[{"article_processing_charge":"No","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"type":"research_data","day":"28","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"oa_version":"Published Version","contributor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","contributor_type":"project_leader","first_name":"Calin C","last_name":"Guet"}],"_id":"7383","year":"2020","file_date_updated":"2020-07-14T12:47:57Z","month":"01","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","corr_author":"1","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","citation":{"apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>","mla":"Grah, Rok. <i>Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>.","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>.","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>.","short":"R. Grah, (2020).","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>"},"author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","first_name":"Rok","last_name":"Grah","full_name":"Grah, Rok"}],"doi":"10.15479/AT:ISTA:7383","status":"public","fulldoi":"https://doi.org/10.15479/AT:ISTA:7383","date_updated":"2025-06-12T07:34:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-01-28T00:00:00Z","related_material":{"record":[{"id":"7652","status":"public","relation":"used_in_publication"}]},"file":[{"date_created":"2020-01-28T10:39:40Z","access_level":"open_access","checksum":"9d292cf5207b3829225f44c044cdb3fd","relation":"main_file","file_id":"7384","file_name":"Scripts.zip","creator":"rgrah","content_type":"application/zip","date_updated":"2020-07-14T12:47:57Z","file_size":73363365},{"content_type":"text/plain","creator":"rgrah","file_size":962,"date_updated":"2020-07-14T12:47:57Z","checksum":"4076ceab32ef588cc233802bab24c1ab","relation":"main_file","access_level":"open_access","date_created":"2020-01-28T10:39:30Z","file_name":"READ_ME_MAIN.txt","file_id":"7385"}],"oa":1,"date_created":"2020-01-28T10:41:49Z","abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}]},{"status":"public","fulldoi":"https://doi.org/10.1090/tran/8113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-08-01T00:00:00Z","project":[{"_id":"26A455A6-B435-11E9-9278-68D0E5697425","grant_number":"846294","name":"Geometric study of Wasserstein spaces and free probability","call_identifier":"H2020"}],"scopus_import":"1","author":[{"full_name":"Geher, Gyorgy Pal","last_name":"Geher","first_name":"Gyorgy Pal"},{"full_name":"Titkos, Tamas","last_name":"Titkos","first_name":"Tamas"},{"orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","full_name":"Virosztek, Daniel","last_name":"Virosztek","first_name":"Daniel"}],"oa":1,"date_created":"2020-01-29T10:20:46Z","oa_version":"Preprint","department":[{"_id":"LaEr"}],"arxiv":1,"quality_controlled":"1","article_type":"original","keyword":["Wasserstein space","isometric embeddings","isometric rigidity","exotic isometry flow"],"article_processing_charge":"No","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/2002.00859","open_access":"1"}],"month":"08","doi":"10.1090/tran/8113","date_updated":"2025-07-10T11:54:32Z","issue":"8","intvolume":"       373","citation":{"ama":"Geher GP, Titkos T, Virosztek D. Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. 2020;373(8):5855-5883. doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>","short":"G.P. Geher, T. Titkos, D. Virosztek, Transactions of the American Mathematical Society 373 (2020) 5855–5883.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2020. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>.","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Isometric study of Wasserstein spaces - the real line,” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8. American Mathematical Society, pp. 5855–5883, 2020.","ista":"Geher GP, Titkos T, Virosztek D. 2020. Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. 373(8), 5855–5883.","mla":"Geher, Gyorgy Pal, et al. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8, American Mathematical Society, 2020, pp. 5855–83, doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>.","apa":"Geher, G. P., Titkos, T., &#38; Virosztek, D. (2020). Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>"},"abstract":[{"text":"Recently Kloeckner described the structure of the isometry group of the quadratic Wasserstein space W_2(R^n). It turned out that the case of the real line is exceptional in the sense that there exists an exotic isometry flow. Following this line of investigation, we compute Isom(W_p(R)), the isometry group of the Wasserstein space\r\nW_p(R) for all p \\in [1,\\infty) \\setminus {2}. We show that W_2(R) is also exceptional regarding the\r\nparameter p: W_p(R) is isometrically rigid if and only if p is not equal to 2. Regarding the underlying\r\nspace, we prove that the exceptionality of p = 2 disappears if we replace R by the compact\r\ninterval [0,1]. Surprisingly, in that case, W_p([0,1]) is isometrically rigid if and only if\r\np is not equal to 1. Moreover, W_1([0,1]) admits isometries that split mass, and Isom(W_1([0,1]))\r\ncannot be embedded into Isom(W_1(R)).","lang":"eng"}],"publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"day":"01","publication_status":"published","ddc":["515"],"type":"journal_article","volume":373,"ec_funded":1,"external_id":{"arxiv":["2002.00859"],"isi":["000551418100018"]},"publisher":"American Mathematical Society","language":[{"iso":"eng"}],"page":"5855-5883","_id":"7389","year":"2020","title":"Isometric study of Wasserstein spaces - the real line","publication":"Transactions of the American Mathematical Society"},{"external_id":{"isi":["000557689300003"],"arxiv":["1808.07350"]},"volume":2256,"ec_funded":1,"publisher":"Springer Nature","year":"2020","_id":"74","page":"1-27","language":[{"iso":"eng"}],"publication":"Geometric Aspects of Functional Analysis","title":"Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures","day":"21","publication_status":"published","type":"book_chapter","abstract":[{"text":"We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean  space,  motivated  by  the  famous  theorem  of  Gromov  about  the  waist  of  radially symmetric Gaussian measures.  In particular, it turns our possible to extend Gromov’s original result  to  the  case  of  not  necessarily  radially  symmetric  Gaussian  measure.   We  also  provide examples of measures having no t-neighborhood waist property, including a rather wide class\r\nof compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2.\r\nWe  use  a  simpler  form  of  Gromov’s  pancake  argument  to  produce  some  estimates  of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for reader’s convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian\r\nmeasures.","lang":"eng"}],"publication_identifier":{"isbn":["9783030360191"],"eissn":["1617-9692"],"issn":["0075-8434"],"eisbn":["9783030360207"]},"doi":"10.1007/978-3-030-36020-7_1","date_updated":"2025-07-10T11:54:33Z","citation":{"short":"A. Akopyan, R. Karasev, in:, B. Klartag, E. Milman (Eds.), Geometric Aspects of Functional Analysis, Springer Nature, 2020, pp. 1–27.","ama":"Akopyan A, Karasev R. Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Klartag B, Milman E, eds. <i>Geometric Aspects of Functional Analysis</i>. Vol 2256. LNM. Springer Nature; 2020:1-27. doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>","ieee":"A. Akopyan and R. Karasev, “Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures,” in <i>Geometric Aspects of Functional Analysis</i>, vol. 2256, B. Klartag and E. Milman, Eds. Springer Nature, 2020, pp. 1–27.","chicago":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” In <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, 2256:1–27. LNM. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>.","ista":"Akopyan A, Karasev R. 2020.Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Geometric Aspects of Functional Analysis. vol. 2256, 1–27.","mla":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, vol. 2256, Springer Nature, 2020, pp. 1–27, doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>.","apa":"Akopyan, A., &#38; Karasev, R. (2020). Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In B. Klartag &#38; E. Milman (Eds.), <i>Geometric Aspects of Functional Analysis</i> (Vol. 2256, pp. 1–27). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>"},"intvolume":"      2256","main_file_link":[{"url":"https://arxiv.org/abs/1808.07350","open_access":"1"}],"month":"06","quality_controlled":"1","arxiv":1,"oa_version":"Preprint","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"article_processing_charge":"No","isi":1,"oa":1,"editor":[{"last_name":"Klartag","full_name":"Klartag, Bo'az","first_name":"Bo'az"},{"first_name":"Emanuel","full_name":"Milman, Emanuel","last_name":"Milman"}],"date_created":"2018-12-11T11:44:29Z","series_title":"LNM","status":"public","fulldoi":"https://doi.org/10.1007/978-3-030-36020-7_1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-06-21T00:00:00Z","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"first_name":"Roman","last_name":"Karasev","full_name":"Karasev, Roman"}],"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"scopus_import":"1"},{"date_created":"2020-01-30T09:24:06Z","editor":[{"first_name":"Lilianna ","last_name":"Solnica-Krezel","full_name":"Solnica-Krezel, Lilianna "}],"scopus_import":"1","author":[{"last_name":"Bruce","full_name":"Bruce, Ashley E.E.","first_name":"Ashley E.E."},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"date_published":"2020-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","fulldoi":"https://doi.org/10.1016/bs.ctdb.2019.07.001","series_title":"Current Topics in Developmental Biology","month":"01","isi":1,"article_processing_charge":"No","department":[{"_id":"CaHe"}],"oa_version":"None","quality_controlled":"1","publication_identifier":{"isbn":["9780128127988"],"issn":["0070-2153"]},"abstract":[{"text":"Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed.","lang":"eng"}],"intvolume":"       136","pmid":1,"citation":{"mla":"Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>.","apa":"Bruce, A. E. E., &#38; Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish epiboly: A current view. In L. Solnica-Krezel (Ed.), <i>Gastrulation: From Embryonic Pattern to Form</i> (Vol. 136, pp. 319–341). Elsevier. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>","short":"A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.","ama":"Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view. In: Solnica-Krezel L, ed. <i>Gastrulation: From Embryonic Pattern to Form</i>. Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>","ieee":"A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly: A current view,” in <i>Gastrulation: From Embryonic Pattern to Form</i>, vol. 136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341.","ista":"Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.","chicago":"Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” In <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, 136:319–41. Current Topics in Developmental Biology. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>."},"date_updated":"2025-06-12T07:03:19Z","doi":"10.1016/bs.ctdb.2019.07.001","title":"Mechanisms of zebrafish epiboly: A current view","publication":"Gastrulation: From Embryonic Pattern to Form","page":"319-341","language":[{"iso":"eng"}],"_id":"7410","year":"2020","publisher":"Elsevier","volume":136,"external_id":{"pmid":["31959293"],"isi":["000611830600012"]},"type":"book_chapter","publication_status":"published","day":"01"},{"article_type":"original","quality_controlled":"1","oa_version":"Submitted Version","department":[{"_id":"JiFr"}],"isi":1,"article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054","open_access":"1"}],"month":"01","date_published":"2020-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1080/15592324.2019.1687175","status":"public","author":[{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4566-0593","first_name":"Scott A","full_name":"Sinclair, Scott A","last_name":"Sinclair"},{"full_name":"Krämer, U.","last_name":"Krämer","first_name":"U."}],"scopus_import":"1","date_created":"2020-01-30T10:12:04Z","oa":1,"publication_status":"published","day":"01","type":"journal_article","publisher":"Taylor & Francis","external_id":{"isi":["000494909300001"],"pmid":["31696764"]},"volume":15,"publication":"Plant Signaling & Behavior","title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","_id":"7416","year":"2020","language":[{"iso":"eng"}],"issue":"1","date_updated":"2023-10-17T09:01:48Z","doi":"10.1080/15592324.2019.1687175","citation":{"chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>.","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Taylor &#38; Francis, 2020.","ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling &#38; Behavior. 15(1), 1687175.","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>","short":"S.A. Sinclair, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","apa":"Sinclair, S. A., &#38; Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>","mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, 1687175, Taylor &#38; Francis, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>."},"pmid":1,"intvolume":"        15","abstract":[{"lang":"eng","text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements."}],"article_number":"1687175","publication_identifier":{"issn":["1559-2324"]}},{"date_created":"2020-01-30T10:14:14Z","oa":1,"author":[{"orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","full_name":"Sinclair, Scott A","last_name":"Sinclair","first_name":"Scott A"},{"first_name":"S.","full_name":"Gille, S.","last_name":"Gille"},{"first_name":"M.","full_name":"Pauly, M.","last_name":"Pauly"},{"first_name":"U.","full_name":"Krämer, U.","last_name":"Krämer"}],"scopus_import":"1","date_published":"2020-01-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","fulldoi":"https://doi.org/10.1080/15592324.2019.1687185","month":"01","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154"}],"isi":1,"article_processing_charge":"No","article_type":"original","quality_controlled":"1","department":[{"_id":"JiFr"}],"oa_version":"Submitted Version","article_number":"e1687185","publication_identifier":{"issn":["1559-2324"]},"abstract":[{"text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development.","lang":"eng"}],"citation":{"short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Informa UK Limited, 2020.","chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling &#38; Behavior. 15(1), e1687185.","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>.","apa":"Sinclair, S. A., Gille, S., Pauly, M., &#38; Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>"},"pmid":1,"intvolume":"        15","date_updated":"2023-09-06T15:23:04Z","issue":"1","doi":"10.1080/15592324.2019.1687185","publication":"Plant Signaling & Behavior","title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","_id":"7417","year":"2020","language":[{"iso":"eng"}],"publisher":"Informa UK Limited","external_id":{"pmid":["31696770"],"isi":["000494907500001"]},"volume":15,"type":"journal_article","publication_status":"published","day":"01"},{"oa":1,"date_created":"2020-02-02T23:01:01Z","scopus_import":"1","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan"},{"first_name":"P. L.S.","full_name":"Lopes, P. L.S.","last_name":"Lopes"},{"last_name":"Hosur","full_name":"Hosur, Pavan","first_name":"Pavan"},{"full_name":"Gilbert, Matthew J.","last_name":"Gilbert","first_name":"Matthew J."},{"first_name":"Pouyan","full_name":"Ghaemi, Pouyan","last_name":"Ghaemi"}],"fulldoi":"https://doi.org/10.1103/PhysRevB.101.020504","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-01-13T00:00:00Z","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.02077"}],"article_processing_charge":"No","isi":1,"department":[{"_id":"MiLe"}],"arxiv":1,"oa_version":"Preprint","quality_controlled":"1","article_type":"original","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"article_number":"020504","abstract":[{"text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex.","lang":"eng"}],"intvolume":"       101","citation":{"ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. <i>Physical Review B</i>. 