---
_id: '1806'
abstract:
- lang: eng
text: The generation of asymmetry, at both cellular and tissue level, is one of
the most essential capabilities of all eukaryotic organisms. It mediates basically
all multicellular development ranging from embryogenesis and de novo organ formation
till responses to various environmental stimuli. In plants, the awe-inspiring
number of such processes is regulated by phytohormone auxin and its directional,
cell-to-cell transport. The mediators of this transport, PIN auxin transporters,
are asymmetrically localized at the plasma membrane, and this polar localization
determines the directionality of intercellular auxin flow. Thus, auxin transport
contributes crucially to the generation of local auxin gradients or maxima, which
instruct given cell to change its developmental program. Here, we introduce and
discuss the molecular components and cellular mechanisms regulating the generation
and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity
in plants.
author:
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In:
Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development.
Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8'
apa: Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular
PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin
and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8
chicago: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular
PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva
Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8.
ieee: P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,”
in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek,
and E. Benková, Eds. Springer, 2014, pp. 143–170.
ista: 'Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity.
In: Auxin and Its Role in Plant Development. , 143–170.'
mla: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN
Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová
et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8.
short: P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.),
Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.
date_created: 2018-12-11T11:54:07Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:19Z
day: '01'
department:
- _id: JiFr
doi: 10.1007/978-3-7091-1526-8_8
editor:
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
language:
- iso: eng
month: '04'
oa_version: None
page: 143 - 170
publication: Auxin and Its Role in Plant Development
publication_status: published
publisher: Springer
publist_id: '5304'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin on the road navigated by cellular PIN polarity
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1816'
abstract:
- lang: eng
text: Watermarking techniques for vector graphics dislocate vertices in order to
embed imperceptible, yet detectable, statistical features into the input data.
The embedding process may result in a change of the topology of the input data,
e.g., by introducing self-intersections, which is undesirable or even disastrous
for many applications. In this paper we present a watermarking framework for two-dimensional
vector graphics that employs conventional watermarking techniques but still provides
the guarantee that the topology of the input data is preserved. The geometric
part of this framework computes so-called maximum perturbation regions (MPR) of
vertices. We propose two efficient algorithms to compute MPRs based on Voronoi
diagrams and constrained triangulations. Furthermore, we present two algorithms
to conditionally correct the watermarked data in order to increase the watermark
embedding capacity and still guarantee topological correctness. While we focus
on the watermarking of input formed by straight-line segments, one of our approaches
can also be extended to circular arcs. We conclude the paper by demonstrating
and analyzing the applicability of our framework in conjunction with two well-known
watermarking techniques.
acknowledgement: 'Work by Martin Held and Stefan Huber was supported by Austrian Science
Fund (FWF): L367-N15 and P25816-N15.'
author:
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Peter
full_name: Meerwald, Peter
last_name: Meerwald
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
citation:
ama: Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector
graphics. International Journal of Computational Geometry and Applications.
2014;24(1):61-86. doi:10.1142/S0218195914500034
apa: Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving
watermarking of vector graphics. International Journal of Computational Geometry
and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034
chicago: Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving
Watermarking of Vector Graphics.” International Journal of Computational Geometry
and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034.
ieee: S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking
of vector graphics,” International Journal of Computational Geometry and Applications,
vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014.
ista: Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking
of vector graphics. International Journal of Computational Geometry and Applications.
24(1), 61–86.
mla: Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.”
International Journal of Computational Geometry and Applications, vol.
24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034.
short: S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational
Geometry and Applications 24 (2014) 61–86.
date_created: 2018-12-11T11:54:10Z
date_published: 2014-03-16T00:00:00Z
date_updated: 2021-01-12T06:53:23Z
day: '16'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1142/S0218195914500034
file:
- access_level: open_access
checksum: be45c133ab4d43351260e21beaa8f4b1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:43Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4704'
file_name: IST-2016-443-v1+1_S0218195914500034.pdf
file_size: 991734
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 61 - 86
publication: International Journal of Computational Geometry and Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '5290'
pubrep_id: '443'
quality_controlled: '1'
scopus_import: 1
status: public
title: Topology-preserving watermarking of vector graphics
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
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2014'
...
