[{"file":[{"relation":"supplementary_material","checksum":"bc1b285edca9e98a2c63d153c79bb75b","creator":"dernst","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-07T13:37:19Z","file_size":33202743,"content_type":"application/zip","access_level":"open_access","file_name":"Setd5_paper.zip","file_id":"6084"}],"year":"2019","department":[{"_id":"GaNo"}],"date_published":"2019-01-09T00:00:00Z","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter","full_name":"Dotter, Christoph"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","date_created":"2019-03-07T13:32:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2020-07-14T12:47:18Z","has_accepted_license":"1","ddc":["570"],"oa_version":"Published Version","related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"month":"01","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":"2025-04-15T07:50:27Z","day":"09","_id":"6074","status":"public","type":"research_data","doi":"10.15479/AT:ISTA:6074","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","citation":{"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>","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>","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>.","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>.","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.","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>.","short":"C. Dotter, G. Novarino, (2019)."}},{"publisher":"Cambridge University Press","arxiv":1,"doi":"10.1017/etds.2017.52","day":"01","scopus_import":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-03-10T22:59:18Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["1601.06118"],"isi":["000459725600012"]},"intvolume":"        39","year":"2019","department":[{"_id":"LaEr"}],"project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1601.06118","open_access":"1"}],"article_processing_charge":"No","citation":{"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>","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.","short":"C. Sadel, D. Xu, Ergodic Theory and Dynamical Systems 39 (2019) 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>.","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>.","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."},"type":"journal_article","_id":"6086","status":"public","month":"04","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"}],"volume":39,"issue":"4","date_updated":"2025-04-15T06:50:24Z","oa_version":"Preprint","isi":1,"title":"Singular analytic linear cocycles with negative infinite Lyapunov exponents","date_published":"2019-04-01T00:00:00Z","author":[{"full_name":"Sadel, Christian","last_name":"Sadel","orcid":"0000-0001-8255-3968","first_name":"Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xu","full_name":"Xu, Disheng","first_name":"Disheng"}],"page":"1082-1098","publication_status":"published","publication":"Ergodic Theory and Dynamical Systems","quality_controlled":"1"},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-03-10T22:59:19Z","external_id":{"isi":["000460509600013"],"pmid":["30773315"]},"language":[{"iso":"eng"}],"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020"}],"intvolume":"       176","department":[{"_id":"CaHe"},{"_id":"EM-Fac"}],"year":"2019","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.01.019","open_access":"1"}],"publisher":"Elsevier","doi":"10.1016/j.cell.2019.01.019","day":"07","scopus_import":"1","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.).","ddc":["570"],"title":"Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"author":[{"first_name":"Peng","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","full_name":"Xia, Peng","orcid":"0000-0002-5419-7756","last_name":"Xia"},{"full_name":"Gütl, Daniel J","last_name":"Gütl","first_name":"Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","last_name":"Zheden","orcid":"0000-0002-9438-4783"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"date_published":"2019-03-07T00:00:00Z","page":"1379-1392.e14","publication_status":"published","publication":"Cell","pmid":1,"quality_controlled":"1","citation":{"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.","short":"P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14.","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>.","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>.","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.","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>","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>"},"article_processing_charge":"No","type":"journal_article","status":"public","_id":"6087","date_updated":"2026-06-18T18:59:54Z","issue":"6","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"}],"month":"03","volume":176,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/in-zebrafish-eggs-most-rapidly-growing-cell-inhibits-its-neighbours-through-mechanical-signals/","relation":"press_release","description":"News on IST Homepage"}]},"article_type":"original","oa_version":"Published Version","isi":1},{"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"intvolume":"        36","year":"2019","project":[{"call_identifier":"FWF","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["30590559"],"isi":["000462585100006"]},"date_created":"2019-03-10T22:59:19Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"scopus_import":"1","day":"01","doi":"10.1093/molbev/msy246","publisher":"Oxford University Press","quality_controlled":"1","pmid":1,"publication":"Molecular biology and evolution","page":"500-515","publication_status":"published","date_published":"2019-03-01T00:00:00Z","author":[{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","oa_version":"Submitted Version","isi":1,"related_material":{"record":[{"relation":"popular_science","id":"5757","status":"public"}]},"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."