2020;101(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020).","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” <i>Physical Review B</i>, vol. 101, no. 2. American Physical Society, 2020.","ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>.","mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” <i>Physical Review B</i>, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>.","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., &#38; Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>"},"doi":"10.1103/PhysRevB.101.020504","date_updated":"2025-07-10T11:54:37Z","issue":"2","language":[{"iso":"eng"}],"_id":"7428","year":"2020","title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","publication":"Physical Review B","volume":101,"external_id":{"arxiv":["1907.02077"],"isi":["000506843500001"]},"publisher":"American Physical Society","type":"journal_article","day":"13","publication_status":"published"},{"publication_status":"published","day":"10","type":"dissertation","ddc":["514"],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","corr_author":"1","title":"The hole system of triangulated shapes","file_date_updated":"2020-07-14T12:47:58Z","_id":"7460","year":"2020","page":"155","language":[{"iso":"eng"}],"date_updated":"2026-04-08T07:23:21Z","doi":"10.15479/AT:ISTA:7460","citation":{"ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>","apa":"Ölsböck, K. (2020). <i>The hole system of triangulated shapes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>","mla":"Ölsböck, Katharina. <i>The Hole System of Triangulated Shapes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>."},"abstract":[{"text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"OA_place":"publisher","oa_version":"Published Version","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"article_processing_charge":"No","has_accepted_license":"1","month":"02","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2020-02-10T00:00:00Z","status":"public","fulldoi":"https://doi.org/10.15479/AT:ISTA:7460","author":[{"orcid":"0000-0002-4672-8297","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","full_name":"Ölsböck, Katharina","last_name":"Ölsböck","first_name":"Katharina"}],"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"degree_awarded":"PhD","date_created":"2020-02-06T14:56:53Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6608"}]},"oa":1,"file":[{"file_id":"7461","file_name":"thesis_ist-final_noack.pdf","date_created":"2020-02-06T14:43:54Z","access_level":"open_access","relation":"main_file","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","date_updated":"2020-07-14T12:47:58Z","file_size":76195184,"creator":"koelsboe","content_type":"application/pdf"},{"relation":"source_file","checksum":"7a52383c812b0be64d3826546509e5a4","access_level":"closed","date_created":"2020-02-06T14:52:45Z","description":"latex source files, figures","file_name":"latex-files.zip","file_id":"7462","content_type":"application/x-zip-compressed","creator":"koelsboe","file_size":122103715,"date_updated":"2020-07-14T12:47:58Z"}]},{"article_number":"e1008277","publication_identifier":{"issn":["1553-7374"]},"abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"pmid":1,"citation":{"apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>.","ieee":"R. A. Dick <i>et al.</i>, “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” <i>PLOS Pathogens</i>, vol. 16, no. 1. Public Library of Science, 2020.","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>.","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. 2020;16(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>"},"intvolume":"        16","doi":"10.1371/journal.ppat.1008277","issue":"1","date_updated":"2025-04-15T08:24:51Z","year":"2020","_id":"7464","file_date_updated":"2020-07-14T12:47:59Z","language":[{"iso":"eng"}],"publication":"PLOS Pathogens","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","corr_author":"1","external_id":{"isi":["000510746400010"],"pmid":["31986188"]},"volume":16,"publisher":"Public Library of Science","ddc":["570"],"type":"journal_article","day":"27","publication_status":"published","related_material":{"record":[{"relation":"research_data","id":"9723","status":"deleted"}]},"file":[{"date_updated":"2020-07-14T12:47:59Z","file_size":4551246,"creator":"dernst","content_type":"application/pdf","file_name":"2020_PLOSPatho_Dick.pdf","file_id":"7484","access_level":"open_access","date_created":"2020-02-11T10:07:28Z","relation":"main_file","checksum":"a297f54d1fef0efe4789ca00f37f241e"}],"oa":1,"date_created":"2020-02-06T18:47:17Z","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."},{"full_name":"Xu, Chaoyi","last_name":"Xu","first_name":"Chaoyi"},{"full_name":"Morado, Dustin R.","last_name":"Morado","first_name":"Dustin R."},{"first_name":"Vladyslav","last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9523-9089"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"full_name":"Lyddon, Terri D.","last_name":"Lyddon","first_name":"Terri D."},{"full_name":"Broad, Arianna M.","last_name":"Broad","first_name":"Arianna M."},{"full_name":"Feathers, J. Ryan","last_name":"Feathers","first_name":"J. Ryan"},{"first_name":"Marc C.","last_name":"Johnson","full_name":"Johnson, Marc C."},{"first_name":"Volker M.","last_name":"Vogt","full_name":"Vogt, Volker M."},{"full_name":"Perilla, Juan R.","last_name":"Perilla","first_name":"Juan R."},{"first_name":"John A. G.","full_name":"Briggs, John A. G.","last_name":"Briggs"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"fulldoi":"https://doi.org/10.1371/journal.ppat.1008277","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-01-27T00:00:00Z","month":"01","has_accepted_license":"1","article_processing_charge":"No","isi":1,"quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"FlSc"}],"article_type":"original"},{"month":"04","has_accepted_license":"1","isi":1,"article_processing_charge":"No","article_type":"original","oa_version":"Published Version","department":[{"_id":"JiFr"}],"quality_controlled":"1","date_created":"2020-02-09T23:00:50Z","file":[{"file_size":3499069,"date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","creator":"dernst","file_id":"7471","file_name":"2020_PlantScience_Mazur.pdf","relation":"main_file","checksum":"f7f27c6a8fea985ceb9279be2204461c","date_created":"2020-02-10T08:59:36Z","access_level":"open_access"}],"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"author":[{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","full_name":"Adamowski, Maciek","last_name":"Adamowski"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin"},{"last_name":"Robert","full_name":"Robert, Hélène S.","first_name":"Hélène S."},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2020-04-01T00:00:00Z","status":"public","fulldoi":"https://doi.org/10.1016/j.plantsci.2020.110414","title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","corr_author":"1","publication":"Plant Science","language":[{"iso":"eng"}],"_id":"7465","year":"2020","file_date_updated":"2020-07-14T12:47:59Z","publisher":"Elsevier","volume":293,"ec_funded":1,"external_id":{"pmid":["32081263"],"isi":["000520609800009"]},"type":"journal_article","ddc":["580"],"publication_status":"published","day":"01","publication_identifier":{"eissn":["1873-2259"],"issn":["0168-9452"]},"article_number":"110414","abstract":[{"lang":"eng","text":"The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization."}],"intvolume":"       293","citation":{"mla":"Mazur, Ewa, et al. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>, vol. 293, no. 4, 110414, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>.","apa":"Mazur, E., Gallei, M. C., Adamowski, M., Han, H., Robert, H. S., &#38; Friml, J. (2020). Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>","short":"E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020).","ama":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. 2020;293(4). doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>","ieee":"E. Mazur, M. C. Gallei, M. Adamowski, H. Han, H. S. Robert, and J. Friml, “Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis,” <i>Plant Science</i>, vol. 293, no. 4. Elsevier, 2020.","chicago":"Mazur, Ewa, Michelle C Gallei, Maciek Adamowski, Huibin Han, Hélène S. Robert, and Jiří Friml. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>.","ista":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. 2020. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 293(4), 110414."