[{"year":"2019","day":"09","abstract":[{"lang":"eng","text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS."}],"date_updated":"2024-02-21T13:41:01Z","_id":"6074","file":[{"relation":"supplementary_material","content_type":"application/zip","file_size":33202743,"checksum":"bc1b285edca9e98a2c63d153c79bb75b","creator":"dernst","file_id":"6084","access_level":"open_access","file_name":"Setd5_paper.zip","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-07T13:37:19Z"}],"author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","orcid":"0000-0002-9033-9096","first_name":"Christoph","full_name":"Dotter, Christoph"},{"full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178"}],"oa":1,"title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","status":"public","month":"01","date_created":"2019-03-07T13:32:35Z","doi":"10.15479/AT:ISTA:6074","has_accepted_license":"1","date_published":"2019-01-09T00:00:00Z","department":[{"_id":"GaNo"}],"type":"research_data","oa_version":"Published Version","ddc":["570"],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:18Z","related_material":{"record":[{"status":"public","relation":"research_paper","id":"3"}]},"citation":{"chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6074\">https://doi.org/10.15479/AT:ISTA:6074</a>.","ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:6074\">10.15479/AT:ISTA:6074</a>.","apa":"Dotter, C., &#38; Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6074\">https://doi.org/10.15479/AT:ISTA:6074</a>","mla":"Dotter, Christoph, and Gaia Novarino. <i>Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.”</i> Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6074\">10.15479/AT:ISTA:6074</a>.","short":"C. Dotter, G. Novarino, (2019).","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6074\">10.15479/AT:ISTA:6074</a>"}},{"publication":"Ergodic Theory and Dynamical Systems","page":"1082-1098","date_created":"2019-03-10T22:59:18Z","type":"journal_article","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":39,"quality_controlled":"1","external_id":{"isi":["000459725600012"],"arxiv":["1601.06118"]},"day":"01","isi":1,"author":[{"full_name":"Sadel, Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","last_name":"Sadel","first_name":"Christian","orcid":"0000-0001-8255-3968"},{"last_name":"Xu","first_name":"Disheng","full_name":"Xu, Disheng"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Cambridge University Press","title":"Singular analytic linear cocycles with negative infinite Lyapunov exponents","doi":"10.1017/etds.2017.52","publication_status":"published","oa_version":"Preprint","date_published":"2019-04-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1601.06118","open_access":"1"}],"scopus_import":"1","intvolume":"        39","citation":{"ieee":"C. Sadel and D. Xu, “Singular analytic linear cocycles with negative infinite Lyapunov exponents,” <i>Ergodic Theory and Dynamical Systems</i>, vol. 39, no. 4. Cambridge University Press, pp. 1082–1098, 2019.","ama":"Sadel C, Xu D. Singular analytic linear cocycles with negative infinite Lyapunov exponents. <i>Ergodic Theory and Dynamical Systems</i>. 2019;39(4):1082-1098. doi:<a href=\"https://doi.org/10.1017/etds.2017.52\">10.1017/etds.2017.52</a>","short":"C. Sadel, D. Xu, Ergodic Theory and Dynamical Systems 39 (2019) 1082–1098.","chicago":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” <i>Ergodic Theory and Dynamical Systems</i>. Cambridge University Press, 2019. <a href=\"https://doi.org/10.1017/etds.2017.52\">https://doi.org/10.1017/etds.2017.52</a>.","apa":"Sadel, C., &#38; Xu, D. (2019). Singular analytic linear cocycles with negative infinite Lyapunov exponents. <i>Ergodic Theory and Dynamical Systems</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/etds.2017.52\">https://doi.org/10.1017/etds.2017.52</a>","ista":"Sadel C, Xu D. 2019. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 39(4), 1082–1098.","mla":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” <i>Ergodic Theory and Dynamical Systems</i>, vol. 39, no. 4, Cambridge University Press, 2019, pp. 1082–98, doi:<a href=\"https://doi.org/10.1017/etds.2017.52\">10.1017/etds.2017.52</a>."},"issue":"4","arxiv":1,"abstract":[{"text":"We show that linear analytic cocycles where all Lyapunov exponents are negative infinite are nilpotent. For such one-frequency cocycles we show that they can be analytically conjugated to an upper triangular cocycle or a Jordan normal form. As a consequence, an arbitrarily small analytic perturbation leads to distinct Lyapunov exponents. Moreover, in the one-frequency case where the th Lyapunov exponent is finite and the st negative infinite, we obtain a simple criterion for domination in which case there is a splitting into a nilpotent part and an invertible part.","lang":"eng"}],"date_updated":"2023-08-25T08:03:30Z","year":"2019","_id":"6086","status":"public","oa":1,"month":"04","ec_funded":1},{"intvolume":"       176","citation":{"chicago":"Xia, Peng, Daniel J Gütl, Vanessa Zheden, and Carl-Philipp J Heisenberg. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.01.019\">https://doi.org/10.1016/j.cell.2019.01.019</a>.","mla":"Xia, Peng, et al. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” <i>Cell</i>, vol. 176, no. 6, Elsevier, 2019, p. 1379–1392.e14, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.01.019\">10.1016/j.cell.2019.01.019</a>.","ista":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. 2019. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 176(6), 1379–1392.e14.","apa":"Xia, P., Gütl, D. J., Zheden, V., &#38; Heisenberg, C.-P. J. (2019). Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.01.019\">https://doi.org/10.1016/j.cell.2019.01.019</a>","short":"P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14.","ama":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. <i>Cell</i>. 2019;176(6):1379-1392.e14. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.01.019\">10.1016/j.cell.2019.01.019</a>","ieee":"P. Xia, D. J. Gütl, V. Zheden, and C.-P. J. Heisenberg, “Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity,” <i>Cell</i>, vol. 176, no. 6. Elsevier, p. 1379–1392.e14, 2019."},"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.01.019","open_access":"1"}],"date_published":"2019-03-07T00:00:00Z","oa_version":"Published Version","doi":"10.1016/j.cell.2019.01.019","publication_status":"published","ec_funded":1,"month":"03","oa":1,"status":"public","_id":"6087","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"year":"2019","abstract":[{"text":"Cell fate specification by lateral inhibition typically involves contact signaling through the Delta-Notch signaling pathway. However, whether this is the only signaling mode mediating lateral inhibition remains unclear. Here we show that in zebrafish oogenesis, a group of cells within the granulosa cell layer at the oocyte animal pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei. One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly, relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear TAZ accumulation in neighboring cells, eventually leading to MPC re-specification from these cells. Conversely, MPC specification is defective in taz−/− follicles. These findings uncover a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity.","lang":"eng"}],"issue":"6","date_updated":"2023-08-25T08:02:23Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/in-zebrafish-eggs-most-rapidly-growing-cell-inhibits-its-neighbours-through-mechanical-signals/"}]},"quality_controlled":"1","volume":176,"external_id":{"isi":["000460509600013"],"pmid":["30773315"]},"article_type":"original","article_processing_charge":"No","department":[{"_id":"CaHe"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Cell","date_created":"2019-03-10T22:59:19Z","page":"1379-1392.e14","title":"Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","isi":1,"author":[{"full_name":"Xia, Peng","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xia","orcid":"0000-0002-5419-7756","first_name":"Peng"},{"full_name":"Gütl, Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87","last_name":"Gütl","first_name":"Daniel J"},{"full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"day":"07","acknowledgement":"We thank Roland Dosch, Makoto Furutani-Seiki, Brian Link, Mary Mullins, and Masazumi Tada for providing transgenic and/or mutant zebrafish lines; Alexandra Schauer, Shayan Shami-Pour, and the rest of the Heisenberg lab for technical assistance and feedback on the manuscript; and the Bioimaging, Electron Microscopy, and Zebrafish facilities of IST Austria for continuous support. This work was supported by an ERC advanced grant ( MECSPEC to C.