---
_id: '1821'
abstract:
- lang: eng
text: We review recent progress towards a rigorous understanding of the Bogoliubov
approximation for bosonic quantum many-body systems. We focus, in particular,
on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A
list of open problems will be discussed at the end.
article_number: '1.4881536'
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation.
Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536
apa: Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation. Journal of Mathematical Physics. American Institute of Physics.
https://doi.org/10.1063/1.4881536
chicago: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov
Approximation.” Journal of Mathematical Physics. American Institute of
Physics, 2014. https://doi.org/10.1063/1.4881536.
ieee: R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American
Institute of Physics, 2014.
ista: Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation. Journal of Mathematical Physics. 55(7), 1.4881536.
mla: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov
Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536,
American Institute of Physics, 2014, doi:10.1063/1.4881536.
short: R. Seiringer, Journal of Mathematical Physics 55 (2014).
date_created: 2018-12-11T11:54:11Z
date_published: 2014-06-26T00:00:00Z
date_updated: 2021-01-12T06:53:25Z
day: '26'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1063/1.4881536
file:
- access_level: open_access
checksum: ed0efc93c10f1341155f0316af617b82
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:49Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5172'
file_name: IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf
file_size: 269171
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Journal of Mathematical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5285'
pubrep_id: '532'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '1822'
article_number: '075101'
author:
- first_name: Vojkan
full_name: Jakšić, Vojkan
last_name: Jakšić
- first_name: Claude
full_name: Pillet, Claude
last_name: Pillet
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics.
2014;55(7). doi:10.1063/1.4884877
apa: Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal
of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877
chicago: Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal
of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877.
ieee: V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical
Physics, vol. 55, no. 7. American Institute of Physics, 2014.
ista: Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical
Physics. 55(7), 075101.
mla: Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics,
vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877.
short: V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).
date_created: 2018-12-11T11:54:12Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:25Z
day: '01'
department:
- _id: RoSe
doi: 10.1063/1.4884877
intvolume: ' 55'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
publication: Journal of Mathematical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5284'
quality_controlled: '1'
scopus_import: 1
status: public
title: Introduction
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '1829'
abstract:
- lang: eng
text: Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or
baseball batting, depend on predictions where the ball can be intercepted and
how it can properly be returned to the opponent. These predictions get more accurate
over time, hence the behaviors need to be continuously modified. As a result,
movement templates with a learned global shape need to be adapted during the execution
so that the racket reaches a target position and velocity that will return the
ball over to the other side of the net or court. It requires altering learned
movements to hit a varying target with the necessary velocity at a specific instant
in time. Such a task cannot be incorporated straightforwardly in most movement
representations suitable for learning. For example, the standard formulation of
the dynamical system based motor primitives (introduced by Ijspeert et al (2002b))
does not satisfy this property despite their flexibility which has allowed learning
tasks ranging from locomotion to kendama. In order to fulfill this requirement,
we reformulate the Ijspeert framework to incorporate the possibility of specifying
a desired hitting point and a desired hitting velocity while maintaining all advantages
of the original formulation.We show that the proposed movement template formulation
works well in two scenarios, i.e., for hitting a ball on a string with a table
tennis racket at a specified velocity and for returning balls launched by a ball
gun successfully over the net using forehand movements.
alternative_title:
- Springer Tracts in Advanced Robotics
author:
- first_name: Katharina
full_name: Muelling, Katharina
last_name: Muelling
- first_name: Oliver
full_name: Kroemer, Oliver
last_name: Kroemer
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning
of hitting and batting. In: Kober J, Peters J, eds. Learning Motor Skills.
Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:10.1007/978-3-319-03194-1_3'
apa: Muelling, K., Kroemer, O., Lampert, C., & Schölkopf, B. (2014). Movement
templates for learning of hitting and batting. In J. Kober & J. Peters (Eds.),
Learning Motor Skills (Vol. 97, pp. 69–82). Springer. https://doi.org/10.1007/978-3-319-03194-1_3
chicago: Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf.