},"pmid":1,"issue":"4","date_updated":"2026-04-07T14:18:57Z","doi":"10.1016/j.plantsci.2020.110414"},{"publication":"eLife","title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","_id":"7466","year":"2020","file_date_updated":"2020-07-14T12:47:59Z","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","external_id":{"isi":["000512304800001"]},"volume":9,"type":"journal_article","ddc":["570"],"publication_status":"published","day":"20","article_number":"e51595","publication_identifier":{"eissn":["2050-084X"]},"abstract":[{"text":"Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis.","lang":"eng"}],"citation":{"apa":"Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou, J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>","mla":"Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>, vol. 9, e51595, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>.","chicago":"Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent, Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>.","ista":"Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595.","ieee":"K. Kierdorf <i>et al.</i>, “Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","short":"K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou, A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020).","ama":"Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>"},"intvolume":"         9","date_updated":"2026-04-03T09:24:34Z","doi":"10.7554/eLife.51595","month":"01","has_accepted_license":"1","isi":1,"article_processing_charge":"No","article_type":"original","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"DaSi"}],"date_created":"2020-02-09T23:00:51Z","oa":1,"file":[{"content_type":"application/pdf","creator":"dernst","file_size":4959933,"date_updated":"2020-07-14T12:47:59Z","checksum":"3a072be843f416c7a7d532a51dc0addb","relation":"main_file","date_created":"2020-02-10T08:53:16Z","access_level":"open_access","file_id":"7470","file_name":"2020_eLife_Kierdorf.pdf"}],"author":[{"first_name":"Katrin","last_name":"Kierdorf","full_name":"Kierdorf, Katrin"},{"last_name":"Hersperger","full_name":"Hersperger, Fabian","first_name":"Fabian"},{"full_name":"Sharrock, Jessica","last_name":"Sharrock","first_name":"Jessica"},{"first_name":"Crystal M.","last_name":"Vincent","full_name":"Vincent, Crystal M."},{"full_name":"Ustaoglu, Pinar","last_name":"Ustaoglu","first_name":"Pinar"},{"first_name":"Jiawen","full_name":"Dou, Jiawen","last_name":"Dou"},{"orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila","last_name":"György","first_name":"Attila"},{"full_name":"Groß, Olaf","last_name":"Groß","first_name":"Olaf"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","full_name":"Siekhaus, Daria E","last_name":"Siekhaus"},{"first_name":"Marc S.","full_name":"Dionne, Marc S.","last_name":"Dionne"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","project":[{"call_identifier":"FWF","name":"The role of Drosophila TNF alpha in immune cell invasion","grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2020-01-20T00:00:00Z","fulldoi":"https://doi.org/10.7554/eLife.51595","status":"public"},{"file":[{"file_size":4703751,"date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","creator":"dernst","file_name":"2020_ScientificReport_Lopez.pdf","file_id":"7495","checksum":"c780bd87476a9c9e12668ff66de3dc96","relation":"main_file","access_level":"open_access","date_created":"2020-02-18T07:43:21Z"}],"oa":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-020-80651-0"}]},"date_created":"2020-02-16T23:00:49Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"author":[{"last_name":"López De La Oliva","full_name":"López De La Oliva, Amada R.","first_name":"Amada R."},{"last_name":"Campos-Sandoval","full_name":"Campos-Sandoval, José A.","first_name":"José A."},{"first_name":"María C.","full_name":"Gómez-García, María C.","last_name":"Gómez-García"},{"full_name":"Cardona, Carolina","last_name":"Cardona","first_name":"Carolina"},{"last_name":"Martín-Rufián","full_name":"Martín-Rufián, Mercedes","first_name":"Mercedes"},{"first_name":"Fernando J.","last_name":"Sialana","full_name":"Sialana, Fernando J."},{"first_name":"Laura","full_name":"Castilla, Laura","last_name":"Castilla"},{"first_name":"Narkhyun","full_name":"Bae, Narkhyun","last_name":"Bae","id":"3A5F7CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carolina","last_name":"Lobo","full_name":"Lobo, Carolina"},{"full_name":"Peñalver, Ana","last_name":"Peñalver","first_name":"Ana"},{"full_name":"García-Frutos, Marina","last_name":"García-Frutos","first_name":"Marina"},{"first_name":"David","last_name":"Carro","full_name":"Carro, David"},{"first_name":"Victoria","full_name":"Enrique, Victoria","last_name":"Enrique"},{"first_name":"José C.","last_name":"Paz","full_name":"Paz, José C."},{"first_name":"Raghavendra G.","full_name":"Mirmira, Raghavendra G.","last_name":"Mirmira"},{"last_name":"Gutiérrez","full_name":"Gutiérrez, Antonia","first_name":"Antonia"},{"first_name":"Francisco J.","last_name":"Alonso","full_name":"Alonso, Francisco J."},{"last_name":"Segura","full_name":"Segura, Juan A.","first_name":"Juan A."},{"first_name":"José M.","last_name":"Matés","full_name":"Matés, José M."},{"first_name":"Gert","full_name":"Lubec, Gert","last_name":"Lubec"},{"full_name":"Márquez, Javier","last_name":"Márquez","first_name":"Javier"}],"fulldoi":"https://doi.org/10.1038/s41598-020-58264-4","status":"public","date_published":"2020-02-10T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"02","has_accepted_license":"1","article_processing_charge":"No","isi":1,"department":[{"_id":"CaBe"}],"oa_version":"Published Version","quality_controlled":"1","article_type":"original","publication_identifier":{"eissn":["2045-2322"]},"article_number":"2259","abstract":[{"lang":"eng","text":"Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis playing a key role in cancer metabolic reprogramming. Humans express two types of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2 is repressed in many tumor cells and a better understanding of its function in tumorigenesis may further the development of new therapeutic approaches. We analyzed GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7 cells. We studied GLS2 expression after induction of differentiation with phorbol ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we investigated cell cycle progression and levels of p53, p21 and c-Myc proteins. Using the baculovirus system, human GLS2 protein was overexpressed, purified and analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform. We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry and subcellular fractionation gave consistent results demonstrating nuclear and mitochondrial locations, with the latter being predominant. Nuclear targeting was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins. We assessed the subnuclear location finding a widespread distribution of GLS2 in the nucleoplasm without clear overlapping with specific nuclear substructures. GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore, human GLS2 was identified as being hypusinated by MS analysis, a posttranslational modification which may be relevant for its nuclear targeting and/or function. Our studies provide evidence for a tumor suppressor role of GLS2 in certain types of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in cancer cells induced an antiproliferative response with cell cycle arrest at the G2/M phase."}],"intvolume":"        10","citation":{"short":"A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona, M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M. García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J. Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020).","ama":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. <i>Scientific reports</i>. 2020;10(1). doi:<a href=\"https://doi.org/10.1038/s41598-020-58264-4\">10.1038/s41598-020-58264-4</a>","chicago":"López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García, Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla, et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-58264-4\">https://doi.org/10.1038/s41598-020-58264-4</a>.","ista":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D, Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 10(1), 2259.","ieee":"A. R. López De La Oliva <i>et al.