-P.H.).","pmid":1},{"_id":"6088","date_updated":"2023-08-25T08:02:51Z","issue":"3","abstract":[{"lang":"eng","text":"P-Glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) are two efflux transporters at the blood–brain barrier (BBB), which effectively restrict brain distribution of diverse drugs, such as tyrosine kinase inhibitors. There is a crucial need for pharmacological ABCB1 and ABCG2 inhibition protocols for a more effective treatment of brain diseases. In the present study, seven marketed drugs (osimertinib, erlotinib, nilotinib, imatinib, lapatinib, pazopanib, and cyclosporine A) and one nonmarketed drug (tariquidar), with known in vitro ABCB1/ABCG2 inhibitory properties, were screened for their inhibitory potency at the BBB in vivo. Positron emission tomography (PET) using the model ABCB1/ABCG2 substrate [11C]erlotinib was performed in mice. Tested inhibitors were administered as i.v. bolus injections at 30 min before the start of the PET scan, followed by a continuous i.v. infusion for the duration of the PET scan. Five of the tested drugs increased total distribution volume of [11C]erlotinib in the brain (VT,brain) compared to vehicle-treated animals (tariquidar, + 69%; erlotinib, + 19% and +23% for the 21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 22%; lapatinib, + 25%; and cyclosporine A, + 49%). For all drugs, increases in [11C]erlotinib brain distribution were lower than in Abcb1a/b(−/−)Abcg2(−/−) mice (+149%), which suggested that only partial ABCB1/ABCG2 inhibition was reached at the mouse BBB. The plasma concentrations of the tested drugs at the time of the PET scan were higher than clinically achievable plasma concentrations. Some of the tested drugs led to significant increases in blood radioactivity concentrations measured at the end of the PET scan (erlotinib, + 103% and +113% for the 21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 125%; and cyclosporine A, + 101%), which was most likely caused by decreased hepatobiliary excretion of radioactivity. Taken together, our data suggest that some marketed tyrosine kinase inhibitors may be repurposed to inhibit ABCB1 and ABCG2 at the BBB. From a clinical perspective, moderate increases in brain delivery despite the administration of high i.v. doses as well as peripheral drug–drug interactions due to transporter inhibition in clearance organs question the translatability of this concept."}],"year":"2019","month":"03","status":"public","oa_version":"None","date_published":"2019-03-04T00:00:00Z","publication_status":"published","doi":"10.1021/acs.molpharmaceut.8b01217","intvolume":"        16","citation":{"short":"A. Traxl, S. Mairinger, T. Filip, M. Sauberer, J. Stanek, S. Poschner, W. Jäger, V. Zoufal, G. Novarino, N. Tournier, M. Bauer, T. Wanek, O. Langer, Molecular Pharmaceutics 16 (2019) 1282–1293.","ieee":"A. Traxl <i>et al.</i>, “Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” <i>Molecular Pharmaceutics</i>, vol. 16, no. 3. American Chemical Society, pp. 1282–1293, 2019.","ama":"Traxl A, Mairinger S, Filip T, et al. Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. <i>Molecular Pharmaceutics</i>. 2019;16(3):1282-1293. doi:<a href=\"https://doi.org/10.1021/acs.molpharmaceut.8b01217\">10.1021/acs.molpharmaceut.8b01217</a>","ista":"Traxl A, Mairinger S, Filip T, Sauberer M, Stanek J, Poschner S, Jäger W, Zoufal V, Novarino G, Tournier N, Bauer M, Wanek T, Langer O. 2019. Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. 16(3), 1282–1293.","apa":"Traxl, A., Mairinger, S., Filip, T., Sauberer, M., Stanek, J., Poschner, S., … Langer, O. (2019). Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. <i>Molecular Pharmaceutics</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.molpharmaceut.8b01217\">https://doi.org/10.1021/acs.molpharmaceut.8b01217</a>","mla":"Traxl, Alexander, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” <i>Molecular Pharmaceutics</i>, vol. 16, no. 3, American Chemical Society, 2019, pp. 1282–93, doi:<a href=\"https://doi.org/10.1021/acs.molpharmaceut.8b01217\">10.1021/acs.molpharmaceut.8b01217</a>.","chicago":"Traxl, Alexander, Severin Mairinger, Thomas Filip, Michael Sauberer, Johann Stanek, Stefan Poschner, Walter Jäger, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” <i>Molecular Pharmaceutics</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/acs.molpharmaceut.8b01217\">https://doi.org/10.1021/acs.molpharmaceut.8b01217</a>."},"scopus_import":"1","isi":1,"author":[{"full_name":"Traxl, Alexander","last_name":"Traxl","first_name":"Alexander"},{"last_name":"Mairinger","first_name":"Severin","full_name":"Mairinger, Severin"},{"first_name":"Thomas","last_name":"Filip","full_name":"Filip, Thomas"},{"full_name":"Sauberer, Michael","first_name":"Michael","last_name":"Sauberer"},{"first_name":"Johann","last_name":"Stanek","full_name":"Stanek, Johann"},{"full_name":"Poschner, Stefan","first_name":"Stefan","last_name":"Poschner"},{"first_name":"Walter","last_name":"Jäger","full_name":"Jäger, Walter"},{"last_name":"Zoufal","first_name":"Viktoria","full_name":"Zoufal, Viktoria"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"full_name":"Tournier, Nicolas","last_name":"Tournier","first_name":"Nicolas"},{"first_name":"Martin","last_name":"Bauer","full_name":"Bauer, Martin"},{"full_name":"Wanek, Thomas","first_name":"Thomas","last_name":"Wanek"},{"full_name":"Langer, Oliver","last_name":"Langer","first_name":"Oliver"}],"pmid":1,"day":"04","publisher":"American Chemical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"page":"1282-1293","date_created":"2019-03-10T22:59:19Z","publication":"Molecular Pharmaceutics","external_id":{"isi":["000460600400031"],"pmid":["30694684"]},"volume":16,"quality_controlled":"1","article_processing_charge":"No"},{"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","publisher":"Oxford University Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","pmid":1,"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"isi":1,"author":[{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"first_name":"Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"article_processing_charge":"No","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5757"}]},"external_id":{"pmid":["30590559"],"isi":["000462585100006"]},"quality_controlled":"1","volume":36,"page":"500-515","date_created":"2019-03-10T22:59:19Z","publication":"Molecular biology and evolution","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"type":"journal_article","oa":1,"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"status":"public","month":"03","year":"2019","date_updated":"2024-02-21T13:59:17Z","issue":"3","abstract":[{"lang":"eng","text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general."}],"_id":"6089","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"citation":{"apa":"Fraisse, C., Puixeu Sala, G., &#38; Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>.","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” <i>Molecular biology and evolution</i>, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular biology and evolution</i>. 2019;36(3):500-515. doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515."},"intvolume":"        36","publication_status":"published","doi":"10.1093/molbev/msy246","date_published":"2019-03-01T00:00:00Z","oa_version":"Submitted Version"},{"_id":"6090","article_number":"022423","year":"2019","date_updated":"2024-02-28T13:12:06Z","abstract":[{"lang":"eng","text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing."}],"issue":"2","month":"02","oa":1,"status":"public","date_published":"2019-02-26T00:00:00Z","oa_version":"Preprint","publication_status":"published","doi":"10.1103/PhysRevE.99.022423","intvolume":"        99","citation":{"ieee":"M. Carballo-Pacheco <i>et al.</i>, “Receptor crosstalk improves concentration sensing of multiple ligands,” <i>Physical Review E</i>, vol. 99, no. 2. American Physical Society, 2019.","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. <i>Physical Review E</i>. 2019;99(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.99.022423\">10.1103/PhysRevE.99.022423</a>","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.99.022423\">https://doi.org/10.1103/PhysRevE.99.022423</a>","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” <i>Physical Review E</i>, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevE.99.022423\">10.1103/PhysRevE.99.022423</a>.","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” <i>Physical Review E</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevE.99.022423\">https://doi.org/10.1103/PhysRevE.99.022423</a>."