--- _id: '1730' abstract: - lang: eng 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. author: - first_name: Éric full_name: Colin De Verdière, Éric last_name: Colin De Verdière - first_name: Alfredo full_name: Hubard, Alfredo last_name: Hubard - first_name: Arnaud N full_name: De Mesmay, Arnaud N id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87 last_name: De Mesmay citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:53:42Z date_published: 2015-04-02T00:00:00Z date_updated: 2021-01-12T06:52:49Z day: '02' department: - _id: UlWa doi: 10.1007/s00454-015-9679-9 intvolume: ' 53' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1408.4036 month: '04' oa: 1 oa_version: Preprint page: 587 - 620 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5397' quality_controlled: '1' scopus_import: 1 status: public title: Discrete systolic inequalities and decompositions of triangulated surfaces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2015' ... --- _id: '1728' abstract: - lang: eng 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.' 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). author: - first_name: Michael full_name: Cohen, Michael H last_name: Cohen - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Ana full_name: Ribeiro, Ana C last_name: Ribeiro - first_name: Robert full_name: Blassberg, Robert A last_name: Blassberg - first_name: Karen full_name: Page, Karen M last_name: Page - first_name: Chris full_name: Barnes, Chris P last_name: Barnes - first_name: James full_name: Briscoe, James last_name: Briscoe citation: 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 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 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. ieee: M. Cohen et al., “Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms,” Nature Communications, vol. 6. Nature Publishing Group, 2015. 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. 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). date_created: 2018-12-11T11:53:42Z date_published: 2015-04-02T00:00:00Z date_updated: 2021-01-12T06:52:48Z day: '02' doi: 10.1038/ncomms7709 extern: 1 intvolume: ' 6' month: '04' publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5399' quality_controlled: 0 status: public title: Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 6 year: '2015' ... --- _id: '1735' 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. acknowledgement: The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad author: - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando - first_name: Nils full_name: Thürey, Nils last_name: Thürey - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 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 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 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. 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. ista: Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480. 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. date_created: 2018-12-11T11:53:44Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-23T10:12:11Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12576 file: - access_level: open_access checksum: 590752bf977855b337a80f78a9bc2404 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:30Z date_updated: 2020-07-14T12:45:15Z file_id: '5218' file_name: IST-2016-607-v1+1_coarsegrid.pdf file_size: 6312352 relation: main_file file_date_updated: 2020-07-14T12:45:15Z has_accepted_license: '1' intvolume: ' 34' issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 473 - 480 publication: Computer Graphics Forum publication_status: published publisher: Wiley publist_id: '5389' pubrep_id: '607' quality_controlled: '1' scopus_import: 1 status: public title: A dimension-reduced pressure solver for liquid simulations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1734' 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. author: - first_name: Oliver full_name: Klehm, Oliver last_name: Klehm - first_name: Fabrice full_name: Rousselle, Fabrice last_name: Rousselle - first_name: Marios full_name: Papas, Marios last_name: Papas - first_name: Derek full_name: Bradley, Derek last_name: Bradley - first_name: Christophe full_name: Hery, Christophe last_name: Hery - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Wojciech full_name: Jarosz, Wojciech last_name: Jarosz - first_name: Thabo full_name: Beeler, Thabo last_name: Beeler citation: 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 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 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. ieee: O. Klehm et al., “Recent advances in facial appearance capture,” Computer Graphics Forum, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015. 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. 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. short: O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz, T. Beeler, Computer Graphics Forum 34 (2015) 709–733. date_created: 2018-12-11T11:53:43Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:52:52Z day: '01' department: - _id: BeBi doi: 10.1111/cgf.12594 intvolume: ' 34' issue: '2' language: - iso: eng main_file_link: - url: https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf month: '05' oa_version: None page: 709 - 733 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '5391' quality_controlled: '1' scopus_import: 1 status: public title: Recent advances in facial appearance capture type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1789' 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. author: - first_name: Alma full_name: Kuechler, Alma last_name: Kuechler - first_name: Alexander full_name: Zink, Alexander last_name: Zink - first_name: Thomas full_name: Wieland, Thomas last_name: Wieland - first_name: Hermann full_name: Lüdecke, Hermann last_name: Lüdecke - first_name: Kirsten full_name: Cremer, Kirsten last_name: Cremer - first_name: Leonardo full_name: Salviati, Leonardo last_name: Salviati - first_name: Pamela full_name: Magini, Pamela last_name: Magini - first_name: Kimia full_name: Najafi, Kimia last_name: Najafi - first_name: Christiane full_name: Zweier, Christiane last_name: Zweier - first_name: Johanna full_name: Czeschik, Johanna last_name: Czeschik - first_name: Stefan full_name: Aretz, Stefan last_name: Aretz - first_name: Sabine full_name: Endele, Sabine last_name: Endele - first_name: Federica full_name: Tamburrino, Federica last_name: Tamburrino - first_name: Claudia full_name: Pinato, Claudia last_name: Pinato - first_name: Maurizio full_name: Clementi, Maurizio last_name: Clementi - first_name: Jasmin full_name: Gundlach, Jasmin last_name: Gundlach - first_name: Carina full_name: Maylahn, Carina last_name: Maylahn - first_name: Laura full_name: Mazzanti, Laura last_name: Mazzanti - first_name: Eva full_name: Wohlleber, Eva last_name: Wohlleber - first_name: Thomas full_name: Schwarzmayr, Thomas last_name: Schwarzmayr - first_name: Roxana full_name: Kariminejad, Roxana last_name: Kariminejad - first_name: Avner full_name: Schlessinger, Avner last_name: Schlessinger - first_name: Dagmar full_name: Wieczorek, Dagmar last_name: Wieczorek - first_name: Tim full_name: Strom, Tim last_name: Strom - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Hartmut full_name: Engels, Hartmut last_name: Engels citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:54:01Z date_published: 2015-06-15T00:00:00Z date_updated: 2021-01-12T06:53:12Z day: '15' department: - _id: GaNo doi: 10.1038/ejhg.2014.165 external_id: pmid: - '25138099' intvolume: ' 23' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/ month: '06' oa: 1 oa_version: Submitted Version page: 753 - 760 pmid: 1 publication: European Journal of Human Genetics publication_status: published publisher: Nature Publishing Group publist_id: '5324' quality_controlled: '1' status: public title: Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2015' ...