</i>, “Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation,” <i>Scientific reports</i>, vol. 10, no. 1. Springer Nature, 2020.","mla":"López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” <i>Scientific Reports</i>, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-58264-4\">10.1038/s41598-020-58264-4</a>.","apa":"López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona, C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-58264-4\">https://doi.org/10.1038/s41598-020-58264-4</a>"},"pmid":1,"doi":"10.1038/s41598-020-58264-4","issue":"1","date_updated":"2026-04-02T11:51:06Z","language":[{"iso":"eng"}],"_id":"7487","year":"2020","file_date_updated":"2020-07-14T12:47:59Z","title":"Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation","publication":"Scientific reports","volume":10,"external_id":{"pmid":["32042057"],"isi":["000560694800012"]},"publisher":"Springer Nature","ddc":["570"],"type":"journal_article","day":"10","publication_status":"published"},{"oa_version":"Published Version","department":[{"_id":"GaNo"}],"quality_controlled":"1","article_type":"original","article_processing_charge":"No","isi":1,"has_accepted_license":"1","month":"02","fulldoi":"https://doi.org/10.3390/ijms21031042","status":"public","date_published":"2020-02-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"author":[{"full_name":"Latorre-Pellicer, Ana","last_name":"Latorre-Pellicer","first_name":"Ana"},{"full_name":"Ascaso, Ángela","last_name":"Ascaso","first_name":"Ángela"},{"full_name":"Trujillano, Laura","last_name":"Trujillano","first_name":"Laura"},{"first_name":"Marta","last_name":"Gil-Salvador","full_name":"Gil-Salvador, Marta"},{"full_name":"Arnedo, Maria","last_name":"Arnedo","first_name":"Maria"},{"last_name":"Lucia-Campos","full_name":"Lucia-Campos, Cristina","first_name":"Cristina"},{"first_name":"Rebeca","full_name":"Antoñanzas-Pérez, Rebeca","last_name":"Antoñanzas-Pérez"},{"last_name":"Marcos-Alcalde","full_name":"Marcos-Alcalde, Iñigo","first_name":"Iñigo"},{"id":"D93538B0-5B71-11E9-AC62-02EBE5697425","first_name":"Ilaria","full_name":"Parenti, Ilaria","last_name":"Parenti"},{"full_name":"Bueno-Lozano, Gloria","last_name":"Bueno-Lozano","first_name":"Gloria"},{"full_name":"Musio, Antonio","last_name":"Musio","first_name":"Antonio"},{"first_name":"Beatriz","last_name":"Puisac","full_name":"Puisac, Beatriz"},{"first_name":"Frank J.","last_name":"Kaiser","full_name":"Kaiser, Frank J."},{"full_name":"Ramos, Feliciano J.","last_name":"Ramos","first_name":"Feliciano J."},{"last_name":"Gómez-Puertas","full_name":"Gómez-Puertas, Paulino","first_name":"Paulino"},{"first_name":"Juan","full_name":"Pié, Juan","last_name":"Pié"}],"oa":1,"file":[{"content_type":"application/pdf","creator":"dernst","file_size":4271234,"date_updated":"2020-07-14T12:47:59Z","relation":"main_file","checksum":"0e6658c4fe329d55d4d9bef01c5b15d0","date_created":"2020-02-18T07:49:22Z","access_level":"open_access","file_id":"7496","file_name":"2020_IntMolecSciences_Latorre.pdf"}],"date_created":"2020-02-16T23:00:49Z","day":"04","publication_status":"published","ddc":["570"],"type":"journal_article","volume":21,"external_id":{"isi":["000522551606028"]},"publisher":"MDPI","language":[{"iso":"eng"}],"_id":"7488","year":"2020","file_date_updated":"2020-07-14T12:47:59Z","title":"Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes","corr_author":"1","publication":"International Journal of Molecular Sciences","doi":"10.3390/ijms21031042","date_updated":"2025-07-10T11:54:41Z","issue":"3","intvolume":"        21","citation":{"short":"A. Latorre-Pellicer, Á. Ascaso, L. Trujillano, M. Gil-Salvador, M. Arnedo, C. Lucia-Campos, R. Antoñanzas-Pérez, I. Marcos-Alcalde, I. Parenti, G. Bueno-Lozano, A. Musio, B. Puisac, F.J. Kaiser, F.J. Ramos, P. Gómez-Puertas, J. Pié, International Journal of Molecular Sciences 21 (2020).","ama":"Latorre-Pellicer A, Ascaso Á, Trujillano L, et al. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. <i>International Journal of Molecular Sciences</i>. 2020;21(3). doi:<a href=\"https://doi.org/10.3390/ijms21031042\">10.3390/ijms21031042</a>","ieee":"A. Latorre-Pellicer <i>et al.</i>, “Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 3. MDPI, 2020.","chicago":"Latorre-Pellicer, Ana, Ángela Ascaso, Laura Trujillano, Marta Gil-Salvador, Maria Arnedo, Cristina Lucia-Campos, Rebeca Antoñanzas-Pérez, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21031042\">https://doi.org/10.3390/ijms21031042</a>.","ista":"Latorre-Pellicer A, Ascaso Á, Trujillano L, Gil-Salvador M, Arnedo M, Lucia-Campos C, Antoñanzas-Pérez R, Marcos-Alcalde I, Parenti I, Bueno-Lozano G, Musio A, Puisac B, Kaiser FJ, Ramos FJ, Gómez-Puertas P, Pié J. 2020. Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. International Journal of Molecular Sciences. 21(3), 1042.","mla":"Latorre-Pellicer, Ana, et al. “Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 3, 1042, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21031042\">10.3390/ijms21031042</a>.","apa":"Latorre-Pellicer, A., Ascaso, Á., Trujillano, L., Gil-Salvador, M., Arnedo, M., Lucia-Campos, C., … Pié, J. (2020). Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21031042\">https://doi.org/10.3390/ijms21031042</a>"},"abstract":[{"text":"Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS.","lang":"eng"}],"publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"article_number":"1042"},{"has_accepted_license":"1","month":"05","oa_version":"Published Version","department":[{"_id":"JuFi"}],"quality_controlled":"1","article_type":"original","article_processing_charge":"Yes (via OA deal)","isi":1,"file":[{"creator":"dernst","content_type":"application/pdf","success":1,"date_updated":"2020-11-20T09:14:22Z","file_size":1897571,"access_level":"open_access","date_created":"2020-11-20T09:14:22Z","relation":"main_file","checksum":"f107e21b58f5930876f47144be37cf6c","file_name":"2020_ArchRatMechAn_Fischer.pdf","file_id":"8779"}],"oa":1,"related_material":{"record":[{"id":"10007","status":"public","relation":"dissertation_contains"}]},"date_created":"2020-02-16T23:00:50Z","status":"public","fulldoi":"https://doi.org/10.1007/s00205-019-01486-2","date_published":"2020-05-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"author":[{"full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7252-8072","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","last_name":"Hensel","full_name":"Hensel, Sebastian","first_name":"Sebastian"}],"ec_funded":1,"volume":236,"external_id":{"isi":["000511060200001"]},"publisher":"Springer Nature","page":"967-1087","language":[{"iso":"eng"}],"_id":"7489","year":"2020","file_date_updated":"2020-11-20T09:14:22Z","corr_author":"1","title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension","publication":"Archive for Rational Mechanics and Analysis","day":"01","publication_status":"published","ddc":["530","532"],"type":"journal_article","abstract":[{"lang":"eng","text":"In the present work, we consider the evolution of two fluids separated by a sharp interface in the presence of surface tension—like, for example, the evolution of oil bubbles in water. Our main result is a weak–strong uniqueness principle for the corresponding free boundary problem for the incompressible Navier–Stokes equation: as long as a strong solution exists, any varifold solution must coincide with it. In particular, in the absence of physical singularities, the concept of varifold solutions—whose global in time existence has been shown by Abels (Interfaces Free Bound 9(1):31–65, 2007) for general initial data—does not introduce a mechanism for non-uniqueness. The key ingredient of our approach is the construction of a relative entropy functional capable of controlling the interface error. If the viscosities of the two fluids do not coincide, even for classical (strong) solutions the gradient of the velocity field becomes discontinuous at the interface, introducing the need for a careful additional adaption of the relative entropy."}],"publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"doi":"10.1007/s00205-019-01486-2","date_updated":"2026-04-08T07:01:01Z","intvolume":"       236","citation":{"apa":"Fischer, J. L., &#38; Hensel, S. (2020). Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-019-01486-2\">https://doi.org/10.1007/s00205-019-01486-2</a>","mla":"Fischer, Julian L., and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 236, Springer Nature, 2020, pp. 967–1087, doi:<a href=\"https://doi.org/10.1007/s00205-019-01486-2\">10.1007/s00205-019-01486-2</a>.","ieee":"J. L. Fischer and S. Hensel, “Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 236. Springer Nature, pp. 967–1087, 2020.","ista":"Fischer JL, Hensel S. 2020. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 236, 967–1087.","chicago":"Fischer, Julian L, and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00205-019-01486-2\">https://doi.org/10.1007/s00205-019-01486-2</a>.","short":"J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087.","ama":"Fischer JL, Hensel S. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. <i>Archive for Rational Mechanics and Analysis</i>. 2020;236:967-1087. doi:<a href=\"https://doi.org/10.1007/s00205-019-01486-2\">10.1007/s00205-019-01486-2</a>"}},{"isi":1,"article_processing_charge":"No","article_type":"original","oa_version":"Published Version","department":[{"_id":"JiFr"},{"_id":"GaTk"},{"_id":"EM-Fac"},{"_id":"SyCr"}],"quality_controlled":"1","month":"01","has_accepted_license":"1","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","author":[{"full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"last_name":"Prizak","full_name":"Prizak, Roshan","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","full_name":"Kaufmann, Walter","first_name":"Walter"},{"first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285"},{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","first_name":"Barbara E"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"date_published":"2020-01-23T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","fulldoi":"https://doi.org/10.7554/eLife.52067","status":"public","date_created":"2020-02-16T23:00:50Z","oa":1,"file":[{"date_created":"2020-02-18T07:21:16Z","access_level":"open_access","checksum":"2052daa4be5019534f3a42f200a09f32","relation":"main_file","file_id":"7494","file_name":"2020_eLife_Narasimhan.pdf","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:47:59Z","file_size":7247468}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"type":"journal_article","ddc":["570","580"],"publication_status":"published","day":"23","title":"Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants","publication":"eLife","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:59Z","_id":"7490","year":"2020","publisher":"eLife Sciences Publications","volume":9,"ec_funded":1,"external_id":{"pmid":["31971511"],"isi":["000514104100001"]},"intvolume":"         9","pmid":1,"citation":{"chicago":"Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann, Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.52067\">https://doi.org/10.7554/eLife.52067</a>.","ieee":"M. Narasimhan <i>et al.</i>, “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","ista":"Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE, Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 9, e52067.","short":"M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020).","ama":"Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.52067\">10.7554/eLife.52067</a>","apa":"Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas Perez, B. E., &#38; Friml, J. (2020). Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.52067\">https://doi.org/10.7554/eLife.52067</a>","mla":"Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” <i>ELife</i>, vol. 9, e52067, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.52067\">10.7554/eLife.52067</a>."},"date_updated":"2025-04-14T07:45:03Z","doi":"10.7554/eLife.52067","publication_identifier":{"eissn":["2050-084X"]},"article_number":"e52067","abstract":[{"text":"In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.","lang":"eng"}]},{"publication":"Journal of Integrative Plant Biology","title":"Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid","year":"2020","_id":"7497","page":"1433-1451","language":[{"iso":"eng"}],"publisher":"Wiley","external_id":{"pmid":["31912615"],"isi":["000515803000001"]},"volume":62,"type":"journal_article","ddc":["580"],"publication_status":"published","day":"01","publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"abstract":[{"lang":"eng","text":"Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover, the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross‐talk between JA signalling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants."}],"pmid":1,"citation":{"mla":"Han, L., et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9, Wiley, 2020, pp. 1433–51, doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>.","apa":"Han, L., Zhou, X., Zhao, Y., Zhu, S., Wu, L., He, Y., … Du, Y. (2020). Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>","short":"L. Han, X. Zhou, Y. Zhao, S. Zhu, L. Wu, Y. He, X. Ping, X. Lu, W. Huang, J. Qian, L. Zhang, X. Jiang, D. Zhu, C. Luo, S. Li, Q. Dong, Q. Fu, K. Deng, X. Wang, L. Wang, S. Peng, J. Wu, W. Li, J. Friml, Y. Zhu, X. He, Y. Du, Journal of Integrative Plant Biology 62 (2020) 1433–1451.","ama":"Han L, Zhou X, Zhao Y, et al. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. <i>Journal of Integrative Plant Biology</i>. 2020;62(9):1433-1451. doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>","ieee":"L. Han <i>et al.</i>, “Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid,” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9. Wiley, pp. 1433–1451, 2020.","ista":"Han L, Zhou X, Zhao Y, Zhu S, Wu L, He Y, Ping X, Lu X, Huang W, Qian J, Zhang L, Jiang X, Zhu D, Luo C, Li S, Dong Q, Fu Q, Deng K, Wang X, Wang L, Peng S, Wu J, Li W, Friml J, Zhu Y, He X, Du Y. 2020. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. 62(9), 1433–1451.","chicago":"Han, L, X Zhou, Y Zhao, S Zhu, L Wu, Y He, X Ping, et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>."},"intvolume":"        62","issue":"9","date_updated":"2026-06-18T19:22:29Z","doi":"10.1111/jipb.12905","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.12905"}],"isi":1,"article_processing_charge":"No","article_type":"original","quality_controlled":"1","department":[{"_id":"JiFr"}],"oa_version":"Published Version","date_created":"2020-02-18T10:02:25Z","oa":1,"acknowledgement":"We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for providing generous support with the IAA and JA measurements. We thank Professor Guohua Xu (Nanjing Agricultural University) for generously providing the Nipponbare rice expressing DR5::GUS. We thank Professor Muyuan Zhu (Zhejiang University) for generously providing a rice line expressing 35S::miR393b. We thank Professor Yinong Yang (Pennsylvania State University) for generously providing the rice line coi1-18. This work was supported by grants from the National Natural Science Foundation of China (31660501, 31460453, 31860064 and 31470382), the Major Special Program for Scientific Research, Education Department of Yunnan Province (ZD2015005), the Project sponsored by SRF for ROCS, SEM ([2013] 1792), the Major Science and Technique Programs in Yunnan Province (2016ZF001), the Key Projects of the Applied Basic Research Plan of Yunnan Province (2017FA018), the National Key R&D Program of China (2018YFD0201100) and the China Agriculture Research System (CARS-21).","author":[{"first_name":"L","full_name":"Han, L","last_name":"Han"},{"last_name":"Zhou","full_name":"Zhou, X","first_name":"X"},{"first_name":"Y","full_name":"Zhao, Y","last_name":"Zhao"},{"last_name":"Zhu","full_name":"Zhu, S","first_name":"S"},{"full_name":"Wu, L","last_name":"Wu","first_name":"L"},{"last_name":"He","full_name":"He, Y","first_name":"Y"},{"last_name":"Ping","full_name":"Ping, X","first_name":"X"},{"first_name":"X","full_name":"Lu, X","last_name":"Lu"},{"first_name":"W","last_name":"Huang","full_name":"Huang, W"},{"first_name":"J","last_name":"Qian","full_name":"Qian, J"},{"first_name":"L","last_name":"Zhang","full_name":"Zhang, L"},{"first_name":"X","full_name":"Jiang, X","last_name":"Jiang"},{"first_name":"D","full_name":"Zhu, D","last_name":"Zhu"},{"last_name":"Luo","full_name":"Luo, C","first_name":"C"},{"last_name":"Li","full_name":"Li, S","first_name":"S"},{"first_name":"Q","full_name":"Dong, Q","last_name":"Dong"},{"first_name":"Q","last_name":"Fu","full_name":"Fu, Q"},{"first_name":"K","last_name":"Deng","full_name":"Deng, K"},{"last_name":"Wang","full_name":"Wang, X","first_name":"X"},{"last_name":"Wang","full_name":"Wang, L","first_name":"L"},{"full_name":"Peng, S","last_name":"Peng","first_name":"S"},{"full_name":"Wu, J","last_name":"Wu","first_name":"J"},{"first_name":"W","full_name":"Li, W","last_name":"Li"},{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Y","last_name":"Zhu","full_name":"Zhu, Y"},{"first_name":"X","full_name":"He, X","last_name":"He"},{"last_name":"Du","full_name":"Du, Y","first_name":"Y"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-09-01T00:00:00Z","status":"public","fulldoi":"https://doi.org/10.1111/jipb.12905"},{"corr_author":"1","title":"Outside