},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract"}],"scopus_import":"1","author":[{"full_name":"Carballo-Pacheco, Martín","last_name":"Carballo-Pacheco","first_name":"Martín"},{"full_name":"Desponds, Jonathan","last_name":"Desponds","first_name":"Jonathan"},{"last_name":"Gavrilchenko","first_name":"Tatyana","full_name":"Gavrilchenko, Tatyana"},{"last_name":"Mayer","first_name":"Andreas","full_name":"Mayer, Andreas"},{"full_name":"Prizak, Roshan","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak"},{"first_name":"Gautam","last_name":"Reddy","full_name":"Reddy, Gautam"},{"full_name":"Nemenman, Ilya","last_name":"Nemenman","first_name":"Ilya"},{"full_name":"Mora, Thierry","first_name":"Thierry","last_name":"Mora"}],"isi":1,"day":"26","title":"Receptor crosstalk improves concentration sensing of multiple ligands","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"type":"journal_article","date_created":"2019-03-10T22:59:20Z","publication":"Physical Review E","external_id":{"isi":["000459916500007"]},"volume":99,"quality_controlled":"1","article_processing_charge":"No"},{"publication_status":"published","doi":"10.7554/eLife.41563","oa_version":"Published Version","date_published":"2019-02-21T00:00:00Z","file_date_updated":"2020-07-14T12:47:19Z","scopus_import":"1","ddc":["570"],"intvolume":"         8","citation":{"chicago":"Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer, Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.41563\">https://doi.org/10.7554/eLife.41563</a>.","ista":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 8, e41563.","apa":"Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L., &#38; Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.41563\">https://doi.org/10.7554/eLife.41563</a>","mla":"Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” <i>ELife</i>, vol. 8, e41563, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.41563\">10.7554/eLife.41563</a>.","short":"N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B. Dalva, ELife 8 (2019).","ieee":"N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ama":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.41563\">10.7554/eLife.41563</a>"},"date_updated":"2023-08-24T14:50:50Z","abstract":[{"lang":"eng","text":"Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons."}],"year":"2019","article_number":"e41563","_id":"6091","status":"public","oa":1,"month":"02","has_accepted_license":"1","date_created":"2019-03-10T22:59:20Z","publication":"eLife","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"article_processing_charge":"No","external_id":{"pmid":["30789343"],"isi":["000459380600001"]},"volume":8,"quality_controlled":"1","pmid":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"21","isi":1,"author":[{"first_name":"Nathan T.","last_name":"Henderson","full_name":"Henderson, Nathan T."},{"first_name":"Sylvain J.","last_name":"Le Marchand","full_name":"Le Marchand, Sylvain J."},{"last_name":"Hruska","first_name":"Martin","full_name":"Hruska, Martin"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"},{"full_name":"Dalva, Matthew B.","first_name":"Matthew B.","last_name":"Dalva"}],"file":[{"date_created":"2019-03-11T16:15:37Z","date_updated":"2020-07-14T12:47:19Z","file_name":"2019_eLife_Henderson.pdf","access_level":"open_access","file_id":"6098","checksum":"7b0800d003f14cd06b1802dea0c52941","creator":"dernst","file_size":7260753,"relation":"main_file","content_type":"application/pdf"}],"publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs"},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01638"}],"citation":{"chicago":"Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevB.99.064428\">https://doi.org/10.1103/PhysRevB.99.064428</a>.","mla":"Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” <i>Physical Review B</i>, vol. 99, no. 6, 064428, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevB.99.064428\">10.1103/PhysRevB.99.064428</a>.","ista":"Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 99(6), 064428.","apa":"Mentink, J. H., Katsnelson, M., &#38; Lemeshko, M. (2019). Quantum many-body dynamics of the Einstein-de Haas effect. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.99.064428\">https://doi.org/10.1103/PhysRevB.99.064428</a>","short":"J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).","ieee":"J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics of the Einstein-de Haas effect,” <i>Physical Review B</i>, vol. 99, no. 6. American Physical Society, 2019.","ama":"Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de Haas effect. <i>Physical Review B</i>. 2019;99(6). doi:<a href=\"https://doi.org/10.1103/PhysRevB.99.064428\">10.1103/PhysRevB.99.064428</a>"},"intvolume":"        99","doi":"10.1103/PhysRevB.99.064428","publication_status":"published","date_published":"2019-02-01T00:00:00Z","oa_version":"Preprint","oa":1,"status":"public","month":"02","year":"2019","issue":"6","arxiv":1,"abstract":[{"lang":"eng","text":"In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization of a magnetic material results in mechanical rotation and vice versa. At the microscopic level, this effect governs the transfer between electron spin and orbital angular momentum, and lattice degrees of freedom, understanding which is key for molecular magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now, the timescales of electron-to-lattice angular momentum transfer remain unclear, since modeling this process on a microscopic level requires the addition of an infinite amount of quantum angular momenta. We show that this problem can be solved by reformulating it in terms of the recently discovered angulon quasiparticles, which results in a rotationally invariant quantum many-body theory. In particular, we demonstrate that nonperturbative effects take place even if the electron-phonon coupling is weak and give rise to angular momentum transfer on femtosecond timescales."}],"date_updated":"2024-02-28T13:11:54Z","_id":"6092","article_number":"064428","article_processing_charge":"No","volume":99,"quality_controlled":"1","external_id":{"isi":["000459223400004"],"arxiv":["1802.01638"]},"publication":"Physical Review B","date_created":"2019-03-10T22:59:20Z","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"type":"journal_article","title":"Quantum many-body dynamics of the Einstein-de Haas effect","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","day":"01","isi":1,"author":[{"first_name":"Johann H","last_name":"Mentink","full_name":"Mentink, Johann H"},{"full_name":"Katsnelson, Mikhail","last_name":"Katsnelson","first_name":"Mikhail"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail"}],"project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"}]},{"date_published":"2019-02-26T00:00:00Z","oa_version":"Published Version","doi":"10.1371/journal.pone.0212699","publication_status":"published","intvolume":"        14","citation":{"chicago":"Goudarzi, Mohammad, Aleix Boquet-Pujadas, Jean Christophe Olivo-Marin, and Erez Raz. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” <i>PLOS ONE</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pone.0212699\">https://doi.org/10.1371/journal.pone.0212699</a>.","ista":"Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. 2019. Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. 14(2), e0212699.","apa":"Goudarzi, M., Boquet-Pujadas, A., Olivo-Marin, J. C., &#38; Raz, E. (2019). Fluid dynamics during bleb formation in migrating cells in vivo. <i>PLOS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0212699\">https://doi.org/10.1371/journal.pone.0212699</a>","mla":"Goudarzi, Mohammad, et al. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” <i>PLOS ONE</i>, vol. 14, no. 2, e0212699, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pone.0212699\">10.1371/journal.pone.0212699</a>.","ieee":"M. Goudarzi, A. Boquet-Pujadas, J. C. Olivo-Marin, and E. Raz, “Fluid dynamics during bleb formation in migrating cells in vivo,” <i>PLOS ONE</i>, vol. 14, no. 2. Public Library of Science, 2019.","ama":"Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. Fluid dynamics during bleb formation in migrating cells in vivo. <i>PLOS ONE</i>. 2019;14(2). doi:<a href=\"https://doi.org/10.1371/journal.pone.0212699\">10.1371/journal.pone.0212699</a>","short":"M. Goudarzi, A. Boquet-Pujadas, J.C. Olivo-Marin, E. Raz, PLOS ONE 14 (2019)."