}],"volume":36,"month":"03","date_updated":"2025-04-15T08:18:38Z","issue":"3","_id":"6089","status":"public","type":"journal_article","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"article_processing_charge":"No","citation":{"short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","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.","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.","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>.","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>.","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>","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>"}},{"year":"2019","intvolume":"        99","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-03-10T22:59:20Z","language":[{"iso":"eng"}],"external_id":{"isi":["000459916500007"]},"scopus_import":"1","publisher":"American Physical Society","doi":"10.1103/PhysRevE.99.022423","day":"26","publication_status":"published","publication":"Physical Review E","quality_controlled":"1","title":"Receptor crosstalk improves concentration sensing of multiple ligands","date_published":"2019-02-26T00:00:00Z","article_number":"022423","author":[{"first_name":"Martín","last_name":"Carballo-Pacheco","full_name":"Carballo-Pacheco, Martín"},{"first_name":"Jonathan","full_name":"Desponds, Jonathan","last_name":"Desponds"},{"first_name":"Tatyana","last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana"},{"first_name":"Andreas","full_name":"Mayer, Andreas","last_name":"Mayer"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak","full_name":"Prizak, Roshan"},{"first_name":"Gautam","full_name":"Reddy, Gautam","last_name":"Reddy"},{"last_name":"Nemenman","full_name":"Nemenman, Ilya","first_name":"Ilya"},{"first_name":"Thierry","full_name":"Mora, Thierry","last_name":"Mora"}],"volume":99,"month":"02","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."}],"date_updated":"2024-02-28T13:12:06Z","issue":"2","oa_version":"Preprint","isi":1,"article_processing_charge":"No","citation":{"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.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","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>.","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.","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>.","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>","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>"},"type":"journal_article","status":"public","_id":"6090"},{"title":"Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs","date_published":"2019-02-21T00:00:00Z","article_number":"e41563","author":[{"last_name":"Henderson","full_name":"Henderson, Nathan T.","first_name":"Nathan T."},{"full_name":"Le Marchand, Sylvain J.","last_name":"Le Marchand","first_name":"Sylvain J."},{"first_name":"Martin","last_name":"Hruska","full_name":"Hruska, Martin"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"},{"first_name":"Matthew B.","last_name":"Dalva","full_name":"Dalva, Matthew B."}],"publication_status":"published","file":[{"checksum":"7b0800d003f14cd06b1802dea0c52941","relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:47:19Z","file_size":7260753,"date_created":"2019-03-11T16:15:37Z","file_id":"6098","file_name":"2019_eLife_Henderson.pdf","access_level":"open_access","content_type":"application/pdf"}],"publication":"eLife","quality_controlled":"1","pmid":1,"article_processing_charge":"No","citation":{"short":"N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B. Dalva, ELife 8 (2019).","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.","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>.","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.","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>.","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>","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>"},"type":"journal_article","status":"public","_id":"6091","month":"02","volume":8,"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."}],"date_updated":"2023-08-24T14:50:50Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","oa":1,"file_date_updated":"2020-07-14T12:47:19Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-03-10T22:59:20Z","language":[{"iso":"eng"}],"external_id":{"pmid":["30789343"],"isi":["000459380600001"]},"intvolume":"         8","department":[{"_id":"SiHi"}],"year":"2019","publisher":"eLife Sciences Publications","doi":"10.7554/eLife.41563","day":"21","scopus_import":"1","ddc":["570"]},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-03-10T22:59:20Z","external_id":{"isi":["000459223400004"],"arxiv":["1802.01638"]},"language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"year":"2019","intvolume":"        99","department":[{"_id":"MiLe"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01638"}],"publisher":"American Physical Society","doi":"10.1103/PhysRevB.99.064428","arxiv":1,"day":"01","scopus_import":"1","title":"Quantum many-body dynamics of the Einstein-de Haas effect","author":[{"full_name":"Mentink, Johann H","last_name":"Mentink","first_name":"Johann H"},{"first_name":"Mikhail","full_name":"Katsnelson, Mikhail","last_name":"Katsnelson"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"date_published":"2019-02-01T00:00:00Z","article_number":"064428","publication_status":"published","publication":"Physical Review B","quality_controlled":"1","citation":{"ista":"Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 99(6), 064428.","short":"J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).","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>.","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.","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>.","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>","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>"},"article_processing_charge":"No","type":"journal_article","_id":"6092","status":"public","date_updated":"2025-04-15T07:59:29Z","issue":"6","volume":99,"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."