_name":"Ionas","last_name":"Erb","full_name":"Erb, Ionas"},{"full_name":"Mansouri, Leila","first_name":"Leila","last_name":"Mansouri"},{"full_name":"Baltzis, Athanasios","first_name":"Athanasios","last_name":"Baltzis"},{"full_name":"Laayouni, Hafid","first_name":"Hafid","last_name":"Laayouni"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"full_name":"Floden, Evan","first_name":"Evan","last_name":"Floden"},{"full_name":"Notredame, Cedric","last_name":"Notredame","first_name":"Cedric"}],"ec_funded":1,"project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/","open_access":"1"}],"oa":1,"external_id":{"pmid":["31792410"],"isi":["000500748900021"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41587-019-0333-6","publication_identifier":{"issn":["10870156"],"eissn":["15461696"]},"month":"12"},{"date_published":"2019-11-18T00:00:00Z","article_type":"original","citation":{"ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8. doi:10.7554/eLife.51381","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381.","ieee":"A. Llorca et al., “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife Sciences Publications, 2019, doi:10.7554/eLife.51381.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019).","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381."},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_eLife_Llorca.pdf","content_type":"application/pdf","file_size":2960543,"creator":"dernst","relation":"main_file","file_id":"7503","checksum":"b460ecc33e1a68265e7adea775021f3a","date_created":"2020-02-18T15:19:26Z","date_updated":"2020-07-14T12:47:53Z"}],"intvolume":" 8","title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","ddc":["570"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7202","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.7554/eLife.51381","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416"}],"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":{"isi":["000508156800001"],"pmid":["31736464"]},"publication_identifier":{"eissn":["2050084X"]},"month":"11","volume":8,"date_updated":"2023-09-06T14:38:39Z","date_created":"2019-12-22T23:00:42Z","author":[{"first_name":"Alfredo","last_name":"Llorca","full_name":"Llorca, Alfredo"},{"first_name":"Gabriele","last_name":"Ciceri","full_name":"Ciceri, Gabriele"},{"last_name":"Beattie","first_name":"Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","full_name":"Beattie, Robert J"},{"full_name":"Wong, Fong Kuan","first_name":"Fong Kuan","last_name":"Wong"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"full_name":"Serafeimidou-Pouliou, Eleni","last_name":"Serafeimidou-Pouliou","first_name":"Eleni"},{"last_name":"Fernández-Otero","first_name":"Marian","full_name":"Fernández-Otero, Marian"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"full_name":"Arnold, Sebastian J.","last_name":"Arnold","first_name":"Sebastian J."},{"full_name":"Meyer, Martin","last_name":"Meyer","first_name":"Martin"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Miguel","last_name":"Maravall","full_name":"Maravall, Miguel"},{"first_name":"Oscar","last_name":"Marín","full_name":"Marín, Oscar"}],"department":[{"_id":"SiHi"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:53Z","article_number":"e51381"},{"publication_identifier":{"eissn":["15306860"]},"month":"12","doi":"10.1096/fj.201901543R","language":[{"iso":"eng"}],"external_id":{"pmid":["31585509"],"isi":["000507466100054"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-12-06T17:30:09Z","author":[{"full_name":"Klotz, Lisa","first_name":"Lisa","last_name":"Klotz"},{"last_name":"Wendler","first_name":"Olaf","full_name":"Wendler, Olaf"},{"full_name":"Frischknecht, Renato","last_name":"Frischknecht","first_name":"Renato"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"full_name":"Schulze, Holger","last_name":"Schulze","first_name":"Holger"},{"last_name":"Enz","first_name":"Ralf","full_name":"Enz, Ralf"}],"volume":33,"date_updated":"2023-09-06T14:34:36Z","date_created":"2019-12-15T23:00:42Z","pmid":1,"year":"2019","publisher":"FASEB","department":[{"_id":"RySh"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","citation":{"mla":"Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R.","short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","chicago":"Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R.","ama":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 2019;33(12):13734-13746. doi:10.1096/fj.201901543R","ista":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746.","ieee":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” FASEB Journal, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.","apa":"Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., & Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. FASEB. https://doi.org/10.1096/fj.201901543R"},"publication":"FASEB Journal","page":"13734-13746","article_type":"original","issue":"12","abstract":[{"text":"Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"8922","date_created":"2020-12-06T17:30:09Z","date_updated":"2020-12-06T17:30:09Z","checksum":"79e3b72481dc32489911121cf3b7d8d0","success":1,"file_name":"Klotz et al 2019 EMBO Reports.pdf","access_level":"open_access","file_size":4766789,"content_type":"application/pdf","creator":"shigemot"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7179","intvolume":" 33","status":"public","ddc":["571","599"],"title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses"},{"publication_identifier":{"isbn":["9781450362290"],"eissn":["21674337"],"issn":["21674329"]},"month":"11","oa":1,"external_id":{"arxiv":["1802.08021"],"isi":["000545976800011"]},"main_file_link":[{"url":"https://arxiv.org/abs/1802.08021","open_access":"1"}],"project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1145/3295500.3356222","conference":{"end_date":"2019-11-19","start_date":"2019-11-17","location":"Denver, CO, Unites States","name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis"},"language":[{"iso":"eng"}],"article_number":"a11","ec_funded":1,"year":"2019","department":[{"_id":"DaAl"}],"publisher":"ACM","publication_status":"published","author":[{"full_name":"Renggli, Cedric","first_name":"Cedric","last_name":"Renggli"},{"full_name":"Ashkboos, Saleh","first_name":"Saleh","last_name":"Ashkboos","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A"},{"full_name":"Aghagolzadeh, Mehdi","last_name":"Aghagolzadeh","first_name":"Mehdi"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"}],"date_created":"2019-12-22T23:00:42Z","date_updated":"2023-09-06T14:37:55Z","scopus_import":"1","article_processing_charge":"No","day":"17","citation":{"apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in International Conference for High Performance Computing, Networking, Storage and Analysis, SC, Denver, CO, Unites States, 2019.","ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11.","ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019. doi:10.1145/3295500.3356222","chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019.","mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” International Conference for High Performance Computing, Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222."