},"ddc":["570"],"file_date_updated":"2020-07-14T12:47:19Z","scopus_import":"1","_id":"6093","article_number":"e0212699","year":"2019","abstract":[{"lang":"eng","text":"Blebs are cellular protrusions observed in migrating cells and in cells undergoing spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm during bleb formation and the concurrent changes in cell volume using zebrafish primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation occurs concomitantly with cytoplasmic inflow into it and that during this process the total cell volume does not change. We thus show that bleb formation in primordial germ cells results primarily from redistribution of material within the cell rather than being driven by flow of water from an external source."}],"issue":"2","date_updated":"2023-09-19T14:46:47Z","month":"02","oa":1,"status":"public","department":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"PLOS ONE","date_created":"2019-03-10T22:59:21Z","has_accepted_license":"1","quality_controlled":"1","volume":14,"external_id":{"isi":["000459712100022"]},"article_processing_charge":"No","file":[{"file_name":"2019_PLoSOne_Goudarzi.pdf","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-11T16:09:23Z","creator":"dernst","checksum":"b885de050ed4bb3c86f706487a47197f","file_id":"6096","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":2967731}],"isi":1,"author":[{"id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi","first_name":"Mohammad","full_name":"Goudarzi, Mohammad"},{"last_name":"Boquet-Pujadas","first_name":"Aleix","full_name":"Boquet-Pujadas, Aleix"},{"full_name":"Olivo-Marin, Jean Christophe","last_name":"Olivo-Marin","first_name":"Jean Christophe"},{"first_name":"Erez","last_name":"Raz","full_name":"Raz, Erez"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"26","title":"Fluid dynamics during bleb formation in migrating cells in vivo","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Public Library of Science"},{"doi":"10.1111/mec.14972","publication_status":"published","oa_version":"Published Version","date_published":"2019-03-01T00:00:00Z","scopus_import":"1","file_date_updated":"2020-07-14T12:47:19Z","ddc":["570"],"intvolume":"        28","citation":{"mla":"Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” <i>Molecular Ecology</i>, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:<a href=\"https://doi.org/10.1111/mec.14972\">10.1111/mec.14972</a>.","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14972\">https://doi.org/10.1111/mec.14972</a>","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.14972\">https://doi.org/10.1111/mec.14972</a>.","ama":"Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. <i>Molecular Ecology</i>. 2019;28(6):1375-1393. doi:<a href=\"https://doi.org/10.1111/mec.14972\">10.1111/mec.14972</a>","ieee":"R. Faria <i>et al.</i>, “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” <i>Molecular Ecology</i>, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393."},"issue":"6","abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}],"date_updated":"2023-08-24T14:50:27Z","year":"2019","_id":"6095","status":"public","oa":1,"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"month":"03","has_accepted_license":"1","publication":"Molecular Ecology","page":"1375-1393","date_created":"2019-03-10T22:59:21Z","type":"journal_article","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","volume":28,"external_id":{"isi":["000465219200013"]},"related_material":{"record":[{"relation":"research_data","status":"public","id":"9837"}]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","isi":1,"author":[{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"first_name":"Tomas","last_name":"Larsson","full_name":"Larsson, Tomas"},{"last_name":"Lemmon","first_name":"Alan R.","full_name":"Lemmon, Alan R."},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"file":[{"checksum":"f915885756057ec0ca5912a41f46a887","creator":"dernst","file_id":"6097","access_level":"open_access","file_name":"2019_MolecularEcology_Faria.pdf","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-11T16:12:54Z","relation":"main_file","content_type":"application/pdf","file_size":1510715}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes"},{"citation":{"ama":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. A full vectorial mapping of nanophotonic light fields. <i>Light: Science and Applications</i>. 2019;8(1). doi:<a href=\"https://doi.org/10.1038/s41377-019-0124-3\">10.1038/s41377-019-0124-3</a>","ieee":"B. Le Feber, J. E. Sipe, M. Wulf, L. Kuipers, and N. Rotenberg, “A full vectorial mapping of nanophotonic light fields,” <i>Light: Science and Applications</i>, vol. 8, no. 1. Springer Nature, 2019.","short":"B. Le Feber, J.E. Sipe, M. Wulf, L. Kuipers, N. Rotenberg, Light: Science and Applications 8 (2019).","chicago":"Le Feber, B., J. E. Sipe, Matthias Wulf, L. Kuipers, and N. Rotenberg. “A Full Vectorial Mapping of Nanophotonic Light Fields.” <i>Light: Science and Applications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41377-019-0124-3\">https://doi.org/10.1038/s41377-019-0124-3</a>.","mla":"Le Feber, B., et al. “A Full Vectorial Mapping of Nanophotonic Light Fields.” <i>Light: Science and Applications</i>, vol. 8, no. 1, 28, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41377-019-0124-3\">10.1038/s41377-019-0124-3</a>.","apa":"Le Feber, B., Sipe, J. E., Wulf, M., Kuipers, L., &#38; Rotenberg, N. (2019). A full vectorial mapping of nanophotonic light fields. <i>Light: Science and Applications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41377-019-0124-3\">https://doi.org/10.1038/s41377-019-0124-3</a>","ista":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. 2019. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 8(1), 28."},"intvolume":"         8","ddc":["530"],"file_date_updated":"2020-07-14T12:47:19Z","scopus_import":"1","date_published":"2019-03-06T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1038/s41377-019-0124-3","month":"03","publication_identifier":{"eissn":["20477538"],"issn":["20955545"]},"oa":1,"status":"public","_id":"6102","article_number":"28","year":"2019","date_updated":"2023-08-25T08:06:10Z","issue":"1","abstract":[{"lang":"eng","text":"Light is a union of electric and magnetic fields, and nowhere is the complex relationship between these fields more evident than in the near fields of nanophotonic structures. There, complicated electric and magnetic fields varying over subwavelength scales are generally present, which results in photonic phenomena such as extraordinary optical momentum, superchiral fields, and a complex spatial evolution of optical singularities. An understanding of such phenomena requires nanoscale measurements of the complete optical field vector. Although the sensitivity of near- field scanning optical microscopy to the complete electromagnetic field was recently demonstrated, a separation of different components required a priori knowledge of the sample. Here, we introduce a robust algorithm that can disentangle all six electric and magnetic field components from a single near-field measurement without any numerical modeling of the structure. As examples, we unravel the fields of two prototypical nanophotonic structures: a photonic crystal waveguide and a plasmonic nanowire. These results pave the way for new studies of complex photonic phenomena at the nanoscale and for the design of structures that optimize their optical behavior."}],"arxiv":1,"external_id":{"isi":["000460470700004"],"arxiv":["1803.10145"]},"volume":8,"quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"type":"journal_article","date_created":"2019-03-17T22:59:13Z","publication":"Light: Science and Applications","has_accepted_license":"1","title":"A full vectorial mapping of nanophotonic light fields","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","checksum":"d71e528cff9c56f70ccc29dd7005257f","file_id":"6108","creator":"dernst","date_created":"2019-03-18T08:08:22Z","file_name":"2019_Light_LeFeber.pdf","date_updated":"2020-07-14T12:47:19Z","file_size":1119947,"relation":"main_file","content_type":"application/pdf"}],"isi":1,"author":[{"first_name":"B.","last_name":"Le Feber","full_name":"Le Feber, B."},{"first_name":"J. E.","last_name":"Sipe","full_name":"Sipe, J. E."},{"orcid":"0000-0001-6613-1378","first_name":"Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias"},{"last_name":"Kuipers","first_name":"L.","full_name":"Kuipers, L."},{"full_name":"Rotenberg, N.","first_name":"N.","last_name":"Rotenberg"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"06"},{"author":[{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"full_name":"Bielach, Agnieszka","first_name":"Agnieszka","last_name":"Bielach"},{"full_name":"Tamizhselvan, Prashanth","first_name":"Prashanth","last_name":"Tamizhselvan"},{"first_name":"Sharmila","last_name":"Madhavan","full_name":"Madhavan, Sharmila"},{"full_name":"Ryad, Eman Elrefaay","last_name":"Ryad","first_name":"Eman Elrefaay"},{"full_name":"Tan, Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285"},{"first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","last_name":"Hrtyan","full_name":"Hrtyan, Mónika"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"first_name":"Radomira","last_name":"Vanková","full_name":"Vanková, Radomira"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"},{"last_name":"Tognetti","first_name":"Vanesa B.","full_name":"Tognetti, Vanesa B."