}],"month":"02","oa_version":"Preprint","isi":1},{"type":"journal_article","article_processing_charge":"No","citation":{"short":"M. Goudarzi, A. Boquet-Pujadas, J.C. Olivo-Marin, E. Raz, PLOS ONE 14 (2019).","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.","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.","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>.","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>.","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>","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>"},"_id":"6093","status":"public","month":"02","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."}],"volume":14,"date_updated":"2023-09-19T14:46:47Z","issue":"2","has_accepted_license":"1","isi":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"title":"Fluid dynamics during bleb formation in migrating cells in vivo","date_published":"2019-02-26T00:00:00Z","article_number":"e0212699","author":[{"last_name":"Goudarzi","full_name":"Goudarzi, Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","first_name":"Mohammad"},{"first_name":"Aleix","last_name":"Boquet-Pujadas","full_name":"Boquet-Pujadas, Aleix"},{"full_name":"Olivo-Marin, Jean Christophe","last_name":"Olivo-Marin","first_name":"Jean Christophe"},{"first_name":"Erez","full_name":"Raz, Erez","last_name":"Raz"}],"publication_status":"published","quality_controlled":"1","file":[{"file_name":"2019_PLoSOne_Goudarzi.pdf","access_level":"open_access","file_id":"6096","content_type":"application/pdf","file_size":2967731,"date_created":"2019-03-11T16:09:23Z","date_updated":"2020-07-14T12:47:19Z","relation":"main_file","checksum":"b885de050ed4bb3c86f706487a47197f","creator":"dernst"}],"publication":"PLOS ONE","doi":"10.1371/journal.pone.0212699","publisher":"Public Library of Science","day":"26","ddc":["570"],"scopus_import":"1","date_created":"2019-03-10T22:59:21Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"file_date_updated":"2020-07-14T12:47:19Z","language":[{"iso":"eng"}],"external_id":{"isi":["000459712100022"]},"intvolume":"        14","year":"2019","department":[{"_id":"Bio"}]},{"day":"01","publisher":"Wiley","doi":"10.1111/mec.14972","scopus_import":"1","ddc":["570"],"external_id":{"isi":["000465219200013"]},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:19Z","oa":1,"date_created":"2019-03-10T22:59:21Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","department":[{"_id":"NiBa"}],"intvolume":"        28","status":"public","_id":"6095","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>.","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>.","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.","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.","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.","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>","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>"},"article_processing_charge":"No","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","isi":1,"has_accepted_license":"1","issue":"6","date_updated":"2023-08-24T14:50:27Z","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."}],"volume":28,"month":"03","related_material":{"record":[{"status":"public","id":"9837","relation":"research_data"}]},"author":[{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"last_name":"Chaube","full_name":"Chaube, Pragya","first_name":"Pragya"},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"last_name":"Larsson","full_name":"Larsson, Tomas","first_name":"Tomas"},{"last_name":"Lemmon","full_name":"Lemmon, Alan R.","first_name":"Alan R."},{"first_name":"Emily M.","full_name":"Lemmon, Emily M.","last_name":"Lemmon"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"date_published":"2019-03-01T00:00:00Z","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","publication":"Molecular Ecology","file":[{"date_updated":"2020-07-14T12:47:19Z","checksum":"f915885756057ec0ca5912a41f46a887","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_MolecularEcology_Faria.pdf","file_id":"6097","date_created":"2019-03-11T16:12:54Z","file_size":1510715}],"quality_controlled":"1","publication_status":"published","page":"1375-1393"},{"_id":"6102","status":"public","citation":{"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>","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>","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>.","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.","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>.","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.","short":"B. Le Feber, J.E. Sipe, M. Wulf, L. Kuipers, N. Rotenberg, Light: Science and Applications 8 (2019)."},"article_processing_charge":"No","publication_identifier":{"issn":["2095-5545"],"eissn":["2047-7538"]},"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","isi":1,"has_accepted_license":"1","date_updated":"2025-07-10T11:53:10Z","issue":"1","volume":8,"month":"03","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."}],"author":[{"last_name":"Le Feber","full_name":"Le Feber, B.","first_name":"B."},{"first_name":"J. E.","last_name":"Sipe","full_name":"Sipe, J. E."},{"orcid":"0000-0001-6613-1378","last_name":"Wulf","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"last_name":"Kuipers","full_name":"Kuipers, L.","first_name":"L."