[{"scopus_import":1,"day":"14","publication":"Society for Industrial and Applied Mathematics","citation":{"ista":"Akopyan A, Plakhov A. 2015. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 47(4), 2754–2769.","apa":"Akopyan, A., & Plakhov, A. (2015). Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. SIAM. https://doi.org/10.1137/140993843","ieee":"A. Akopyan and A. Plakhov, “Minimal resistance of curves under the single impact assumption,” Society for Industrial and Applied Mathematics, vol. 47, no. 4. SIAM, pp. 2754–2769, 2015.","ama":"Akopyan A, Plakhov A. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 2015;47(4):2754-2769. doi:10.1137/140993843","chicago":"Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics. SIAM, 2015. https://doi.org/10.1137/140993843.","mla":"Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics, vol. 47, no. 4, SIAM, 2015, pp. 2754–69, doi:10.1137/140993843.","short":"A. Akopyan, A. Plakhov, Society for Industrial and Applied Mathematics 47 (2015) 2754–2769."},"page":"2754 - 2769","date_published":"2015-07-14T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞."}],"issue":"4","_id":"1710","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Minimal resistance of curves under the single impact assumption","intvolume":" 47","oa_version":"Preprint","month":"07","main_file_link":[{"url":"http://arxiv.org/abs/1410.3736","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"doi":"10.1137/140993843","language":[{"iso":"eng"}],"publist_id":"5423","ec_funded":1,"year":"2015","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"SIAM","author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"full_name":"Plakhov, Alexander","last_name":"Plakhov","first_name":"Alexander"}],"date_updated":"2021-01-12T06:52:41Z","date_created":"2018-12-11T11:53:36Z","volume":47},{"quality_controlled":"1","page":"587 - 620","publication":"Discrete & Computational Geometry","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.4036"}],"citation":{"mla":"Colin De Verdière, Éric, et al. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry, vol. 53, no. 3, Springer, 2015, pp. 587–620, doi:10.1007/s00454-015-9679-9.","short":"É. Colin De Verdière, A. Hubard, A.N. de Mesmay, Discrete & Computational Geometry 53 (2015) 587–620.","chicago":"Colin De Verdière, Éric, Alfredo Hubard, and Arnaud N de Mesmay. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9679-9.","ama":"Colin De Verdière É, Hubard A, de Mesmay AN. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 2015;53(3):587-620. doi:10.1007/s00454-015-9679-9","ista":"Colin De Verdière É, Hubard A, de Mesmay AN. 2015. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 53(3), 587–620.","ieee":"É. Colin De Verdière, A. Hubard, and A. N. de Mesmay, “Discrete systolic inequalities and decompositions of triangulated surfaces,” Discrete & Computational Geometry, vol. 53, no. 3. Springer, pp. 587–620, 2015.","apa":"Colin De Verdière, É., Hubard, A., & de Mesmay, A. N. (2015). Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9679-9"},"oa":1,"language":[{"iso":"eng"}],"date_published":"2015-04-02T00:00:00Z","doi":"10.1007/s00454-015-9679-9","scopus_import":1,"month":"04","day":"02","publication_status":"published","status":"public","title":"Discrete systolic inequalities and decompositions of triangulated surfaces","department":[{"_id":"UlWa"}],"intvolume":" 53","publisher":"Springer","_id":"1730","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:53:42Z","date_updated":"2021-01-12T06:52:49Z","oa_version":"Preprint","volume":53,"author":[{"first_name":"Éric","last_name":"Colin De Verdière","full_name":"Colin De Verdière, Éric"},{"full_name":"Hubard, Alfredo","last_name":"Hubard","first_name":"Alfredo"},{"id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","last_name":"De Mesmay","first_name":"Arnaud N","full_name":"De Mesmay, Arnaud N"}],"type":"journal_article","abstract":[{"text":"How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations.","lang":"eng"}],"issue":"3","publist_id":"5397"},{"abstract":[{"text":"In the vertebrate neural tube, the morphogen Sonic Hedgehog (Shh) establishes a characteristic pattern of gene expression. Here we quantify the Shh gradient in the developing mouse neural tube and show that while the amplitude of the gradient increases over time, the activity of the pathway transcriptional effectors, Gli proteins, initially increases but later decreases. Computational analysis of the pathway suggests three mechanisms that could contribute to this adaptation: transcriptional upregulation of the inhibitory receptor Ptch1, transcriptional downregulation of Gli and the differential stability of active and inactive Gli isoforms. Consistent with this, Gli2 protein expression is downregulated during neural tube patterning and adaptation continues when the pathway is stimulated downstream of Ptch1. Moreover, the Shh-induced upregulation of Gli2 transcription prevents Gli activity levels from adapting in a different cell type, NIH3T3 fibroblasts, despite the upregulation of Ptch1. Multiple mechanisms therefore contribute to the intracellular dynamics of Shh signalling, resulting in different signalling dynamics in different cell types.","lang":"eng"}],"publist_id":"5399","extern":1,"type":"journal_article","author":[{"full_name":"Cohen, Michael H","last_name":"Cohen","first_name":"Michael"},{"full_name":"Anna Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna"},{"full_name":"Ribeiro, Ana C","first_name":"Ana","last_name":"Ribeiro"},{"full_name":"Blassberg, Robert A","last_name":"Blassberg","first_name":"Robert"},{"full_name":"Page, Karen M","last_name":"Page","first_name":"Karen"},{"first_name":"Chris","last_name":"Barnes","full_name":"Barnes, Chris P"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"}],"date_created":"2018-12-11T11:53:42Z","date_updated":"2021-01-12T06:52:48Z","volume":6,"acknowledgement":"C.P.B. gratefully acknowledges funding from the Wellcome Trust through a Research Career Development Fellowship (097319/Z/11/Z). This work was supported by the Medical Research Council (U117560541) and Wellcome Trust (WT098326MA, WT098325MA).","_id":"1728","year":"2015","title":"Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms","status":"public","publication_status":"published","publisher":"Nature Publishing Group","intvolume":" 6","month":"04","day":"02","doi":"10.1038/ncomms7709","date_published":"2015-04-02T00:00:00Z","publication":"Nature Communications","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"mla":"Cohen, Michael, et al. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” Nature Communications, vol. 6, Nature Publishing Group, 2015, doi:10.1038/ncomms7709.","short":"M. Cohen, A. Kicheva, A. Ribeiro, R. Blassberg, K. Page, C. Barnes, J. Briscoe, Nature Communications 6 (2015).","chicago":"Cohen, Michael, Anna Kicheva, Ana Ribeiro, Robert Blassberg, Karen Page, Chris Barnes, and James Briscoe. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7709.","ama":"Cohen M, Kicheva A, Ribeiro A, et al. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. 2015;6. doi:10.1038/ncomms7709","ista":"Cohen M, Kicheva A, Ribeiro A, Blassberg R, Page K, Barnes C, Briscoe J. 2015. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. 6.","ieee":"M. Cohen et al., “Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Cohen, M., Kicheva, A., Ribeiro, A., Blassberg, R., Page, K., Barnes, C., & Briscoe, J. (2015). Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7709"},"quality_controlled":0},{"intvolume":" 34","status":"public","ddc":["000"],"title":"A dimension-reduced pressure solver for liquid simulations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1735","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2016-607-v1+1_coarsegrid.pdf","file_size":6312352,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5218","checksum":"590752bf977855b337a80f78a9bc2404","date_created":"2018-12-12T10:16:30Z","date_updated":"2020-07-14T12:45:15Z"}],"pubrep_id":"607","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations."}],"page":"473 - 480","citation":{"ama":"Ando R, Thürey N, Wojtan C. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 2015;34(2):473-480. doi:10.1111/cgf.12576","ista":"Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480.","apa":"Ando, R., Thürey, N., & Wojtan, C. (2015). A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12576","ieee":"R. Ando, N. Thürey, and C. Wojtan, “A dimension-reduced pressure solver for liquid simulations,” Computer Graphics Forum, vol. 34, no. 2. Wiley, pp. 473–480, 2015.","mla":"Ando, Ryoichi, et al. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum, vol. 34, no. 2, Wiley, 2015, pp. 473–80, doi:10.1111/cgf.12576.","short":"R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 473–480.","chicago":"Ando, Ryoichi, Nils Thürey, and Chris Wojtan. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum. Wiley, 2015. https://doi.org/10.1111/cgf.12576."},"publication":"Computer Graphics Forum","date_published":"2015-05-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","department":[{"_id":"ChWo"}],"publisher":"Wiley","publication_status":"published","year":"2015","acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad","volume":34,"date_created":"2018-12-11T11:53:44Z","date_updated":"2023-02-23T10:12:11Z","author":[{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"},{"last_name":"Thürey","first_name":"Nils","full_name":"Thürey, Nils"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"publist_id":"5389","file_date_updated":"2020-07-14T12:45:15Z","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/cgf.12576","month":"05"},{"publist_id":"5391","issue":"2","abstract":[{"lang":"eng","text":"Facial appearance capture is now firmly established within academic research and used extensively across various application domains, perhaps most prominently in the entertainment industry through the design of virtual characters in video games and films. While significant progress has occurred over the last two decades, no single survey currently exists that discusses the similarities, differences, and practical considerations of the available appearance capture techniques as applied to human faces. A central difficulty of facial appearance capture is the way light interacts with skin-which has a complex multi-layered structure-and the interactions that occur below the skin surface can, by definition, only be observed indirectly. In this report, we distinguish between two broad strategies for dealing with this complexity. "Image-based methods" try to exhaustively capture the exact face appearance under different lighting and viewing conditions, and then render the face through weighted image combinations. "Parametric methods" instead fit the captured reflectance data to some parametric appearance model used during rendering, allowing for a more lightweight and flexible representation but at the cost of potentially increased rendering complexity or inexact reproduction. The goal of this report is to provide an overview that can guide practitioners and researchers in assessing the tradeoffs between current approaches and identifying directions for future advances in facial appearance capture."}],"type":"journal_article","volume":34,"oa_version":"None","date_created":"2018-12-11T11:53:43Z","date_updated":"2021-01-12T06:52:52Z","author":[{"full_name":"Klehm, Oliver","last_name":"Klehm","first_name":"Oliver"},{"last_name":"Rousselle","first_name":"Fabrice","full_name":"Rousselle, Fabrice"},{"full_name":"Papas, Marios","last_name":"Papas","first_name":"Marios"},{"first_name":"Derek","last_name":"Bradley","full_name":"Bradley, Derek"},{"last_name":"Hery","first_name":"Christophe","full_name":"Hery, Christophe"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"full_name":"Jarosz, Wojciech","first_name":"Wojciech","last_name":"Jarosz"},{"first_name":"Thabo","last_name":"Beeler","full_name":"Beeler, Thabo"}],"publisher":"Wiley-Blackwell","intvolume":" 34","department":[{"_id":"BeBi"}],"title":"Recent advances in facial appearance capture","publication_status":"published","status":"public","_id":"1734","year":"2015","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","month":"05","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2015-05-01T00:00:00Z","doi":"10.1111/cgf.12594","page":"709 - 733","quality_controlled":"1","main_file_link":[{"url":"https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf"}],"citation":{"short":"O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz, T. Beeler, Computer Graphics Forum 34 (2015) 709–733.","mla":"Klehm, Oliver, et al. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum, vol. 34, no. 2, Wiley-Blackwell, 2015, pp. 709–33, doi:10.1111/cgf.12594.","chicago":"Klehm, Oliver, Fabrice Rousselle, Marios Papas, Derek Bradley, Christophe Hery, Bernd Bickel, Wojciech Jarosz, and Thabo Beeler. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum. Wiley-Blackwell, 2015. https://doi.org/10.1111/cgf.12594.","ama":"Klehm O, Rousselle F, Papas M, et al. Recent advances in facial appearance capture. Computer Graphics Forum. 2015;34(2):709-733. doi:10.1111/cgf.12594","ieee":"O. Klehm et al., “Recent advances in facial appearance capture,” Computer Graphics Forum, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015.","apa":"Klehm, O., Rousselle, F., Papas, M., Bradley, D., Hery, C., Bickel, B., … Beeler, T. (2015). Recent advances in facial appearance capture. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12594","ista":"Klehm O, Rousselle F, Papas M, Bradley D, Hery C, Bickel B, Jarosz W, Beeler T. 2015. Recent advances in facial appearance capture. Computer Graphics Forum. 34(2), 709–733."},"publication":"Computer Graphics Forum"},{"page":"753 - 760","citation":{"ista":"Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760.","ieee":"A. Kuechler et al., “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” European Journal of Human Genetics, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015.","apa":"Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. Nature Publishing Group. https://doi.org/10.1038/ejhg.2014.165","ama":"Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 2015;23(6):753-760. doi:10.1038/ejhg.2014.165","chicago":"Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics. Nature Publishing Group, 2015. https://doi.org/10.1038/ejhg.2014.165.","mla":"Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:10.1038/ejhg.2014.165.","short":"A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760."},"publication":"European Journal of Human Genetics","date_published":"2015-06-15T00:00:00Z","day":"15","intvolume":" 23","title":"Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome","status":"public","_id":"1789","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID."}],"quality_controlled":"1","oa":1,"external_id":{"pmid":["25138099"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1038/ejhg.2014.165","month":"06","department":[{"_id":"GaNo"}],"publisher":"Nature Publishing Group","publication_status":"published","pmid":1,"year":"2015","volume":23,"date_updated":"2021-01-12T06:53:12Z","date_created":"2018-12-11T11:54:01Z","author":[{"full_name":"Kuechler, Alma","first_name":"Alma","last_name":"Kuechler"},{"first_name":"Alexander","last_name":"Zink","full_name":"Zink, Alexander"},{"full_name":"Wieland, Thomas","first_name":"Thomas","last_name":"Wieland"},{"full_name":"Lüdecke, Hermann","last_name":"Lüdecke","first_name":"Hermann"},{"last_name":"Cremer","first_name":"Kirsten","full_name":"Cremer, Kirsten"},{"first_name":"Leonardo","last_name":"Salviati","full_name":"Salviati, Leonardo"},{"full_name":"Magini, Pamela","first_name":"Pamela","last_name":"Magini"},{"last_name":"Najafi","first_name":"Kimia","full_name":"Najafi, Kimia"},{"full_name":"Zweier, Christiane","last_name":"Zweier","first_name":"Christiane"},{"full_name":"Czeschik, Johanna","first_name":"Johanna","last_name":"Czeschik"},{"first_name":"Stefan","last_name":"Aretz","full_name":"Aretz, Stefan"},{"full_name":"Endele, Sabine","first_name":"Sabine","last_name":"Endele"},{"full_name":"Tamburrino, Federica","first_name":"Federica","last_name":"Tamburrino"},{"last_name":"Pinato","first_name":"Claudia","full_name":"Pinato, Claudia"},{"first_name":"Maurizio","last_name":"Clementi","full_name":"Clementi, Maurizio"},{"full_name":"Gundlach, Jasmin","last_name":"Gundlach","first_name":"Jasmin"},{"last_name":"Maylahn","first_name":"Carina","full_name":"Maylahn, Carina"},{"full_name":"Mazzanti, Laura","first_name":"Laura","last_name":"Mazzanti"},{"full_name":"Wohlleber, Eva","first_name":"Eva","last_name":"Wohlleber"},{"last_name":"Schwarzmayr","first_name":"Thomas","full_name":"Schwarzmayr, Thomas"},{"last_name":"Kariminejad","first_name":"Roxana","full_name":"Kariminejad, Roxana"},{"last_name":"Schlessinger","first_name":"Avner","full_name":"Schlessinger, Avner"},{"first_name":"Dagmar","last_name":"Wieczorek","full_name":"Wieczorek, Dagmar"},{"full_name":"Strom, Tim","last_name":"Strom","first_name":"Tim"},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Engels, Hartmut","first_name":"Hartmut","last_name":"Engels"}],"publist_id":"5324"},{"type":"journal_article","publist_id":"5325","issue":"3","abstract":[{"lang":"eng","text":"We fabricate and characterize a microscale silicon opto-electromechanical system whose mechanical motion is coupled capacitively to an electrical circuit and optically via radiation pressure to a photonic crystal cavity. To achieve large electromechanical interaction strength, we implement an inverse shadow mask fabrication scheme which obtains capacitor gaps as small as 30 nm while maintaining a silicon surface quality necessary for minimizing optical loss. Using the sensitive optical read-out of the photonic crystal cavity, we characterize the linear and nonlinear capacitive coupling to the fundamental ωm=2π = 63 MHz in-plane flexural motion of the structure, showing that the large electromechanical coupling in such devices may be suitable for realizing efficient microwave-to-optical signal conversion."