}],"isi":1,"pmid":1,"day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford University Press","title":"Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking","type":"journal_article","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publication":"Plant and Cell Physiology","date_created":"2019-03-17T22:59:14Z","page":"255-273","quality_controlled":"1","volume":60,"external_id":{"isi":["000459634300002"],"pmid":["30668780"]},"article_processing_charge":"No","_id":"6104","issue":"2","abstract":[{"text":"Abiotic stress poses constant challenges for plant survival and is a serious problem for global agricultural productivity. On a molecular level, stress conditions result in elevation of reactive oxygen species (ROS) production causing oxidative stress associated with oxidation of proteins and nucleic acids as well as impairment of membrane functions. Adaptation of root growth to ROS accumulation is facilitated through modification of auxin and cytokinin hormone homeostasis. Here, we report that in Arabidopsis root meristem, ROS-induced changes of auxin levels correspond to decreased abundance of PIN auxin efflux carriers at the plasma membrane (PM). Specifically, increase in H2O2 levels affects PIN2 endocytic recycling. We show that the PIN2 intracellular trafficking during adaptation to oxidative stress requires the function of the ADP-ribosylation factor (ARF)-guanine-nucleotide exchange factor (GEF) BEN1, an actin-associated regulator of the trafficking from the PM to early endosomes and, presumably, indirectly, trafficking to the vacuoles. We propose that H2O2 levels affect the actin dynamics thus modulating ARF-GEF-dependent trafficking of PIN2. This mechanism provides a way how root growth acclimates to stress and adapts to a changing environment.","lang":"eng"}],"date_updated":"2023-08-25T08:05:28Z","year":"2019","month":"02","status":"public","publication_identifier":{"issn":["0032-0781"],"eissn":["1471-9053"]},"oa_version":"None","date_published":"2019-02-01T00:00:00Z","doi":"10.1093/pcp/pcz001","publication_status":"published","intvolume":"        60","citation":{"chicago":"Zwiewka, Marta, Agnieszka Bielach, Prashanth Tamizhselvan, Sharmila Madhavan, Eman Elrefaay Ryad, Shutang Tan, Mónika Hrtyan, et al. “Root Adaptation to H2O2-Induced Oxidative Stress by ARF-GEF BEN1- and Cytoskeleton-Mediated PIN2 Trafficking.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/pcp/pcz001\">https://doi.org/10.1093/pcp/pcz001</a>.","mla":"Zwiewka, Marta, et al. “Root Adaptation to H2O2-Induced Oxidative Stress by ARF-GEF BEN1- and Cytoskeleton-Mediated PIN2 Trafficking.” <i>Plant and Cell Physiology</i>, vol. 60, no. 2, Oxford University Press, 2019, pp. 255–73, doi:<a href=\"https://doi.org/10.1093/pcp/pcz001\">10.1093/pcp/pcz001</a>.","apa":"Zwiewka, M., Bielach, A., Tamizhselvan, P., Madhavan, S., Ryad, E. E., Tan, S., … Tognetti, V. B. (2019). Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcz001\">https://doi.org/10.1093/pcp/pcz001</a>","ista":"Zwiewka M, Bielach A, Tamizhselvan P, Madhavan S, Ryad EE, Tan S, Hrtyan M, Dobrev P, Vanková R, Friml J, Tognetti VB. 2019. Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. Plant and Cell Physiology. 60(2), 255–273.","short":"M. Zwiewka, A. Bielach, P. Tamizhselvan, S. Madhavan, E.E. Ryad, S. Tan, M. Hrtyan, P. Dobrev, R. Vanková, J. Friml, V.B. Tognetti, Plant and Cell Physiology 60 (2019) 255–273.","ieee":"M. Zwiewka <i>et al.</i>, “Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking,” <i>Plant and Cell Physiology</i>, vol. 60, no. 2. Oxford University Press, pp. 255–273, 2019.","ama":"Zwiewka M, Bielach A, Tamizhselvan P, et al. Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. <i>Plant and Cell Physiology</i>. 2019;60(2):255-273. doi:<a href=\"https://doi.org/10.1093/pcp/pcz001\">10.1093/pcp/pcz001</a>"},"scopus_import":"1"},{"date_published":"2019-04-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1111/1365-2656.12953","citation":{"mla":"Kutzer, Megan, et al. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” <i>Journal of Animal Ecology</i>, vol. 88, no. 4, Wiley, 2019, pp. 566–78, doi:<a href=\"https://doi.org/10.1111/1365-2656.12953\">10.1111/1365-2656.12953</a>.","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. 88(4), 566–578.","apa":"Kutzer, M., Kurtz, J., &#38; Armitage, S. A. O. (2019). A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. <i>Journal of Animal Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/1365-2656.12953\">https://doi.org/10.1111/1365-2656.12953</a>","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” <i>Journal of Animal Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/1365-2656.12953\">https://doi.org/10.1111/1365-2656.12953</a>.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, Journal of Animal Ecology 88 (2019) 566–578.","ama":"Kutzer M, Kurtz J, Armitage SAO. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. <i>Journal of Animal Ecology</i>. 2019;88(4):566-578. doi:<a href=\"https://doi.org/10.1111/1365-2656.12953\">10.1111/1365-2656.12953</a>","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance,” <i>Journal of Animal Ecology</i>, vol. 88, no. 4. Wiley, pp. 566–578, 2019."},"intvolume":"        88","ddc":["570"],"file_date_updated":"2020-07-14T12:47:19Z","scopus_import":"1","_id":"6105","year":"2019","date_updated":"2023-08-25T08:04:53Z","issue":"4","abstract":[{"text":"    Hosts can alter their strategy towards pathogens during their lifetime; that is, they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e., resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fecundity consequences that result from a high pathogen burden. Finally, previous exposure may also lead to life‐history adjustments, such as terminal investment into reproduction.\r\n    Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested whether previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute‐phase infection (one day post‐challenge). We then asked whether previous pathogen exposure affects chronic‐phase pathogen persistence and longer‐term survival (28 days post‐challenge).\r\n    We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long‐term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses.\r\n    We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection.\r\n    To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi‐faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host–pathogen system and that infection persistence may be bacterium‐specific.\r\n","lang":"eng"}],"ec_funded":1,"month":"04","publication_identifier":{"eissn":["13652656"],"issn":["00218790"]},"oa":1,"status":"public","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"type":"journal_article","date_created":"2019-03-17T22:59:15Z","page":"566-578","publication":"Journal of Animal Ecology","has_accepted_license":"1","related_material":{"record":[{"id":"9806","status":"public","relation":"research_data"}]},"external_id":{"isi":["000467994800007"]},"quality_controlled":"1","volume":88,"article_type":"original","article_processing_charge":"No","file":[{"relation":"main_file","content_type":"application/pdf","file_size":1460662,"file_id":"6107","checksum":"405cde15120de26018b3bd0dfa29986c","creator":"dernst","access_level":"open_access","file_name":"2019_JournalAnimalEcology_Kutzer.pdf","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-18T07:43:06Z"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"isi":1,"author":[{"id":"29D0B332-F248-11E8-B48F-1D18A9856A87","last_name":"Kutzer","orcid":"0000-0002-8696-6978","first_name":"Megan","full_name":"Kutzer, Megan"},{"full_name":"Kurtz, Joachim","first_name":"Joachim","last_name":"Kurtz"},{"full_name":"Armitage, Sophie A.O.","first_name":"Sophie A.O.","last_name":"Armitage"}],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"title":"Kosterlitz-Thouless scaling at many-body localization phase transitions","publisher":"American Physical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Dumitrescu, Philipp T.","last_name":"Dumitrescu","first_name":"Philipp T."},{"full_name":"Goremykina, Anna","last_name":"Goremykina","first_name":"Anna"},{"last_name":"Parameswaran","first_name":"Siddharth A.","full_name":"Parameswaran, Siddharth A."