},{"first_name":"N.","full_name":"Rotenberg, N.","last_name":"Rotenberg"}],"date_published":"2019-03-06T00:00:00Z","article_number":"28","title":"A full vectorial mapping of nanophotonic light fields","file":[{"creator":"dernst","relation":"main_file","checksum":"d71e528cff9c56f70ccc29dd7005257f","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-18T08:08:22Z","file_size":1119947,"access_level":"open_access","file_id":"6108","content_type":"application/pdf","file_name":"2019_Light_LeFeber.pdf"}],"publication":"Light: Science and Applications","quality_controlled":"1","publication_status":"published","day":"06","publisher":"Springer Nature","doi":"10.1038/s41377-019-0124-3","arxiv":1,"scopus_import":"1","ddc":["530"],"external_id":{"arxiv":["1803.10145"],"isi":["000460470700004"]},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:19Z","oa":1,"date_created":"2019-03-17T22:59:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         8","year":"2019","department":[{"_id":"JoFi"}]},{"citation":{"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>","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>","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>.","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.","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>.","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.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, Journal of Animal Ecology 88 (2019) 566–578."},"article_processing_charge":"No","publication_identifier":{"issn":["0021-8790"],"eissn":["1365-2656"]},"type":"journal_article","_id":"6105","status":"public","date_updated":"2025-07-10T11:53:10Z","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"}],"month":"04","volume":88,"related_material":{"record":[{"relation":"research_data","id":"9806","status":"public"}]},"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"oa_version":"Published Version","has_accepted_license":"1","title":"A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","author":[{"first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","full_name":"Kutzer, Megan","last_name":"Kutzer","orcid":"0000-0002-8696-6978"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"},{"full_name":"Armitage, Sophie A.O.","last_name":"Armitage","first_name":"Sophie A.O."}],"date_published":"2019-04-01T00:00:00Z","publication_status":"published","page":"566-578","file":[{"file_size":1460662,"date_created":"2019-03-18T07:43:06Z","content_type":"application/pdf","access_level":"open_access","file_id":"6107","file_name":"2019_JournalAnimalEcology_Kutzer.pdf","creator":"dernst","relation":"main_file","checksum":"405cde15120de26018b3bd0dfa29986c","date_updated":"2020-07-14T12:47:19Z"}],"publication":"Journal of Animal Ecology","quality_controlled":"1","publisher":"Wiley","doi":"10.1111/1365-2656.12953","day":"01","scopus_import":"1","ddc":["570"],"file_date_updated":"2020-07-14T12:47:19Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-03-17T22:59:15Z","external_id":{"isi":["000467994800007"]},"language":[{"iso":"eng"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"intvolume":"        88","year":"2019","department":[{"_id":"SyCr"}],"ec_funded":1},{"_id":"6174","status":"public","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"type":"journal_article","citation":{"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>","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>","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>.","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>.","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.","ista":"Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. 2019. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 99(9), 094205.","short":"P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur, Physical Review B 99 (2019)."},"article_processing_charge":"No","isi":1,"oa_version":"Preprint","article_type":"original","issue":"9","date_updated":"2023-09-05T12:11:13Z","month":"03","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."}],"volume":99,"author":[{"last_name":"Dumitrescu","full_name":"Dumitrescu, Philipp T.","first_name":"Philipp T."},{"first_name":"Anna","last_name":"Goremykina","full_name":"Goremykina, Anna"},{"last_name":"Parameswaran","full_name":"Parameswaran, Siddharth A.","first_name":"Siddharth A."},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"},{"full_name":"Vasseur, Romain","last_name":"Vasseur","first_name":"Romain"}],"article_number":"094205","date_published":"2019-03-22T00:00:00Z","title":"Kosterlitz-Thouless scaling at many-body localization phase transitions","quality_controlled":"1","publication":"Physical Review B","publication_status":"published","day":"22","doi":"10.1103/physrevb.99.094205","arxiv":1,"publisher":"American Physical Society","scopus_import":"1","external_id":{"arxiv":["1811.03103"],"isi":["000462883200001"]},"language":[{"iso":"eng"}],"date_created":"2019-03-25T07:32:08Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1811.03103","open_access":"1"}],"intvolume":"        99","department":[{"_id":"MaSe"}],"year":"2019"},{"external_id":{"isi":["000460099800012"],"pmid":["30552233"]},"language":[{"iso":"eng"}],"oa":1,"date_created":"2019-03-31T21:59:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1158/1541-7786.MCR-18-0530"}],"intvolume":"        17","department":[{"_id":"DaSi"}],"year":"2019","day":"01","publisher":"AACR","doi":"10.1158/1541-7786.MCR-18-0530","scopus_import":"1","ddc":["570"],"author":[{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko","last_name":"Roblek","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko"},{"last_name":"Protsyuk","full_name":"Protsyuk, Darya","first_name":"Darya"},{"last_name":"Becker","full_name":"Becker, Paul F.","first_name":"Paul F."