---
_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'
...