},{"full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"},{"full_name":"Vasseur, Romain","last_name":"Vasseur","first_name":"Romain"}],"isi":1,"day":"22","external_id":{"arxiv":["1811.03103"],"isi":["000462883200001"]},"volume":99,"quality_controlled":"1","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"type":"journal_article","date_created":"2019-03-25T07:32:08Z","publication":"Physical Review B","month":"03","oa":1,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"status":"public","_id":"6174","article_number":"094205","year":"2019","date_updated":"2023-09-05T12:11:13Z","abstract":[{"lang":"eng","text":"We propose a scaling theory for the many-body localization (MBL) phase transition in one dimension, building on the idea that it proceeds via a “quantum avalanche.” We argue that the critical properties can be captured at a coarse-grained level by a Kosterlitz-Thouless (KT) renormalization group (RG) flow. On phenomenological grounds, we identify the scaling variables as the density of thermal regions and the length scale that controls the decay of typical matrix elements. Within this KT picture, the MBL phase is a line of fixed points that terminates at the delocalization transition. We discuss two possible scenarios distinguished by the distribution of rare, fractal thermal inclusions within the MBL phase. In the first scenario, these regions have a stretched exponential distribution in the MBL phase. In the second scenario, the near-critical MBL phase hosts rare thermal regions that are power-law-distributed in size. This points to the existence of a second transition within the MBL phase, at which these power laws change to the stretched exponential form expected at strong disorder. We numerically simulate two different phenomenological RGs previously proposed to describe the MBL transition. Both RGs display a universal power-law length distribution of thermal regions at the transition with a critical exponent αc=2, and continuously varying exponents in the MBL phase consistent with the KT picture."}],"arxiv":1,"issue":"9","intvolume":"        99","citation":{"short":"P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur, Physical Review B 99 (2019).","ama":"Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. Kosterlitz-Thouless scaling at many-body localization phase transitions. <i>Physical Review B</i>. 2019;99(9). doi:<a href=\"https://doi.org/10.1103/physrevb.99.094205\">10.1103/physrevb.99.094205</a>","ieee":"P. T. Dumitrescu, A. Goremykina, S. A. Parameswaran, M. Serbyn, and R. Vasseur, “Kosterlitz-Thouless scaling at many-body localization phase transitions,” <i>Physical Review B</i>, vol. 99, no. 9. American Physical Society, 2019.","chicago":"Dumitrescu, Philipp T., Anna Goremykina, Siddharth A. Parameswaran, Maksym Serbyn, and Romain Vasseur. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevb.99.094205\">https://doi.org/10.1103/physrevb.99.094205</a>.","mla":"Dumitrescu, Philipp T., et al. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” <i>Physical Review B</i>, vol. 99, no. 9, 094205, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevb.99.094205\">10.1103/physrevb.99.094205</a>.","ista":"Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. 2019. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 99(9), 094205.","apa":"Dumitrescu, P. T., Goremykina, A., Parameswaran, S. A., Serbyn, M., &#38; Vasseur, R. (2019). Kosterlitz-Thouless scaling at many-body localization phase transitions. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.99.094205\">https://doi.org/10.1103/physrevb.99.094205</a>"},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.03103"}],"date_published":"2019-03-22T00:00:00Z","oa_version":"Preprint","publication_status":"published","doi":"10.1103/physrevb.99.094205"},{"article_processing_charge":"No","keyword":["Program Cost Analysis","Program Termination","Probabilistic Programs","Martingales"],"quality_controlled":"1","external_id":{"arxiv":["1902.04659"],"isi":["000523190300014"]},"related_material":{"record":[{"id":"5457","relation":"earlier_version","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8934"}]},"has_accepted_license":"1","publication":"PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation","page":"204-220","date_created":"2019-03-25T10:13:25Z","type":"conference","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Association for Computing Machinery","title":"Cost analysis of nondeterministic probabilistic programs","day":"08","isi":1,"author":[{"first_name":"Peixin","last_name":"Wang","full_name":"Wang, Peixin"},{"first_name":"Hongfei","last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","full_name":"Fu, Hongfei"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Xudong","last_name":"Qin","full_name":"Qin, Xudong"},{"full_name":"Shi, Wenjun","first_name":"Wenjun","last_name":"Shi"}],"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"file":[{"file_id":"6176","creator":"akafshda","checksum":"703a5e9b8c8587f2a44085ffd9a4db64","access_level":"open_access","file_name":"paper.pdf","date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-25T10:11:22Z","content_type":"application/pdf","relation":"main_file","file_size":4051066}],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:20Z","ddc":["000"],"citation":{"ama":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. Cost analysis of nondeterministic probabilistic programs. In: <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2019:204-220. doi:<a href=\"https://doi.org/10.1145/3314221.3314581\">10.1145/3314221.3314581</a>","ieee":"P. Wang, H. Fu, A. K. Goharshady, K. Chatterjee, X. Qin, and W. Shi, “Cost analysis of nondeterministic probabilistic programs,” in <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, Phoenix, AZ, United States, 2019, pp. 204–220.","short":"P. Wang, H. Fu, A.K. Goharshady, K. Chatterjee, X. Qin, W. Shi, in:, PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–220.","ista":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. 2019. Cost analysis of nondeterministic probabilistic programs. PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Conference on Programming Language Design and Implementation, 204–220.","apa":"Wang, P., Fu, H., Goharshady, A. K., Chatterjee, K., Qin, X., &#38; Shi, W. (2019). Cost analysis of nondeterministic probabilistic programs. In <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i> (pp. 204–220). Phoenix, AZ, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3314221.3314581\">https://doi.org/10.1145/3314221.3314581</a>","mla":"Wang, Peixin, et al. “Cost Analysis of Nondeterministic Probabilistic Programs.” <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2019, pp. 204–20, doi:<a href=\"https://doi.org/10.1145/3314221.3314581\">10.1145/3314221.3314581</a>.","chicago":"Wang, Peixin, Hongfei Fu, Amir Kafshdar Goharshady, Krishnendu Chatterjee, Xudong Qin, and Wenjun Shi. “Cost Analysis of Nondeterministic Probabilistic Programs.” In <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, 204–20. Association for Computing Machinery, 2019. <a href=\"https://doi.org/10.1145/3314221.3314581\">https://doi.org/10.1145/3314221.3314581</a>."},"doi":"10.1145/3314221.3314581","conference":{"end_date":"2019-06-26","location":"Phoenix, AZ, United States","start_date":"2019-06-22","name":"PLDI: Conference on Programming Language Design and Implementation"},"publication_status":"published","oa_version":"Submitted Version","date_published":"2019-06-08T00:00:00Z","status":"public","oa":1,"month":"06","ec_funded":1,"arxiv":1,"abstract":[{"lang":"eng","text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs,\r\nwhich aims at automated methods for analyzing the resource-usage of such programs.\r\nPrevious approaches for this problem could only handle nonnegative bounded costs.\r\nHowever, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols,\r\nboth positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the\r\nexpected accumulated cost of nondeterministic probabilistic programs.\r\nOur approach can handle (a) general positive and negative costs with bounded updates in\r\nvariables; and (b) nonnegative costs with general updates to variables.\r\nWe show that several natural examples which could not be\r\nhandled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no\r\nprevious approach for cost analysis of probabilistic programs could guarantee polynomial runtime.\r\nFinally, we show the effectiveness of our approach using experimental results on a variety of programs for which we efficiently synthesize tight resource-usage bounds."