}],"extern":1,"year":"2015","_id":"1788","acknowledgement":"This work was supported by the DARPA MESO program, the AFOSR Hybrid Nanophotonics MURI, the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. AP gratefully acknowledge funding from EU through Marie Curie Actions, project NEMO (GA 298861). AT acknowledges partial financial support from the ERC through the advanced grant SoulMan","publisher":"Optical Society of America","intvolume":" 23","status":"public","title":"Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity","publication_status":"published","author":[{"full_name":"Pitanti, Alessandro","first_name":"Alessandro","last_name":"Pitanti"},{"full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"},{"last_name":"Safavi Naeini","first_name":"Amir","full_name":"Safavi-Naeini, Amir H"},{"first_name":"Jeff","last_name":"Hill","full_name":"Hill, Jeff T"},{"full_name":"Lei, Chan U","first_name":"Chan","last_name":"Lei"},{"last_name":"Tredicucci","first_name":"Alessandro","full_name":"Tredicucci, Alessandro"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar J"}],"volume":23,"date_created":"2018-12-11T11:54:01Z","date_updated":"2021-01-12T06:53:12Z","day":"09","month":"02","citation":{"chicago":"Pitanti, Alessandro, Johannes M Fink, Amir Safavi Naeini, Jeff Hill, Chan Lei, Alessandro Tredicucci, and Oskar Painter. “Strong Opto-Electro-Mechanical Coupling in a Silicon Photonic Crystal Cavity.” Optics Express. Optical Society of America, 2015. https://doi.org/10.1364/OE.23.003196.","mla":"Pitanti, Alessandro, et al. “Strong Opto-Electro-Mechanical Coupling in a Silicon Photonic Crystal Cavity.” Optics Express, vol. 23, no. 3, Optical Society of America, 2015, pp. 3196–208, doi:10.1364/OE.23.003196.","short":"A. Pitanti, J.M. Fink, A. Safavi Naeini, J. Hill, C. Lei, A. Tredicucci, O. Painter, Optics Express 23 (2015) 3196–3208.","ista":"Pitanti A, Fink JM, Safavi Naeini A, Hill J, Lei C, Tredicucci A, Painter O. 2015. Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity. Optics Express. 23(3), 3196–3208.","ieee":"A. Pitanti et al., “Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity,” Optics Express, vol. 23, no. 3. Optical Society of America, pp. 3196–3208, 2015.","apa":"Pitanti, A., Fink, J. M., Safavi Naeini, A., Hill, J., Lei, C., Tredicucci, A., & Painter, O. (2015). Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity. Optics Express. Optical Society of America. https://doi.org/10.1364/OE.23.003196","ama":"Pitanti A, Fink JM, Safavi Naeini A, et al. Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity. Optics Express. 2015;23(3):3196-3208. doi:10.1364/OE.23.003196"},"publication":"Optics Express","page":"3196 - 3208","quality_controlled":0,"doi":"10.1364/OE.23.003196","date_published":"2015-02-09T00:00:00Z"},{"month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1038/srep10781","language":[{"iso":"eng"}],"article_number":"10781","publist_id":"5306","file_date_updated":"2020-07-14T12:45:16Z","year":"2015","department":[{"_id":"BjHo"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","first_name":"Sebastian","last_name":"Altmeyer","full_name":"Altmeyer, Sebastian"},{"full_name":"Do, Younghae","last_name":"Do","first_name":"Younghae"},{"last_name":"Lai","first_name":"Ying","full_name":"Lai, Ying"}],"volume":5,"date_created":"2018-12-11T11:54:06Z","date_updated":"2021-01-12T06:53:18Z","scopus_import":1,"has_accepted_license":"1","day":"12","citation":{"chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep10781.","mla":"Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports, vol. 5, 10781, Nature Publishing Group, 2015, doi:10.1038/srep10781.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","ista":"Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781.","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep10781","ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 2015;5. doi:10.1038/srep10781"},"publication":"Scientific Reports","date_published":"2015-06-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control."}],"_id":"1804","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","status":"public","ddc":["530"],"title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","pubrep_id":"450","oa_version":"Published Version","file":[{"checksum":"7716f582f8c9d82d8f2bf80bf896b440","date_created":"2018-12-12T10:17:26Z","date_updated":"2020-07-14T12:45:16Z","file_id":"5280","relation":"main_file","creator":"system","file_size":2449723,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-450-v1+1_srep10781.pdf"}]},{"month":"06","day":"09","date_published":"2015-06-09T00:00:00Z","doi":"10.1073/pnas.1415845112","quality_controlled":0,"page":"7291 - 7296","publication":"PNAS","citation":{"ama":"Rei D, Mason X, Seo J, et al. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. PNAS. 2015;112(23):7291-7296. doi:10.1073/pnas.1415845112","apa":"Rei, D., Mason, X., Seo, J., Gräff, J., Rudenko, A., Wang, J., … Tsai, L. (2015). Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1415845112","ieee":"D. Rei et al., “Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway,” PNAS, vol. 112, no. 23. National Academy of Sciences, pp. 7291–7296, 2015.","ista":"Rei D, Mason X, Seo J, Gräff J, Rudenko A, Wang J, Rueda R, Siegert S, Cho S, Canter R, Mungenast A, Deisseroth K, Tsai L. 2015. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. PNAS. 112(23), 7291–7296.","short":"D. Rei, X. Mason, J. Seo, J. Gräff, A. Rudenko, J. Wang, R. Rueda, S. Siegert, S. Cho, R. Canter, A. Mungenast, K. Deisseroth, L. Tsai, PNAS 112 (2015) 7291–7296.","mla":"Rei, Damien, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” PNAS, vol. 112, no. 23, National Academy of Sciences, 2015, pp. 7291–96, doi:10.1073/pnas.1415845112.","chicago":"Rei, Damien, Xenos Mason, Jinsoo Seo, Johannes Gräff, Andrii Rudenko, Jùn Wang, Richard Rueda, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1415845112."