the box: Abstraction-based monitoring of neural networks","publication":"24th European Conference on Artificial Intelligence","language":[{"iso":"eng"}],"page":"2433-2440","year":"2020","_id":"7505","file_date_updated":"2020-09-21T07:12:32Z","publisher":"IOS Press","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"volume":325,"ec_funded":1,"external_id":{"arxiv":["1911.09032"],"isi":["000650971303002"]},"type":"conference","ddc":["000"],"publication_status":"published","day":"24","abstract":[{"lang":"eng","text":"Neural networks have demonstrated unmatched performance in a range of classification tasks. Despite numerous efforts of the research community, novelty detection remains one of the significant limitations of neural networks. The ability to identify previously unseen inputs as novel is crucial for our understanding of the decisions made by neural networks. At runtime, inputs not falling into any of the categories learned during training cannot be classified correctly by the neural network. Existing approaches treat the neural network as a black box and try to detect novel inputs based on the confidence of the output predictions. However, neural networks are not trained to reduce their confidence for novel inputs, which limits the effectiveness of these approaches. We propose a framework to monitor a neural network by observing the hidden layers. We employ a common abstraction from program analysis - boxes - to identify novel behaviors in the monitored layers, i.e., inputs that cause behaviors outside the box. For each neuron, the boxes range over the values seen in training. The framework is efficient and flexible to achieve a desired trade-off between raising false warnings and detecting novel inputs. We illustrate the performance and the robustness to variability in the unknown classes on popular image-classification benchmarks."}],"intvolume":"       325","citation":{"apa":"Henzinger, T. A., Lukina, A., &#38; Schilling, C. (2020). Outside the box: Abstraction-based monitoring of neural networks. In <i>24th European Conference on Artificial Intelligence</i> (Vol. 325, pp. 2433–2440). Santiago de Compostela, Spain: IOS Press. <a href=\"https://doi.org/10.3233/FAIA200375\">https://doi.org/10.3233/FAIA200375</a>","mla":"Henzinger, Thomas A., et al. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” <i>24th European Conference on Artificial Intelligence</i>, vol. 325, IOS Press, 2020, pp. 2433–40, doi:<a href=\"https://doi.org/10.3233/FAIA200375\">10.3233/FAIA200375</a>.","ieee":"T. A. Henzinger, A. Lukina, and C. Schilling, “Outside the box: Abstraction-based monitoring of neural networks,” in <i>24th European Conference on Artificial Intelligence</i>, Santiago de Compostela, Spain, 2020, vol. 325, pp. 2433–2440.","chicago":"Henzinger, Thomas A, Anna Lukina, and Christian Schilling. “Outside the Box: Abstraction-Based Monitoring of Neural Networks.” In <i>24th European Conference on Artificial Intelligence</i>, 325:2433–40. IOS Press, 2020. <a href=\"https://doi.org/10.3233/FAIA200375\">https://doi.org/10.3233/FAIA200375</a>.","ista":"Henzinger TA, Lukina A, Schilling C. 2020. Outside the box: Abstraction-based monitoring of neural networks. 24th European Conference on Artificial Intelligence. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 325, 2433–2440.","short":"T.A. Henzinger, A. Lukina, C. Schilling, in:, 24th European Conference on Artificial Intelligence, IOS Press, 2020, pp. 2433–2440.","ama":"Henzinger TA, Lukina A, Schilling C. Outside the box: Abstraction-based monitoring of neural networks. In: <i>24th European Conference on Artificial Intelligence</i>. Vol 325. IOS Press; 2020:2433-2440. doi:<a href=\"https://doi.org/10.3233/FAIA200375\">10.3233/FAIA200375</a>"},"date_updated":"2025-04-15T06:26:13Z","conference":{"start_date":"2020-08-29","end_date":"2020-09-08","name":"ECAI: European Conference on Artificial Intelligence","location":"Santiago de Compostela, Spain"},"doi":"10.3233/FAIA200375","month":"02","has_accepted_license":"1","isi":1,"article_processing_charge":"No","arxiv":1,"department":[{"_id":"ToHe"}],"oa_version":"Published Version","quality_controlled":"1","date_created":"2020-02-21T16:44:03Z","file":[{"file_name":"2020_ECAI_Henzinger.pdf","file_id":"8540","relation":"main_file","checksum":"80642fa0b6cd7da95dcd87d63789ad5e","access_level":"open_access","date_created":"2020-09-21T07:12:32Z","file_size":1692214,"success":1,"date_updated":"2020-09-21T07:12:32Z","content_type":"application/pdf","creator":"dernst"}],"oa":1,"acknowledgement":"We thank Christoph Lampert and Nikolaus Mayer for fruitful discussions. This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement No. 754411.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"scopus_import":"1","author":[{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Lukina","full_name":"Lukina, Anna","first_name":"Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","first_name":"Christian","full_name":"Schilling, Christian","last_name":"Schilling"}],"date_published":"2020-02-24T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","fulldoi":"https://doi.org/10.3233/FAIA200375"},{"publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"abstract":[{"lang":"eng","text":"In this paper, we introduce a novel method for deriving higher order corrections to the mean-field description of the dynamics of interacting bosons. More precisely, we consider the dynamics of N d-dimensional bosons for large N. The bosons initially form a Bose–Einstein condensate and interact with each other via a pair potential of the form (N−1)−1Ndβv(Nβ·)forβ∈[0,14d). We derive a sequence of N-body functions which approximate the true many-body dynamics in L2(RdN)-norm to arbitrary precision in powers of N−1. The approximating functions are constructed as Duhamel expansions of finite order in terms of the first quantised analogue of a Bogoliubov time evolution."}],"citation":{"mla":"Bossmann, Lea, et al. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” <i>Journal of Statistical Physics</i>, vol. 178, Springer Nature, 2020, pp. 1362–96, doi:<a href=\"https://doi.org/10.1007/s10955-020-02500-8\">10.1007/s10955-020-02500-8</a>.","apa":"Bossmann, L., Pavlović, N., Pickl, P., &#38; Soffer, A. (2020). Higher order corrections to the mean-field description of the dynamics of interacting bosons. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-020-02500-8\">https://doi.org/10.1007/s10955-020-02500-8</a>","short":"L. Bossmann, N. Pavlović, P. Pickl, A. Soffer, Journal of Statistical Physics 178 (2020) 1362–1396.","ama":"Bossmann L, Pavlović N, Pickl P, Soffer A. Higher order corrections to the mean-field description of the dynamics of interacting bosons. <i>Journal of Statistical Physics</i>. 2020;178:1362-1396. doi:<a href=\"https://doi.org/10.1007/s10955-020-02500-8\">10.1007/s10955-020-02500-8</a>","ista":"Bossmann L, Pavlović N, Pickl P, Soffer A. 2020. Higher order corrections to the mean-field description of the dynamics of interacting bosons. Journal of Statistical Physics. 178, 1362–1396.","chicago":"Bossmann, Lea, Nataša Pavlović, Peter Pickl, and Avy Soffer. “Higher Order Corrections to the Mean-Field Description of the Dynamics of Interacting Bosons.” <i>Journal of Statistical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10955-020-02500-8\">https://doi.org/10.1007/s10955-020-02500-8</a>.","ieee":"L. Bossmann, N. Pavlović, P. Pickl, and A. Soffer, “Higher order corrections to the mean-field description of the dynamics of interacting bosons,” <i>Journal of Statistical Physics</i>, vol. 178. Springer Nature, pp. 1362–1396, 2020."