},{"first_name":"Cristina","last_name":"Stefanescu","full_name":"Stefanescu, Cristina"},{"first_name":"Christian","full_name":"Gorzelanny, Christian","last_name":"Gorzelanny"},{"first_name":"Jesus F.","full_name":"Glaus Garzon, Jesus F.","last_name":"Glaus Garzon"},{"first_name":"Lucia","full_name":"Knopfova, Lucia","last_name":"Knopfova"},{"full_name":"Heikenwalder, Mathias","last_name":"Heikenwalder","first_name":"Mathias"},{"first_name":"Bruno","full_name":"Luckow, Bruno","last_name":"Luckow"},{"last_name":"Schneider","full_name":"Schneider, Stefan W.","first_name":"Stefan W."},{"last_name":"Borsig","full_name":"Borsig, Lubor","first_name":"Lubor"}],"date_published":"2019-03-01T00:00:00Z","title":"CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis","publication":"Molecular Cancer Research","pmid":1,"quality_controlled":"1","page":"783-793","publication_status":"published","_id":"6190","status":"public","citation":{"ama":"Roblek M, Protsyuk D, Becker PF, et al. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. <i>Molecular Cancer Research</i>. 2019;17(3):783-793. doi:<a href=\"https://doi.org/10.1158/1541-7786.MCR-18-0530\">10.1158/1541-7786.MCR-18-0530</a>","apa":"Roblek, M., Protsyuk, D., Becker, P. F., Stefanescu, C., Gorzelanny, C., Glaus Garzon, J. F., … Borsig, L. (2019). CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. <i>Molecular Cancer Research</i>. AACR. <a href=\"https://doi.org/10.1158/1541-7786.MCR-18-0530\">https://doi.org/10.1158/1541-7786.MCR-18-0530</a>","ista":"Roblek M, Protsyuk D, Becker PF, Stefanescu C, Gorzelanny C, Glaus Garzon JF, Knopfova L, Heikenwalder M, Luckow B, Schneider SW, Borsig L. 2019. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 17(3), 783–793.","short":"M. Roblek, D. Protsyuk, P.F. Becker, C. Stefanescu, C. Gorzelanny, J.F. Glaus Garzon, L. Knopfova, M. Heikenwalder, B. Luckow, S.W. Schneider, L. Borsig, Molecular Cancer Research 17 (2019) 783–793.","mla":"Roblek, Marko, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” <i>Molecular Cancer Research</i>, vol. 17, no. 3, AACR, 2019, pp. 783–93, doi:<a href=\"https://doi.org/10.1158/1541-7786.MCR-18-0530\">10.1158/1541-7786.MCR-18-0530</a>.","ieee":"M. Roblek <i>et al.</i>, “CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis,” <i>Molecular Cancer Research</i>, vol. 17, no. 3. AACR, pp. 783–793, 2019.","chicago":"Roblek, Marko, Darya Protsyuk, Paul F. Becker, Cristina Stefanescu, Christian Gorzelanny, Jesus F. Glaus Garzon, Lucia Knopfova, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” <i>Molecular Cancer Research</i>. AACR, 2019. <a href=\"https://doi.org/10.1158/1541-7786.MCR-18-0530\">https://doi.org/10.1158/1541-7786.MCR-18-0530</a>."},"article_processing_charge":"No","publication_identifier":{"issn":["1541-7786"],"eissn":["1557-3125"]},"type":"journal_article","isi":1,"oa_version":"Published Version","date_updated":"2026-06-18T19:00:54Z","issue":"3","volume":17,"month":"03","abstract":[{"lang":"eng","text":"Increased levels of the chemokine CCL2 in cancer patients are associated with poor prognosis. Experimental evidence suggests that CCL2 correlates with inflammatory monocyte recruitment and induction of vascular activation, but the functionality remains open. Here, we show that endothelial Ccr2 facilitates pulmonary metastasis using an endothelial-specific Ccr2-deficient mouse model (Ccr2ecKO). Similar levels of circulating monocytes and equal leukocyte recruitment to metastatic lesions of Ccr2ecKO and Ccr2fl/fl littermates were observed. The absence of endothelial Ccr2 strongly reduced pulmonary metastasis, while the primary tumor growth was unaffected. Despite a comparable cytokine milieu in Ccr2ecKO and Ccr2fl/fl littermates the absence of vascular permeability induction was observed only in Ccr2ecKO mice. CCL2 stimulation of pulmonary endothelial cells resulted in increased phosphorylation of MLC2, endothelial cell retraction, and vascular leakiness that was blocked by an addition of a CCR2 inhibitor. These data demonstrate that endothelial CCR2 expression is required for tumor cell extravasation and pulmonary metastasis.\r\n\r\nImplications: The findings provide mechanistic insight into how CCL2–CCR2 signaling in endothelial cells promotes their activation through myosin light chain phosphorylation, resulting in endothelial retraction and enhanced tumor cell migration and metastasis."}],"article_type":"original"},{"isi":1,"oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"link":[{"relation":"supplementary_material","url":"www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental"}]},"date_updated":"2025-07-10T11:53:14Z","issue":"12","volume":116,"month":"03","abstract":[{"lang":"eng","text":"The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis."}],"status":"public","_id":"6191","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"type":"journal_article","citation":{"apa":"Recho, P., Hallou, A., &#38; Hannezo, E. B. (2019). Theory of mechanochemical patterning in biphasic biological tissues. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1813255116\">https://doi.org/10.1073/pnas.1813255116</a>","ama":"Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic biological tissues. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2019;116(12):5344-5349. doi:<a href=\"https://doi.org/10.1073/pnas.1813255116\">10.1073/pnas.1813255116</a>","mla":"Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49, doi:<a href=\"https://doi.org/10.1073/pnas.1813255116\">10.1073/pnas.1813255116</a>.","ieee":"P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning in biphasic biological tissues,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 12. National Academy of Sciences, pp. 5344–5349, 2019.","chicago":"Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1813255116\">https://doi.org/10.1073/pnas.1813255116</a>.","ista":"Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 116(12), 5344–5349.","short":"P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 5344–5349."