},"extern":1,"abstract":[{"text":"Repeated stress has been suggested to underlie learning and memory deficits via the basolateral amygdala (BLA) and the hippocampus; however, the functional contribution of BLA inputs to the hippocampus and their molecular repercussions are not well understood. Here we show that repeated stress is accompanied by generation of the Cdk5 (cyclin-dependent kinase 5)-activator p25, up-regulation and phosphorylation of glucocorticoid receptors, increased HDAC2 expression, and reduced expression of memoryrelated genes in the hippocampus. A combination of optogenetic and pharmacosynthetic approaches shows that BLA activation is both necessary and sufficient for stress-associated molecular changes and memory impairments. Furthermore, we show that this effect relies on direct glutamatergic projections from the BLA to the dorsal hippocampus. Finally, we show that p25 generation is necessary for the stress-induced memory dysfunction. Taken together, our data provide a neural circuit model for stress-induced hippocampal memory deficits through BLA activity-dependent p25 generation.","lang":"eng"}],"issue":"23","publist_id":"5307","type":"journal_article","date_created":"2018-12-11T11:54:06Z","date_updated":"2021-01-12T06:53:18Z","volume":112,"author":[{"full_name":"Rei, Damien","last_name":"Rei","first_name":"Damien"},{"last_name":"Mason","first_name":"Xenos","full_name":"Mason, Xenos"},{"last_name":"Seo","first_name":"Jinsoo","full_name":"Seo, Jinsoo"},{"last_name":"Gräff","first_name":"Johannes","full_name":"Gräff, Johannes"},{"last_name":"Rudenko","first_name":"Andrii","full_name":"Rudenko, Andrii"},{"full_name":"Wang, Jùn","last_name":"Wang","first_name":"Jùn"},{"full_name":"Rueda, Richard","first_name":"Richard","last_name":"Rueda"},{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra","full_name":"Sandra Siegert"},{"full_name":"Cho, Sukhee","first_name":"Sukhee","last_name":"Cho"},{"full_name":"Canter, Rebecca G","first_name":"Rebecca","last_name":"Canter"},{"last_name":"Mungenast","first_name":"Alison","full_name":"Mungenast, Alison E"},{"full_name":"Deisseroth, Karl A","first_name":"Karl","last_name":"Deisseroth"},{"full_name":"Tsai, Lihuei","first_name":"Lihuei","last_name":"Tsai"}],"publication_status":"published","title":"Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway","status":"public","intvolume":" 112","publisher":"National Academy of Sciences","_id":"1803","acknowledgement":"AG047661; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nNS051874; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nSNSF; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung","year":"2015"},{"scopus_import":1,"month":"05","day":"01","quality_controlled":"1","page":"603 - 624","publication":"ESAIM - Control, Optimisation and Calculus of Variations","citation":{"short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624.","mla":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and Calculus of Variations, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:10.1051/cocv/2014040.","chicago":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and Calculus of Variations. EDP Sciences, 2015. https://doi.org/10.1051/cocv/2014040.","ama":"Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 2015;21(3):603-624. doi:10.1051/cocv/2014040","apa":"Goldman, M., & Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. EDP Sciences. https://doi.org/10.1051/cocv/2014040","ieee":"M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” ESAIM - Control, Optimisation and Calculus of Variations, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.","ista":"Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.1727"}],"oa":1,"language":[{"iso":"eng"}],"date_published":"2015-05-01T00:00:00Z","doi":"10.1051/cocv/2014040","type":"journal_article","abstract":[{"text":"We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential.","lang":"eng"}],"publist_id":"5303","issue":"3","status":"public","title":"Sharp interface limit for two components Bose-Einstein condensates","publication_status":"published","intvolume":" 21","department":[{"_id":"RoSe"}],"publisher":"EDP Sciences","_id":"1807","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","date_updated":"2021-01-12T06:53:20Z","date_created":"2018-12-11T11:54:07Z","volume":21,"oa_version":"Preprint","author":[{"full_name":"Goldman, Michael","first_name":"Michael","last_name":"Goldman"},{"full_name":"Royo-Letelier, Jimena","last_name":"Royo-Letelier","first_name":"Jimena","id":"4D3BED28-F248-11E8-B48F-1D18A9856A87"}]},{"author":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert","full_name":"Sandra Siegert"},{"last_name":"Seo","first_name":"Jinsoo","full_name":"Seo, Jinsoo"},{"first_name":"Ester","last_name":"Kwon","full_name":"Kwon, Ester J"},{"full_name":"Rudenko, Andrii","first_name":"Andrii","last_name":"Rudenko"},{"full_name":"Cho, Sukhee","first_name":"Sukhee","last_name":"Cho"},{"last_name":"Wang","first_name":"Wenyuan","full_name":"Wang, Wenyuan"},{"last_name":"Flood","first_name":"Zachary","full_name":"Flood, Zachary C"},{"full_name":"Martorell, Anthony J","first_name":"Anthony","last_name":"Martorell"},{"full_name":"Ericsson, Maria","last_name":"Ericsson","first_name":"Maria"},{"last_name":"Mungenast","first_name":"Alison","full_name":"Mungenast, Alison E"},{"last_name":"Tsai","first_name":"Lihuei","full_name":"Tsai, Lihuei"}],"volume":18,"date_created":"2018-12-11T11:54:05Z","date_updated":"2021-01-12T06:53:18Z","_id":"1802","year":"2015","acknowledgement":"S.S. was supported by a Human Frontier Science Program (HFSP) long-term postdoctoral fellowship and a Swiss National Science Foundation fellowship for prospective researchers. E.J.K. was supported by a Simons Foundation Postdoctoral Fellowship. A.R. was supported by a NARSAD Young Investigator Award. This work was supported by a Seed Grant from the Simons Center for the Social Brain and US National Institutes of Health grant RO1 MH 091115 to L.