}],"date_updated":"2025-06-02T08:53:45Z","year":"2019","_id":"6175"},{"article_processing_charge":"No","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1144"},{"id":"6186","status":"public","relation":"part_of_dissertation"},{"id":"6185","status":"public","relation":"part_of_dissertation"},{"id":"6182","status":"public","relation":"part_of_dissertation"},{"id":"1012","relation":"part_of_dissertation","status":"public"},{"id":"6184","relation":"part_of_dissertation","status":"public"}]},"date_created":"2019-03-28T08:58:59Z","page":"375","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"type":"dissertation","title":"From Dyson to Pearcey: Universal statistics in random matrix theory","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"full_name":"Erdös, László","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","day":"18","file":[{"file_id":"6180","creator":"dernst","checksum":"6926f66f28079a81c4937e3764be00fc","access_level":"closed","file_name":"2019_Schroeder_Thesis.tar.gz","date_updated":"2020-07-14T12:47:21Z","date_created":"2019-03-28T08:53:52Z","relation":"source_file","content_type":"application/x-gzip","file_size":7104482},{"relation":"main_file","content_type":"application/pdf","file_size":4228794,"file_id":"6181","creator":"dernst","checksum":"7d0ebb8d1207e89768cdd497a5bf80fb","access_level":"open_access","date_updated":"2020-07-14T12:47:21Z","file_name":"2019_Schroeder_Thesis.pdf","date_created":"2019-03-28T08:53:52Z"}],"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"author":[{"full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856"}],"ddc":["515","519"],"file_date_updated":"2020-07-14T12:47:21Z","citation":{"chicago":"Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random Matrix Theory.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:th6179\">https://doi.org/10.15479/AT:ISTA:th6179</a>.","apa":"Schröder, D. J. (2019). <i>From Dyson to Pearcey: Universal statistics in random matrix theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th6179\">https://doi.org/10.15479/AT:ISTA:th6179</a>","mla":"Schröder, Dominik J. <i>From Dyson to Pearcey: Universal Statistics in Random Matrix Theory</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th6179\">10.15479/AT:ISTA:th6179</a>.","ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria.","ieee":"D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix theory,” Institute of Science and Technology Austria, 2019.","ama":"Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th6179\">10.15479/AT:ISTA:th6179</a>","short":"D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix Theory, Institute of Science and Technology Austria, 2019."},"publication_status":"published","doi":"10.15479/AT:ISTA:th6179","date_published":"2019-03-18T00:00:00Z","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"oa":1,"status":"public","ec_funded":1,"month":"03","year":"2019","date_updated":"2024-02-22T14:34:33Z","abstract":[{"text":"In the first part of this thesis we consider large random matrices with arbitrary expectation and a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic control of a multivariate cumulant expansion.\r\nIn the second part we consider Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are uni- versal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta universality conjecture for the last remaining universality type. Our analysis holds not only for exact cusps, but approximate cusps as well, where an ex- tended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow- nian motion to the cusp regime.\r\nIn the third and final part we explore the entrywise linear statistics of Wigner ma- trices and identify the fluctuations for a large class of test functions with little regularity. This enables us to study the rectangular Young diagram obtained from the interlacing eigenvalues of the random matrix and its minor, and we find that, despite having the same limit, the fluctuations differ from those of the algebraic Young tableaux equipped with the Plancharel measure.","lang":"eng"}],"_id":"6179"},{"file_date_updated":"2020-07-14T12:47:22Z","scopus_import":"1","ddc":["510"],"citation":{"chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Random Matrices with Slow Correlation Decay.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2019. <a href=\"https://doi.org/10.1017/fms.2019.2\">https://doi.org/10.1017/fms.2019.2</a>.","mla":"Erdös, László, et al. “Random Matrices with Slow Correlation Decay.” <i>Forum of Mathematics, Sigma</i>, vol. 7, e8, Cambridge University Press, 2019, doi:<a href=\"https://doi.org/10.1017/fms.2019.2\">10.1017/fms.2019.2</a>.","ista":"Erdös L, Krüger TH, Schröder DJ. 2019. Random matrices with slow correlation decay. Forum of Mathematics, Sigma. 7, e8.","apa":"Erdös, L., Krüger, T. H., &#38; Schröder, D. J. (2019). Random matrices with slow correlation decay. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2019.2\">https://doi.org/10.1017/fms.2019.2</a>","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Forum of Mathematics, Sigma 7 (2019).","ama":"Erdös L, Krüger TH, Schröder DJ. Random matrices with slow correlation decay. <i>Forum of Mathematics, Sigma</i>. 2019;7. doi:<a href=\"https://doi.org/10.1017/fms.2019.2\">10.1017/fms.2019.2</a>","ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Random matrices with slow correlation decay,” <i>Forum of Mathematics, Sigma</i>, vol. 7. Cambridge University Press, 2019."},"intvolume":"         7","doi":"10.1017/fms.2019.2","publication_status":"published","oa_version":"Published Version","date_published":"2019-03-26T00:00:00Z","status":"public","oa":1,"publication_identifier":{"eissn":["20505094"]},"month":"03","ec_funded":1,"arxiv":1,"abstract":[{"lang":"eng","text":"We consider large random matrices with a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent away from the spectral edges, generalizing the recent result of Ajanki et al. [‘Stability of the matrix Dyson equation and random matrices with correlations’, Probab. Theory Related Fields 173(1–2) (2019), 293–373] to allow slow correlation decay and arbitrary expectation. The main novel tool is\r\na systematic diagrammatic control of a multivariate cumulant expansion."}],"date_updated":"2023-09-07T12:54:12Z","year":"2019","article_number":"e8","_id":"6182","article_type":"original","article_processing_charge":"No","quality_controlled":"1","volume":7,"external_id":{"arxiv":["1705.10661"],"isi":["000488847100001"]},"related_material":{"record":[{"id":"6179","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","publication":"Forum of Mathematics, Sigma","date_created":"2019-03-28T09:05:23Z","type":"journal_article","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Cambridge University Press","title":"Random matrices with slow correlation decay","day":"26","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}],"isi":1,"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"file":[{"file_size":1520344,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"933a472568221c73b2c3ce8c87bf6d15","file_id":"6883","creator":"dernst","date_created":"2019-09-17T14:24:13Z","file_name":"2019_Forum_Erdoes.pdf","date_updated":"2020-07-14T12:47:22Z"}]},{"main_file_link":[{"url":"https://arxiv.org/abs/1811.04055","open_access":"1"}],"intvolume":"         1","citation":{"short":"G. Cipolloni, L. Erdös, T.H. Krüger, D.J. Schröder, Pure and Applied Analysis  1 (2019) 615–707.","ieee":"G. Cipolloni, L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices, II: The real symmetric case,” <i>Pure and Applied Analysis </i>, vol. 1, no. 4. MSP, pp. 615–707, 2019.","ama":"Cipolloni G, Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices, II: The real symmetric case. <i>Pure and Applied Analysis </i>. 2019;1(4):615–707. doi:<a href=\"https://doi.org/10.2140/paa.2019.1.615\">10.2140/paa.2019.1.615</a>","chicago":"Cipolloni, Giorgio, László Erdös, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices, II: The Real Symmetric Case.” <i>Pure and Applied Analysis </i>. MSP, 2019. <a href=\"https://doi.org/10.2140/paa.2019.1.615\">https://doi.org/10.2140/paa.2019.1.615</a>.","apa":"Cipolloni, G., Erdös, L., Krüger, T. H., &#38; Schröder, D. J. (2019). Cusp universality for random matrices, II: The real symmetric case. <i>Pure and Applied Analysis </i>. MSP. <a href=\"https://doi.org/10.2140/paa.2019.1.615\">https://doi.org/10.2140/paa.2019.1.615</a>","ista":"Cipolloni G, Erdös L, Krüger TH, Schröder DJ. 2019. Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . 1(4), 615–707.","mla":"Cipolloni, Giorgio, et al. “Cusp Universality for Random Matrices, II: The Real Symmetric Case.” <i>Pure and Applied Analysis </i>, vol. 1, no. 4, MSP, 2019, pp. 615–707, doi:<a href=\"https://doi.org/10.2140/paa.2019.1.615\">10.2140/paa.2019.1.615</a>."