},"article_processing_charge":"No","pmid":1,"quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","file":[{"date_updated":"2020-07-14T12:47:23Z","creator":"dernst","relation":"main_file","checksum":"8b67eee0ea8e5db61583e4d485215258","content_type":"application/pdf","file_id":"6193","file_name":"2019_PNAS_Recho.pdf","access_level":"open_access","file_size":3456045,"date_created":"2019-04-03T14:10:30Z"}],"page":"5344-5349","publication_status":"published","author":[{"first_name":"Pierre","full_name":"Recho, Pierre","last_name":"Recho"},{"last_name":"Hallou","full_name":"Hallou, Adrien","first_name":"Adrien"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"}],"date_published":"2019-03-19T00:00:00Z","title":"Theory of mechanochemical patterning in biphasic biological tissues","ddc":["570"],"scopus_import":"1","day":"19","doi":"10.1073/pnas.1813255116","publisher":"National Academy of Sciences","project":[{"grant_number":"P31639","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton"}],"intvolume":"       116","year":"2019","department":[{"_id":"EdHa"}],"external_id":{"pmid":["30819884"],"isi":["000461679000027"]},"language":[{"iso":"eng"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-03-31T21:59:13Z","file_date_updated":"2020-07-14T12:47:23Z","oa":1},{"publication_status":"published","quality_controlled":"1","publication":"eLife","file":[{"checksum":"130d7544b57df4a6787e1263c2d7ea43","relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:47:24Z","file_size":298466,"date_created":"2019-04-11T11:43:38Z","content_type":"application/pdf","access_level":"open_access","file_name":"2019_eLife_Barton.pdf","file_id":"6293"}],"title":"Why structure matters","article_number":"e45380","date_published":"2019-03-21T00:00:00Z","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"full_name":"Hermisson, Joachim","last_name":"Hermisson","first_name":"Joachim"},{"last_name":"Nordborg","full_name":"Nordborg, Magnus","first_name":"Magnus"}],"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","relation":"press_release"}]},"volume":8,"month":"03","abstract":[{"text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.","lang":"eng"}],"date_updated":"2026-04-02T14:03:15Z","has_accepted_license":"1","oa_version":"Published Version","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"journal_article","publication_identifier":{"eissn":["2050-084X"]},"article_processing_charge":"No","citation":{"chicago":"Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.45380\">https://doi.org/10.7554/eLife.45380</a>.","ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” <i>ELife</i>, vol. 8, e45380, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.45380\">10.7554/eLife.45380</a>.","short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).","ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","apa":"Barton, N. H., Hermisson, J., &#38; Nordborg, M. (2019). Why structure matters. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.45380\">https://doi.org/10.7554/eLife.45380</a>","ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.45380\">10.7554/eLife.45380</a>"},"status":"public","_id":"6230","year":"2019","intvolume":"         8","department":[{"_id":"NiBa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2019-04-07T21:59:15Z","oa":1,"file_date_updated":"2020-07-14T12:47:24Z","language":[{"iso":"eng"}],"external_id":{"isi":["000461988300001"]},"ddc":["570"],"scopus_import":"1","doi":"10.7554/eLife.45380","publisher":"eLife Sciences Publications","day":"21"},{"year":"2019","intvolume":"        47","department":[{"_id":"JaMa"}],"main_file_link":[{"url":"https://arxiv.org/abs/1705.05364","open_access":"1"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-04-07T21:59:15Z","external_id":{"isi":["000459681900005"],"arxiv":["1705.05364"]},"language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Institute of Mathematical Statistics","doi":"10.1214/18-AOP1272","arxiv":1,"day":"01","publication_status":"published","page":"804-834","publication":"Annals of Probability","quality_controlled":"1","title":"Boundary regularity of stochastic PDEs","author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate"}],"date_published":"2019-03-01T00:00:00Z","date_updated":"2025-07-10T11:53:17Z","issue":"2","volume":47,"abstract":[{"lang":"eng","text":"The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[ SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional constant coefficient linear equation whose solution at the boundary is not α-Hölder continuous.We obtain a positive counterpart of this: under some mild regularity assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are proved to be α-Hölder continuous up to the boundary with some α>0."}],"month":"03","isi":1,"oa_version":"Preprint","citation":{"ista":"Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability. 47(2), 804–834.","short":"M. Gerencser, Annals of Probability 47 (2019) 804–834.","mla":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” <i>Annals of Probability</i>, vol. 47, no. 2, Institute of Mathematical Statistics, 2019, pp. 804–34, doi:<a href=\"https://doi.org/10.1214/18-AOP1272\">10.1214/18-AOP1272</a>.","chicago":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2019. <a href=\"https://doi.org/10.1214/18-AOP1272\">https://doi.org/10.1214/18-AOP1272</a>.","ieee":"M. Gerencser, “Boundary regularity of stochastic PDEs,” <i>Annals of Probability</i>, vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019.","ama":"Gerencser M. Boundary regularity of stochastic PDEs. <i>Annals of Probability</i>. 2019;47(2):804-834. doi:<a href=\"https://doi.org/10.1214/18-AOP1272\">10.1214/18-AOP1272</a>","apa":"Gerencser, M. (2019). Boundary regularity of stochastic PDEs. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AOP1272\">https://doi.org/10.1214/18-AOP1272</a>"},"article_processing_charge":"No","publication_identifier":{"issn":["0091-1798"]},"type":"journal_article","_id":"6232","status":"public"},{"ddc":["580"],"scopus_import":"1","doi":"10.1038/s41586-019-1069-7","publisher":"Springer Nature","day":"11","ec_funded":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"}],"department":[{"_id":"JiFr"}],"intvolume":"       568","year":"2019","date_created":"2019-04-09T08:37:05Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-11-13T07:37:41Z","oa":1,"external_id":{"pmid":["30944466"],"isi":["000464412700050"]},"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/","relation":"press_release","description":"News on IST Homepage"}]},"article_type":"original","date_updated":"2025-04-14T07:45:04Z","abstract":[{"text":"The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes.","lang":"eng"}],"month":"04","volume":568,"isi":1,"oa_version":"Submitted Version","has_accepted_license":"1","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"type":"journal_article","citation":{"apa":"Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated auxin signalling regulates differential growth of the apical hook. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1069-7\">https://doi.org/10.1038/s41586-019-1069-7</a>","ama":"Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential growth of the apical hook. <i>Nature</i>. 2019;568:240-243. doi:<a href=\"https://doi.org/10.1038/s41586-019-1069-7\">10.1038/s41586-019-1069-7</a>","ieee":"M. Cao <i>et al.</i>, “TMK1-mediated auxin signalling regulates differential growth of the apical hook,” <i>Nature</i>, vol. 568. Springer Nature, pp. 240–243, 2019.","chicago":"Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1069-7\">https://doi.org/10.1038/s41586-019-1069-7</a>.","mla":"Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” <i>Nature</i>, vol. 568, Springer Nature, 2019, pp. 240–43, doi:<a href=\"https://doi.org/10.1038/s41586-019-1069-7\">10.1038/s41586-019-1069-7</a>.","short":"M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu, Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243.","ista":"Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z, Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 568, 240–243."},"article_processing_charge":"No","_id":"6259","status":"public","publication_status":"published","page":"240-243","pmid":1,"quality_controlled":"1","file":[{"content_type":"application/pdf","access_level":"open_access","file_id":"8751","file_name":"2019_Nature _Cao_accepted.pdf","file_size":4321328,"date_created":"2020-11-13T07:37:41Z","date_updated":"2020-11-13T07:37:41Z","relation":"main_file","creator":"dernst","success":1,"checksum":"6b84ab602a34382cf0340a37a1378c75"}],"publication":"Nature","title":"TMK1-mediated auxin signalling regulates differential growth of the apical hook","author":[{"full_name":"Cao, Min","last_name":"Cao","first_name":"Min"},{"full_name":"Chen, Rong","last_name":"Chen","first_name":"Rong"},{"first_name":"Pan","last_name":"Li","full_name":"Li, Pan"},{"last_name":"Yu","full_name":"Yu, Yongqiang","first_name":"Yongqiang"},{"last_name":"Zheng","full_name":"Zheng, Rui","first_name":"Rui"},{"first_name":"Danfeng","last_name":"Ge","full_name":"Ge, Danfeng"},{"first_name":"Wei","full_name":"Zheng, Wei","last_name":"Zheng"},{"first_name":"Xuhui","full_name":"Wang, Xuhui","last_name":"Wang"},{"first_name":"Yangtao","last_name":"Gu","full_name":"Gu, Yangtao"},{"last_name":"Gelová","orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Zhang, Heng","last_name":"Zhang","first_name":"Heng"},{"last_name":"Liu","full_name":"Liu, Renyi","first_name":"Renyi"},{"full_name":"He, Jun","last_name":"He","first_name":"Jun"},{"first_name":"Tongda","last_name":"Xu","full_name":"Xu, Tongda"}],"date_published":"2019-04-11T00:00:00Z"},{"status":"public","_id":"6261","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"type":"journal_article","citation":{"ama":"Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of root distal stem cells. <i>Plant Physiology</i>. 2019;180(1):22-25. doi:<a href=\"https://doi.org/10.1104/pp.18.01305\">10.1104/pp.18.01305</a>","apa":"Wang, Y., Gong, Z., Friml, J., &#38; Zhang, J. (2019). Nitrate modulates the differentiation of root distal stem cells. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.18.01305\">https://doi.org/10.1104/pp.18.01305</a>","ista":"Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 180(1), 22–25.","short":"Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25.","mla":"Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” <i>Plant Physiology</i>, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:<a href=\"https://doi.org/10.1104/pp.18.01305\">10.1104/pp.18.01305</a>.","chicago":"Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.18.01305\">https://doi.org/10.1104/pp.18.01305</a>.","ieee":"Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation of root distal stem cells,” <i>Plant Physiology</i>, vol. 180, no. 1. ASPB, pp. 22–25, 2019."},"article_processing_charge":"No","oa_version":"Published Version","isi":1,"article_type":"letter_note","issue":"1","date_updated":"2026-06-18T19:02:50Z","month":"05","abstract":[{"lang":"eng","text":"Nitrate regulation of root stem cell activity is auxin-dependent."