-H.T.","intvolume":" 18","publisher":"Nature Publishing Group","status":"public","publication_status":"published","title":"The schizophrenia risk gene product miR-137 alters presynaptic plasticity","publist_id":"5308","abstract":[{"text":"Noncoding variants in the human MIR137 gene locus increase schizophrenia risk with genome-wide significance. However, the functional consequence of these risk alleles is unknown. Here we examined induced human neurons harboring the minor alleles of four disease-associated single nucleotide polymorphisms in MIR137. We observed increased MIR137 levels compared to those in major allele–carrying cells. microRNA-137 gain of function caused downregulation of the presynaptic target genes complexin-1 (Cplx1), Nsf and synaptotagmin-1 (Syt1), leading to impaired vesicle release. In vivo, miR-137 gain of function resulted in changes in synaptic vesicle pool distribution, impaired induction of mossy fiber long-term potentiation and deficits in hippocampus-dependent learning and memory. By sequestering endogenous miR-137, we were able to ameliorate the synaptic phenotypes. Moreover, reinstatement of Syt1 expression partially restored synaptic plasticity, demonstrating the importance of Syt1 as a miR-137 target. Our data provide new insight into the mechanism by which miR-137 dysregulation can impair synaptic plasticity in the hippocampus.","lang":"eng"}],"extern":1,"type":"journal_article","doi":"10.1038/nn.4023","date_published":"2015-07-01T00:00:00Z","citation":{"chicago":"Siegert, Sandra, Jinsoo Seo, Ester Kwon, Andrii Rudenko, Sukhee Cho, Wenyuan Wang, Zachary Flood, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters Presynaptic Plasticity.” Nature Neuroscience. Nature Publishing Group, 2015. https://doi.org/10.1038/nn.4023.","mla":"Siegert, Sandra, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters Presynaptic Plasticity.” Nature Neuroscience, vol. 18, Nature Publishing Group, 2015, pp. 1008–16, doi:10.1038/nn.4023.","short":"S. Siegert, J. Seo, E. Kwon, A. Rudenko, S. Cho, W. Wang, Z. Flood, A. Martorell, M. Ericsson, A. Mungenast, L. Tsai, Nature Neuroscience 18 (2015) 1008–1016.","ista":"Siegert S, Seo J, Kwon E, Rudenko A, Cho S, Wang W, Flood Z, Martorell A, Ericsson M, Mungenast A, Tsai L. 2015. The schizophrenia risk gene product miR-137 alters presynaptic plasticity. Nature Neuroscience. 18, 1008–1016.","ieee":"S. Siegert et al., “The schizophrenia risk gene product miR-137 alters presynaptic plasticity,” Nature Neuroscience, vol. 18. Nature Publishing Group, pp. 1008–1016, 2015.","apa":"Siegert, S., Seo, J., Kwon, E., Rudenko, A., Cho, S., Wang, W., … Tsai, L. (2015). The schizophrenia risk gene product miR-137 alters presynaptic plasticity. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.4023","ama":"Siegert S, Seo J, Kwon E, et al. The schizophrenia risk gene product miR-137 alters presynaptic plasticity. Nature Neuroscience. 2015;18:1008-1016. doi:10.1038/nn.4023"},"publication":"Nature Neuroscience","page":"1008 - 1016","quality_controlled":0,"month":"07","day":"01"},{"year":"2015","publication_status":"published","department":[{"_id":"ToBo"}],"publisher":"Elsevier","author":[{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"date_updated":"2021-01-12T06:53:21Z","date_created":"2018-12-11T11:54:08Z","volume":27,"file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5298","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"doi":"10.1016/j.mib.2015.05.008","language":[{"iso":"eng"}],"month":"06","_id":"1810","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","ddc":["570"],"status":"public","intvolume":" 27","pubrep_id":"493","file":[{"file_id":"5277","relation":"main_file","date_created":"2018-12-12T10:17:23Z","date_updated":"2020-07-14T12:45:17Z","checksum":"1683bb0f42ef892a5b3b71a050d65d25","file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1047255}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.","lang":"eng"}],"publication":"Current Opinion in Microbiology","citation":{"apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. Elsevier. https://doi.org/10.1016/j.mib.2015.05.008","ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” Current Opinion in Microbiology, vol. 27. Elsevier, pp. 1–9, 2015.","ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9.","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 2015;27:1-9. doi:10.1016/j.mib.2015.05.008","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology. Elsevier, 2015. https://doi.org/10.1016/j.mib.2015.05.008.","short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9.","mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology, vol. 27, Elsevier, 2015, pp. 1–9, doi:10.1016/j.mib.2015.05.008."},"page":"1 - 9","date_published":"2015-06-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1"},{"month":"04","doi":"10.1088/1367-2630/17/4/045005","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5294","article_number":"045005","author":[{"last_name":"Lahrz","first_name":"Martin","full_name":"Lahrz, Martin"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"full_name":"Mathey, Ludwig","last_name":"Mathey","first_name":"Ludwig"}],"date_created":"2018-12-11T11:54:09Z","date_updated":"2021-01-12T06:53:22Z","volume":17,"year":"2015","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"IOP Publishing Ltd.","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"date_published":"2015-04-01T00:00:00Z","publication":"New Journal of Physics","citation":{"ama":"Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 2015;17(4). doi:10.1088/1367-2630/17/4/045005","apa":"Lahrz, M., Lemeshko, M., & Mathey, L. (2015). Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/4/045005","ieee":"M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar Bose–Einstein condensates ,” New Journal of Physics, vol. 17, no. 4. IOP Publishing Ltd., 2015.","ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005.","short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","mla":"Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” New Journal of Physics, vol. 17, no. 4, 045005, IOP Publishing Ltd., 2015, doi:10.1088/1367-2630/17/4/045005.","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” New Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/4/045005."},"abstract":[{"text":"We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.