},"intvolume":"       178","date_updated":"2025-04-14T07:44:03Z","doi":"10.1007/s10955-020-02500-8","publication":"Journal of Statistical Physics","corr_author":"1","title":"Higher order corrections to the mean-field description of the dynamics of interacting bosons","file_date_updated":"2020-11-20T09:26:46Z","_id":"7508","year":"2020","language":[{"iso":"eng"}],"page":"1362-1396","publisher":"Springer Nature","external_id":{"isi":["000516342200001"],"arxiv":["1905.06164"]},"ec_funded":1,"volume":178,"type":"journal_article","ddc":["510"],"publication_status":"published","day":"21","date_created":"2020-02-23T09:45:51Z","oa":1,"file":[{"relation":"main_file","checksum":"643e230bf147e64d9cdb3f6cc573679d","access_level":"open_access","date_created":"2020-11-20T09:26:46Z","file_name":"2020_JournStatPhysics_Bossmann.pdf","file_id":"8780","content_type":"application/pdf","creator":"dernst","file_size":576726,"success":1,"date_updated":"2020-11-20T09:26:46Z"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nL.B. gratefully acknowledges the support by the German Research Foundation (DFG) within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and wishes to thank Stefan Teufel, Sören Petrat and Marcello Porta for helpful discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. N.P. gratefully acknowledges support from NSF grant DMS-1516228 and DMS-1840314. P.P.’s research was funded by DFG Grant no. PI 1114/3-1. Part of this work was done when N.P. and P.P. were visiting CCNU, Wuhan. N.P. and P.P. thank A.S. for his hospitality at CCNU.","author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","orcid":"0000-0002-6854-1343","first_name":"Lea","full_name":"Bossmann, Lea","last_name":"Bossmann"},{"first_name":"Nataša","full_name":"Pavlović, Nataša","last_name":"Pavlović"},{"first_name":"Peter","full_name":"Pickl, Peter","last_name":"Pickl"},{"last_name":"Soffer","full_name":"Soffer, Avy","first_name":"Avy"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"scopus_import":"1","date_published":"2020-02-21T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","fulldoi":"https://doi.org/10.1007/s10955-020-02500-8","status":"public","month":"02","has_accepted_license":"1","isi":1,"article_processing_charge":"Yes (via OA deal)","article_type":"original","quality_controlled":"1","arxiv":1,"oa_version":"Published Version","department":[{"_id":"RoSe"}]},{"article_type":"original","department":[{"_id":"JaMa"}],"oa_version":"Preprint","arxiv":1,"quality_controlled":"1","isi":1,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01205"}],"month":"05","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-05-13T00:00:00Z","status":"public","fulldoi":"https://doi.org/10.1016/j.aim.2020.107053","acknowledgement":"The author would like to thank Quanhua Xu, Adam Skalski, Ke Li and Zhi Yin for their valuable comments. He also would like to thank the anonymous referees for pointing out some errors in an earlier version of this paper and for helpful comments and suggestions that make this paper better. The research was partially supported by the NCN (National Centre of Science) grant 2014/14/E/ST1/00525, the French project ISITE-BFC (contract ANR-15-IDEX-03), NSFC No. 11826012, and the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"author":[{"full_name":"Zhang, Haonan","last_name":"Zhang","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"date_created":"2020-02-23T21:43:50Z","oa":1,"publication_status":"published","day":"13","type":"journal_article","ddc":["515"],"publisher":"Elsevier","volume":365,"ec_funded":1,"external_id":{"isi":["000522798000001"],"arxiv":["1811.01205"]},"title":"From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture","publication":"Advances in Mathematics","language":[{"iso":"eng"}],"_id":"7509","year":"2020","date_updated":"2025-04-14T07:44:03Z","doi":"10.1016/j.aim.2020.107053","intvolume":"       365","citation":{"chicago":"Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” <i>Advances in Mathematics</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.aim.2020.107053\">https://doi.org/10.1016/j.aim.2020.107053</a>.","ieee":"H. Zhang, “From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture,” <i>Advances in Mathematics</i>, vol. 365. Elsevier, 2020.","ista":"Zhang H. 2020. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. Advances in Mathematics. 365, 107053.","ama":"Zhang H. From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. <i>Advances in Mathematics</i>. 2020;365. doi:<a href=\"https://doi.org/10.1016/j.aim.2020.107053\">10.1016/j.aim.2020.107053</a>","short":"H. Zhang, Advances in Mathematics 365 (2020).","apa":"Zhang, H. (2020). From Wigner-Yanase-Dyson conjecture to Carlen-Frank-Lieb conjecture. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2020.107053\">https://doi.org/10.1016/j.aim.2020.107053</a>","mla":"Zhang, Haonan. “From Wigner-Yanase-Dyson Conjecture to Carlen-Frank-Lieb Conjecture.” <i>Advances in Mathematics</i>, vol. 365, 107053, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.aim.2020.107053\">10.1016/j.aim.2020.107053</a>."},"abstract":[{"text":"In this paper we study the joint convexity/concavity of the trace functions Ψp,q,s(A,B)=Tr(Bq2K∗ApKBq2)s,  p,q,s∈R,\r\nwhere A and B are positive definite matrices and K is any fixed invertible matrix. We will give full range of (p,q,s)∈R3 for Ψp,q,s to be jointly convex/concave for all K. As a consequence, we confirm a conjecture of Carlen, Frank and Lieb. In particular, we confirm a weaker conjecture of Audenaert and Datta and obtain the full range of (α,z) for α-z Rényi relative entropies to be monotone under completely positive trace preserving maps. We also give simpler proofs of many known results, including the concavity of Ψp,0,1/p for 0<p<1 which was first proved by Epstein using complex analysis. The key is to reduce the problem to the joint convexity/concavity of the trace functions Ψp,1−p,1(A,B)=TrK∗ApKB1−p,  −1≤p≤1, using a variational method. ","lang":"eng"}],"article_number":"107053"},{"date_created":"2020-02-23T23:00:35Z","file":[{"date_updated":"2020-07-14T12:47:59Z","file_size":2027529,"creator":"dernst","content_type":"application/pdf","file_id":"7517","file_name":"2020_NatureComm_Turonova.pdf","date_created":"2020-02-24T14:00:54Z","access_level":"open_access","checksum":"2c8d10475e1b0d397500760e28bdf561","relation":"main_file"}],"oa":1,"date_published":"2020-02-13T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","fulldoi":"https://doi.org/10.1038/s41467-020-14535-2","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","author":[{"last_name":"Turoňová","full_name":"Turoňová, Beata","first_name":"Beata"},{"last_name":"Hagen","full_name":"Hagen, Wim J.H.","first_name":"Wim J.H."},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","first_name":"Martin","full_name":"Obr, Martin","last_name":"Obr"},{"first_name":"Shyamal","full_name":"Mosalaganti, Shyamal","last_name":"Mosalaganti"},{"first_name":"J. Wouter","last_name":"Beugelink","full_name":"Beugelink, J. Wouter"},{"last_name":"Zimmerli","full_name":"Zimmerli, Christian E.","first_name":"Christian E."},{"last_name":"Kräusslich","full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg"},{"full_name":"Beck, Martin","last_name":"Beck","first_name":"Martin"}],"has_accepted_license":"1","month":"02","article_type":"original","oa_version":"Published Version","department":[{"_id":"FlSc"}],"quality_controlled":"1","isi":1,"article_processing_charge":"No","abstract":[{"text":"Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.","lang":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"article_number":"876","date_updated":"2026-04-03T09:27:26Z","doi":"10.1038/s41467-020-14535-2","intvolume":"        11","citation":{"apa":"Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W., Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>","mla":"Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>, vol. 11, 876, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>.","chicago":"Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>.","ieee":"B. Turoňová <i>et al.</i>, “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 11, 876.","ama":"Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>","short":"B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020)."},"pmid":1,"publisher":"Springer Nature","volume":11,"external_id":{"pmid":["32054835"],"isi":["000514928000017"]},"title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","publication":"Nature Communications","language":[{"iso":"eng"}],"_id":"7511","year":"2020","file_date_updated":"2020-07-14T12:47:59Z","publication_status":"published","day":"13","type":"journal_article","ddc":["570"]}]