},"publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","date_published":"2019-11-17T00:00:00Z","type":"conference","abstract":[{"text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7201","status":"public","title":"SparCML: High-performance sparse communication for machine learning","oa_version":"Preprint"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13067","year":"2019","status":"public","ddc":["570"],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","department":[{"_id":"NiBa"}],"publisher":"Dryad","author":[{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Zagrodzka, Zuzanna","last_name":"Zagrodzka","first_name":"Zuzanna"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7205"}]},"date_created":"2023-05-23T16:36:27Z","date_updated":"2023-09-06T14:48:57Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.tb2rbnzwk","open_access":"1"}],"doi":"10.5061/DRYAD.TB2RBNZWK","date_published":"2019-12-02T00:00:00Z","day":"02","month":"12","article_processing_charge":"No"},{"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":["000511618800007"]},"isi":1,"quality_controlled":"1","doi":"10.1186/s12859-019-3208-4","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14712105"]},"month":"12","year":"2019","department":[{"_id":"DaAl"}],"publisher":"BMC","publication_status":"published","author":[{"full_name":"Aganezov, Sergey","last_name":"Aganezov","first_name":"Sergey"},{"full_name":"Zban, Ilya","first_name":"Ilya","last_name":"Zban"},{"full_name":"Aksenov, Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii","last_name":"Aksenov"},{"full_name":"Alexeev, Nikita","first_name":"Nikita","last_name":"Alexeev"},{"full_name":"Schatz, Michael C.","last_name":"Schatz","first_name":"Michael C."}],"volume":20,"date_updated":"2023-09-06T14:51:06Z","date_created":"2019-12-29T23:00:46Z","article_number":"641","file_date_updated":"2020-07-14T12:47:54Z","citation":{"chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4.","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019.","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4"},"publication":"BMC Bioinformatics","article_type":"original","date_published":"2019-12-17T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"17","_id":"7214","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 20","status":"public","ddc":["570"],"title":"Recovering rearranged cancer chromosomes from karyotype graphs","file":[{"date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-02T16:10:58Z","checksum":"7a30357efdcf8f66587ed495c0927724","file_id":"7221","relation":"main_file","creator":"dernst","file_size":1917374,"content_type":"application/pdf","file_name":"2019_BMCBioinfo_Aganezov.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.","lang":"eng"}]},{"author":[{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack"}],"volume":6,"date_created":"2020-01-05T23:00:45Z","date_updated":"2023-09-06T14:52:49Z","pmid":1,"year":"2019","department":[{"_id":"NanoFab"}],"publisher":"MDPI","publication_status":"published","file_date_updated":"2020-07-14T12:47:54Z","article_number":"109","doi":"10.3390/bioengineering6040109","language":[{"iso":"eng"}],"external_id":{"isi":["000505590000024"],"pmid":["31816954"]},"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,"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["23065354"]},"month":"12","oa_version":"Published Version","file":[{"file_id":"7243","relation":"main_file","checksum":"80f1499e2a4caccdf3aa54b137fd99a0","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:49:59Z","access_level":"open_access","file_name":"2019_Bioengineering_Merrin.pdf","creator":"dernst","file_size":2660780,"content_type":"application/pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7225","intvolume":" 6","status":"public","ddc":["620"],"title":"Frontiers in microfluidics, a teaching resource review","issue":"4","abstract":[{"text":"This is a literature teaching resource review for biologically inspired microfluidics courses\r\nor exploring the diverse applications of microfluidics. The structure is around key papers and model\r\norganisms. While courses gradually change over time, a focus remains on understanding how\r\nmicrofluidics has developed as well as what it can and cannot do for researchers. As a primary\r\nstarting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof applications are discussed using model prokaryotic and eukaryotic organisms from the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics can still be used effectively for specific applications.","lang":"eng"}],"type":"journal_article","date_published":"2019-12-03T00:00:00Z","citation":{"ama":"Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering. 2019;6(4). doi:10.3390/bioengineering6040109","ista":"Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering. 6(4), 109.","ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019.","apa":"Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review. Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109","mla":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering, vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109.","short":"J. Merrin, Bioengineering 6 (2019).","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109."},"publication":"Bioengineering","article_type":"review","has_accepted_license":"1","article_processing_charge":"Yes","day":"03","scopus_import":"1"},{"scopus_import":"1","article_processing_charge":"No","day":"13","page":"123-141","citation":{"ama":"Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8","ista":"Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.","apa":"Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8","ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141.","mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8.","short":"H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.","chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8."},"publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","date_published":"2019-08-13T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature.","lang":"eng"}],"intvolume":" 11750","status":"public","title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","_id":"7231","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0302-9661-2"],"eissn":["1611-3349"]},"month":"08","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1907.11514"],"isi":["000611677700008"]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-29662-9_8","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","end_date":"2019-08-29","location":"Amsterdam, The Netherlands","start_date":"2019-08-27"},"publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2019","volume":11750,"date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:55:15Z","author":[{"full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","first_name":"Hui","last_name":"Kong"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}]}]