\r\n","lang":"eng"}],"issue":"4","type":"journal_article","pubrep_id":"446","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5184","checksum":"551f751a75b39b89a1db2f7f498f9a49","date_created":"2018-12-12T10:15:59Z","date_updated":"2020-07-14T12:45:17Z","access_level":"open_access","file_name":"IST-2016-446-v1+1_document.pdf","file_size":1900925,"content_type":"application/pdf","creator":"system"}],"_id":"1812","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","status":"public","intvolume":" 17"},{"day":"20","scopus_import":1,"date_published":"2015-05-20T00:00:00Z","publication":"Journal of Mathematical Physics","citation":{"ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105.","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., & Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4921227","ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” Journal of Mathematical Physics, vol. 56, no. 5. American Institute of Physics, 2015.","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 2015;56(5). doi:10.1063/1.4921227","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4921227.","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:10.1063/1.4921227.","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015)."},"abstract":[{"text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.","lang":"eng"}],"issue":"5","type":"journal_article","oa_version":"Preprint","status":"public","title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","intvolume":" 56","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1811","month":"05","language":[{"iso":"eng"}],"doi":"10.1063/1.4921227","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"main_file_link":[{"url":"http://arxiv.org/abs/1409.0110","open_access":"1"}],"oa":1,"publist_id":"5295","ec_funded":1,"article_number":"052105","date_created":"2018-12-11T11:54:08Z","date_updated":"2021-01-12T06:53:21Z","volume":56,"author":[{"last_name":"Safari","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh"},{"full_name":"Santos, José","first_name":"José","last_name":"Santos"},{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"first_name":"Kari","last_name":"Jänkälä","full_name":"Jänkälä, Kari"},{"full_name":"Fratini, Filippo","first_name":"Filippo","last_name":"Fratini"}],"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Institute of Physics","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","year":"2015"},{"quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1502.03447","open_access":"1"}],"oa":1,"citation":{"chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.203001.","short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” Physical Review Letters, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.203001.","apa":"Schmidt, R., & Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.203001","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” Physical Review Letters, vol. 114, no. 20. American Physical Society, 2015.","ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001.","ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 2015;114(20). doi:10.1103/PhysRevLett.114.203001"},"publication":"Physical Review Letters","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.114.203001","date_published":"2015-05-18T00:00:00Z","scopus_import":1,"month":"05","day":"18","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","intvolume":" 114","status":"public","publication_status":"published","title":"Rotation of quantum impurities in the presence of a many-body environment","_id":"1813","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","oa_version":"Preprint","volume":114,"date_created":"2018-12-11T11:54:09Z","date_updated":"2021-01-12T06:53:22Z","author":[{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"type":"journal_article","article_number":"203001","issue":"20","publist_id":"5293","abstract":[{"text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.","lang":"eng"}]},{"day":"01","month":"05","date_published":"2015-05-01T00:00:00Z","doi":"10.1145/2745799","language":[{"iso":"eng"}],"publication":"ACM Transactions on Modeling and Computer Simulation","citation":{"short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 7, ACM, 2015, doi:10.1145/2745799.","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2745799.","ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2745799","ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.","apa":"Gupta, A., & Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2745799","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7."},"quality_controlled":"1","issue":"2","publist_id":"5302","article_number":"7","type":"journal_article","author":[{"last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"date_updated":"2021-01-12T06:53:20Z","date_created":"2018-12-11T11:54:07Z","oa_version":"None","volume":25,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1808","year":"2015","title":"Guest editors' introduction to special issue on computational methods in systems biology","status":"public","publication_status":"published","intvolume":" 25","department":[{"_id":"ToHe"}],"publisher":"ACM"},{"author":[{"full_name":"Porazinski, Sean","last_name":"Porazinski","first_name":"Sean"},{"full_name":"Wang, Huijia","last_name":"Wang","first_name":"Huijia"},{"full_name":"Asaoka, Yoichi","first_name":"Yoichi","last_name":"Asaoka"},{"full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Behrndt"},{"full_name":"Miyamoto, Tatsuo","first_name":"Tatsuo","last_name":"Miyamoto"},{"full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita","first_name":"Hitoshi"},{"full_name":"Hata, Shoji","last_name":"Hata","first_name":"Shoji"},{"full_name":"Sasaki, Takashi","last_name":"Sasaki","first_name":"Takashi"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens"},{"last_name":"Osada","first_name":"Yumi","full_name":"Osada, Yumi"},{"last_name":"Asaka","first_name":"Satoshi","full_name":"Asaka, Satoshi"},{"last_name":"Momoi","first_name":"Akihiro","full_name":"Momoi, Akihiro"},{"first_name":"Sarah","last_name":"Linton","full_name":"Linton, Sarah"},{"full_name":"Miesfeld, Joel","last_name":"Miesfeld","first_name":"Joel"},{"first_name":"Brian","last_name":"Link","full_name":"Link, Brian"},{"first_name":"Takeshi","last_name":"Senga","full_name":"Senga, Takeshi"},{"full_name":"Castillo Morales, Atahualpa","first_name":"Atahualpa","last_name":"Castillo