},"doi":"10.2140/paa.2019.1.615","publication_status":"published","oa_version":"Preprint","date_published":"2019-10-12T00:00:00Z","status":"public","publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"oa":1,"month":"10","ec_funded":1,"arxiv":1,"abstract":[{"lang":"eng","text":"We prove that the local eigenvalue statistics of real symmetric Wigner-type\r\nmatrices near the cusp points of the eigenvalue density are universal. Together\r\nwith the companion paper [arXiv:1809.03971], which proves the same result for\r\nthe complex Hermitian symmetry class, this completes the last remaining case of\r\nthe Wigner-Dyson-Mehta universality conjecture after bulk and edge\r\nuniversalities have been established in the last years. We extend the recent\r\nDyson Brownian motion analysis at the edge [arXiv:1712.03881] to the cusp\r\nregime using the optimal local law from [arXiv:1809.03971] and the accurate\r\nlocal shape analysis of the density from [arXiv:1506.05095, arXiv:1804.07752].\r\nWe also present a PDE-based method to improve the estimate on eigenvalue\r\nrigidity via the maximum principle of the heat flow related to the Dyson\r\nBrownian motion."}],"issue":"4","date_updated":"2023-09-07T12:54:12Z","year":"2019","_id":"6186","article_type":"original","article_processing_charge":"No","quality_controlled":"1","volume":1,"external_id":{"arxiv":["1811.04055"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6179"}]},"publication":"Pure and Applied Analysis ","date_created":"2019-03-28T10:21:17Z","page":"615–707","type":"journal_article","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"MSP","title":"Cusp universality for random matrices, II: The real symmetric case","day":"12","author":[{"full_name":"Cipolloni, Giorgio","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László"},{"orcid":"0000-0002-4821-3297","first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H"},{"full_name":"Schröder, Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}]},{"article_processing_charge":"No","external_id":{"isi":["000462530200001"]},"quality_controlled":"1","volume":8,"related_material":{"record":[{"relation":"dissertation_contains","id":"6530"},{"id":"8983","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"6546"}],"link":[{"url":"https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/","relation":"press_release","description":"News on IST Homepage"}]},"has_accepted_license":"1","date_created":"2019-03-28T13:37:45Z","publication":"eLife","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"DaSi"}],"publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"26","project":[{"name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","grant_number":"24283","_id":"253CDE40-B435-11E9-9278-68D0E5697425"},{"name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF","grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Breaking barriers: Investigating the junctional and mechanobiological changes underlying the ability of Drosophila immune cells to invade an epithelium","_id":"25388084-B435-11E9-9278-68D0E5697425","grant_number":"329540"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"isi":1,"author":[{"first_name":"Katarina","last_name":"Valosková","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","full_name":"Valosková, Katarina"},{"full_name":"Biebl, Julia","first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","last_name":"Biebl"},{"last_name":"Roblek","id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko"},{"orcid":"0000-0001-6981-6938","first_name":"Shamsi","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87","full_name":"Emtenani, Shamsi"},{"full_name":"György, Attila","first_name":"Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György"},{"full_name":"Misova, Michaela","first_name":"Michaela","orcid":"0000-0003-2427-6856","last_name":"Misova","id":"495A3C32-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ratheesh, Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","last_name":"Ratheesh","orcid":"0000-0001-7190-0776","first_name":"Aparna"},{"first_name":"Patricia","id":"2CE4065A-F248-11E8-B48F-1D18A9856A87","last_name":"Rodrigues","full_name":"Rodrigues, Patricia"},{"full_name":"Shkarina, Katerina","first_name":"Katerina","last_name":"Shkarina"},{"full_name":"Larsen, Ida Signe Bohse","first_name":"Ida Signe Bohse","last_name":"Larsen"},{"last_name":"Vakhrushev","first_name":"Sergey Y","full_name":"Vakhrushev, Sergey Y"},{"last_name":"Clausen","first_name":"Henrik","full_name":"Clausen, Henrik"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":4496017,"file_name":"2019_eLife_Valoskova.pdf","date_updated":"2020-07-14T12:47:23Z","date_created":"2019-03-28T14:00:41Z","file_id":"6188","checksum":"cc0d1a512559d52e7e7cb0e9b9854b40","creator":"dernst","access_level":"open_access"}],"file_date_updated":"2020-07-14T12:47:23Z","scopus_import":"1","ddc":["570"],"intvolume":"         8","citation":{"mla":"Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” <i>ELife</i>, vol. 8, e41801, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.41801\">10.7554/elife.41801</a>.","apa":"Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M., … Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.41801\">https://doi.org/10.7554/elife.41801</a>","ista":"Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh A, Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. 2019. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.","chicago":"Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.41801\">https://doi.org/10.7554/elife.41801</a>.","ama":"Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.41801\">10.7554/elife.41801</a>","ieee":"K. Valosková <i>et al.</i>, “A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","short":"K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A. Ratheesh, P. Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev, H. Clausen, D.E. Siekhaus, ELife 8 (2019)."},"publication_status":"published","doi":"10.7554/elife.41801","oa_version":"Published Version","date_published":"2019-03-26T00:00:00Z","status":"public","oa":1,"publication_identifier":{"issn":["2050-084X"]},"month":"03","ec_funded":1,"date_updated":"2024-03-25T23:30:15Z","abstract":[{"text":"Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis.","lang":"eng"}],"year":"2019","article_number":"e41801","acknowledged_ssus":[{"_id":"LifeSc"}],"_id":"6187"},{"month":"03","status":"public","oa":1,"publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"article_number":"114502","_id":"6189","abstract":[{"lang":"eng","text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations."}],"arxiv":1,"issue":"11","date_updated":"2024-03-25T23:30:27Z","year":"2019","citation":{"ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. <i>Physical Review Letters</i>. 2019;122(11). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">10.1103/PhysRevLett.122.114502</a>","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” <i>Physical Review Letters</i>, vol. 122, no. 11. American Physical Society, 2019.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” <i>Physical Review Letters</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">https://doi.org/10.1103/PhysRevLett.122.114502</a>.","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” <i>Physical Review Letters</i>, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">10.1103/PhysRevLett.122.114502</a>.","apa":"Agrawal, N., Choueiri, G. H., &#38; Hof, B. (2019). Transition to turbulence in particle laden flows. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">https://doi.org/10.1103/PhysRevLett.122.114502</a>","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502."},"intvolume":"       122","main_file_link":[{"url":"https://arxiv.org/abs/1809.06358","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","date_published":"2019-03-22T00:00:00Z","doi":"10.1103/PhysRevLett.122.114502","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","title":"Transition to turbulence in particle laden flows","isi":1,"author":[{"first_name":"Nishchal","last_name":"Agrawal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","full_name":"Agrawal, Nishchal"},{"full_name":"Choueiri, George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn"}],"day":"22","quality_controlled":"1","volume":122,"external_id":{"isi":["000461922000006"],"arxiv":["1809.06358"]},"related_material":{"record":[{"id":"9728","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","type":"journal_article","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"publication":"Physical Review Letters","date_created":"2019-03-31T21:59:12Z"}]