}],"volume":180,"author":[{"first_name":"Y","last_name":"Wang","full_name":"Wang, Y"},{"full_name":"Gong, Z","last_name":"Gong","first_name":"Z"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"J","last_name":"Zhang","full_name":"Zhang, J"}],"date_published":"2019-05-01T00:00:00Z","title":"Nitrate modulates the differentiation of root distal stem cells","pmid":1,"quality_controlled":"1","publication":"Plant Physiology","publication_status":"published","page":"22-25","day":"01","doi":"10.1104/pp.18.01305","publisher":"ASPB","ddc":["580"],"scopus_import":"1","external_id":{"pmid":["30787134"],"isi":["000466860800010"]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-04-09T08:46:17Z","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.18.01305"}],"year":"2019","department":[{"_id":"JiFr"}],"intvolume":"       180"},{"ec_funded":1,"intvolume":"        98","year":"2019","department":[{"_id":"JiFr"}],"project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7"}],"date_created":"2019-04-09T08:46:44Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"file_date_updated":"2020-07-14T12:47:25Z","language":[{"iso":"eng"}],"external_id":{"isi":["000473644100008"],"pmid":["30821050"]},"ddc":["580"],"scopus_import":"1","doi":"10.1111/tpj.14301","publisher":"Wiley","day":"01","publication_status":"published","page":"1048-1059","quality_controlled":"1","pmid":1,"file":[{"file_size":1383100,"date_created":"2019-04-15T09:38:43Z","file_name":"2019_PlantJournal_Rakusov.pdf","access_level":"open_access","file_id":"6304","content_type":"application/pdf","checksum":"ad3b5e270b67ba2a45f894ce3be27920","creator":"dernst","relation":"main_file","date_updated":"2020-07-14T12:47:25Z"}],"publication":"The Plant Journal","title":"Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls","date_published":"2019-06-01T00:00:00Z","author":[{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"},{"last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Valošek","full_name":"Valošek, Petr"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"article_type":"original","month":"06","abstract":[{"text":"Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and\r\nshoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-\r\nping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell\r\npolarity and plant adaptive development.","lang":"eng"}],"volume":98,"issue":"6","date_updated":"2025-04-15T07:48:04Z","has_accepted_license":"1","oa_version":"Published Version","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"journal_article","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313x"]},"article_processing_charge":"Yes (via OA deal)","citation":{"apa":"Rakusová, H., Han, H., Valošek, P., &#38; Friml, J. (2019). Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. <i>The Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.14301\">https://doi.org/10.1111/tpj.14301</a>","ama":"Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. <i>The Plant Journal</i>. 2019;98(6):1048-1059. doi:<a href=\"https://doi.org/10.1111/tpj.14301\">10.1111/tpj.14301</a>","mla":"Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” <i>The Plant Journal</i>, vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:<a href=\"https://doi.org/10.1111/tpj.14301\">10.1111/tpj.14301</a>.","ieee":"H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,” <i>The Plant Journal</i>, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019.","chicago":"Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” <i>The Plant Journal</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/tpj.14301\">https://doi.org/10.1111/tpj.14301</a>.","ista":"Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 98(6), 1048–1059.","short":"H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059."},"status":"public","_id":"6262"},{"year":"2019","department":[{"_id":"MaLo"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000468707600005"]},"date_created":"2019-04-11T20:55:01Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"file_date_updated":"2020-07-14T12:47:27Z","ddc":["570"],"day":"01","doi":"10.1016/j.matbio.2018.12.002","publisher":"Elsevier","quality_controlled":"1","file":[{"date_updated":"2020-07-14T12:47:27Z","creator":"dernst","checksum":"790878cd78bfc54a147ddcc7c8f286a0","relation":"main_file","file_name":"2018_MatrixBiology_Davies.pdf","file_id":"7825","content_type":"application/pdf","access_level":"open_access","date_created":"2020-05-14T09:02:07Z","file_size":4444339}],"publication":"Matrix Biology","publication_status":"published","page":"47-59","date_published":"2019-05-01T00:00:00Z","author":[{"last_name":"Davies","full_name":"Davies, Heather S.","first_name":"Heather S."},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S."},{"first_name":"Nouha","last_name":"El Amri","full_name":"El Amri, Nouha"},{"full_name":"Coche-Guérente, Liliane","last_name":"Coche-Guérente","first_name":"Liliane"},{"last_name":"Verdier","full_name":"Verdier, Claude","first_name":"Claude"},{"last_name":"Bureau","full_name":"Bureau, Lionel","first_name":"Lionel"},{"last_name":"Richter","full_name":"Richter, Ralf P.","first_name":"Ralf P."},{"first_name":"Delphine","last_name":"Débarre","full_name":"Débarre, Delphine"}],"title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","has_accepted_license":"1","oa_version":"Submitted Version","isi":1,"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","month":"05","volume":"78-79","abstract":[{"lang":"eng","text":"Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow."}],"date_updated":"2023-08-25T10:11:28Z","status":"public","_id":"6297","type":"journal_article","publication_identifier":{"issn":["0945-053X"]},"article_processing_charge":"No","citation":{"mla":"Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>.","ieee":"H. S. Davies <i>et al.</i>, “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” <i>Matrix Biology</i>, vol. 78–79. Elsevier, pp. 47–59, 2019.","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>","ama":"Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. 2019;78-79:47-59. doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>"}}]