Morales"},{"first_name":"Araxi","last_name":"Urrutia","full_name":"Urrutia, Araxi"},{"last_name":"Shimizu","first_name":"Nobuyoshi","full_name":"Shimizu, Nobuyoshi"},{"last_name":"Nagase","first_name":"Hideaki","full_name":"Nagase, Hideaki"},{"full_name":"Matsuura, Shinya","first_name":"Shinya","last_name":"Matsuura"},{"full_name":"Bagby, Stefan","last_name":"Bagby","first_name":"Stefan"},{"full_name":"Kondoh, Hisato","last_name":"Kondoh","first_name":"Hisato"},{"last_name":"Nishina","first_name":"Hiroshi","full_name":"Nishina, Hiroshi"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Furutani Seiki, Makoto","last_name":"Furutani Seiki","first_name":"Makoto"}],"date_created":"2018-12-11T11:54:10Z","date_updated":"2021-01-12T06:53:23Z","volume":521,"year":"2015","pmid":1,"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"CaHe"}],"publist_id":"5289","doi":"10.1038/nature14215","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"external_id":{"pmid":["25778702"]},"oa":1,"quality_controlled":"1","month":"03","oa_version":"Submitted Version","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","_id":"1817","status":"public","title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","intvolume":" 521","abstract":[{"text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. ","lang":"eng"}],"issue":"7551","type":"journal_article","date_published":"2015-03-16T00:00:00Z","publication":"Nature","citation":{"short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:10.1038/nature14215.","chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature14215.","ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 2015;521(7551):217-221. doi:10.1038/nature14215","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. Nature Publishing Group. https://doi.org/10.1038/nature14215","ieee":"S. Porazinski et al., “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” Nature, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221."},"page":"217 - 221","day":"16","scopus_import":1},{"day":"01","scopus_import":1,"date_published":"2015-06-01T00:00:00Z","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","citation":{"ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . Vol 5. AAAI Press; 2015:3496-3502.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , vol. 5, AAAI Press, 2015, pp. 3496–502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , 5:3496–3502. AAAI Press, 2015."},"page":"3496-3502","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples."}],"type":"conference","alternative_title":["Artifical Intelligence"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1820","title":"Optimal cost almost-sure reachability in POMDPs","status":"public","intvolume":" 5","month":"06","conference":{"end_date":"2015-01-30","start_date":"2015-01-25","location":"Austin, TX, USA","name":"IAAI: Innovative Applications of Artificial Intelligence"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1411.3880"]},"main_file_link":[{"url":"http://arxiv.org/abs/1411.3880","open_access":"1"}],"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"ec_funded":1,"publist_id":"5286","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"first_name":"Raghav","last_name":"Gupta","full_name":"Gupta, Raghav"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"}],"related_material":{"record":[{"id":"1529","relation":"later_version","status":"public"}]},"date_created":"2018-12-11T11:54:11Z","date_updated":"2023-02-23T10:02:57Z","volume":5,"year":"2015","acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"AAAI Press"},{"year":"2015","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","author":[{"last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"date_created":"2018-12-11T11:54:09Z","date_updated":"2023-02-23T10:15:40Z","volume":34,"article_number":"27","file_date_updated":"2020-07-14T12:45:17Z","ec_funded":1,"publist_id":"5292","oa":1,"quality_controlled":"1","project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images"},{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"doi":"10.1145/2714572","language":[{"iso":"eng"}],"month":"04","_id":"1814","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"title":"Water wave animation via wavefront parameter interpolation","status":"public","intvolume":" 34","pubrep_id":"575","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"4933","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:12:15Z","checksum":"67c9f4fa370def68cdf31299e48bc91f","file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","access_level":"open_access","file_size":23712153,"content_type":"application/pdf","creator":"system"}],"type":"journal_article","abstract":[{"text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms.","lang":"eng"}],"issue":"3","publication":"ACM Transactions on Graphics","citation":{"short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics, vol. 34, no. 3, 27, ACM, 2015, doi:10.1145/2714572.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics. ACM, 2015. https://doi.org/10.1145/2714572.","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015.","apa":"Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572","ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27."},"date_published":"2015-04-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1"},{"page":"6401 - 6406","publication":"PNAS","citation":{"mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:10.1073/pnas.1421515112.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","apa":"Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112"},"date_published":"2015-05-19T00:00:00Z","scopus_import":1,"day":"19","title":"Limits to adaptation along environmental gradients","status":"public","intvolume":" 112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1818","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible."}],"issue":"20","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["25941385"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1421515112","month":"05","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"National Academy of Sciences","year":"2015","pmid":1,"date_updated":"2021-01-12T06:53:24Z","date_created":"2018-12-11T11:54:11Z","volume":112,"author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova","full_name":"Polechova, Jitka"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publist_id":"5288","ec_funded":1}]