“Movement Templates for Learning of Hitting and Batting.” In Learning Motor
Skills, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to
Robot Experiments. Springer, 2014. https://doi.org/10.1007/978-3-319-03194-1_3.
ieee: K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates
for learning of hitting and batting,” in Learning Motor Skills, vol. 97,
J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82.
ista: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for
learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in
Advanced Robotics, vol. 97, 69–82.'
mla: Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and
Batting.” Learning Motor Skills, edited by Jens Kober and Jan Peters, vol.
97, Springer, 2014, pp. 69–82, doi:10.1007/978-3-319-03194-1_3.
short: K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters
(Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82.
date_created: 2018-12-11T11:54:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:28Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/978-3-319-03194-1_3
editor:
- first_name: Jens
full_name: Kober, Jens
last_name: Kober
- first_name: Jan
full_name: Peters, Jan
last_name: Peters
intvolume: ' 97'
language:
- iso: eng
month: '01'
oa_version: None
page: 69 - 82
publication: Learning Motor Skills
publication_status: published
publisher: Springer
publist_id: '5274'
quality_controlled: '1'
scopus_import: 1
series_title: From Algorithms to Robot Experiments
status: public
title: Movement templates for learning of hitting and batting
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2014'
...
---
_id: '1842'
abstract:
- lang: eng
text: We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2
outerplanar triangulations in both convex and general cases. We also prove that
the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by
O(n3) and O(n10), in the convex and general case, respectively. We then apply
similar methods to prove an (Formula presented.) upper bound on the Ramsey number
of a path with n ordered vertices.
acknowledgement: Marek Krčál was supported by the ERC Advanced Grant No. 267165.
author:
- first_name: Josef
full_name: Cibulka, Josef
last_name: Cibulka
- first_name: Pu
full_name: Gao, Pu
last_name: Gao
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Tomáš
full_name: Valla, Tomáš
last_name: Valla
- first_name: Pavel
full_name: Valtr, Pavel
last_name: Valtr
citation:
ama: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number
of outerplanar graphs. Discrete & Computational Geometry. 2014;53(1):64-79.
doi:10.1007/s00454-014-9646-x
apa: Cibulka, J., Gao, P., Krcál, M., Valla, T., & Valtr, P. (2014). On the
geometric ramsey number of outerplanar graphs. Discrete & Computational
Geometry. Springer. https://doi.org/10.1007/s00454-014-9646-x
chicago: Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On
the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational
Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9646-x.
ieee: J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey
number of outerplanar graphs,” Discrete & Computational Geometry, vol.
53, no. 1. Springer, pp. 64–79, 2014.
ista: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey
number of outerplanar graphs. Discrete & Computational Geometry. 53(1), 64–79.
mla: Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.”
Discrete & Computational Geometry, vol. 53, no. 1, Springer, 2014,
pp. 64–79, doi:10.1007/s00454-014-9646-x.
short: J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete & Computational
Geometry 53 (2014) 64–79.
date_created: 2018-12-11T11:54:18Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2021-01-12T06:53:33Z
day: '14'
department:
- _id: UlWa
- _id: HeEd
doi: 10.1007/s00454-014-9646-x
intvolume: ' 53'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1310.7004
month: '11'
oa: 1
oa_version: Submitted Version
page: 64 - 79
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '5260'
scopus_import: 1
status: public
title: On the geometric ramsey number of outerplanar graphs
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2014'
...
---
_id: '1844'
abstract:
- lang: eng
text: 'Local protein interactions ("molecular context" effects) dictate
amino acid replacements and can be described in terms of site-specific, energetic
preferences for any different amino acid. It has been recently debated whether
these preferences remain approximately constant during evolution or whether, due
to coevolution of sites, they change strongly. Such research highlights an unresolved
and fundamental issue with far-reaching implications for phylogenetic analysis
and molecular evolution modeling. Here, we take advantage of the recent availability
of phenotypically supported laboratory resurrections of Precambrian thioredoxins
and β-lactamases to experimentally address the change of site-specific amino acid
preferences over long geological timescales. Extensive mutational analyses support
the notion that evolutionary adjustment to a new amino acid may occur, but to
a large extent this is insufficient to erase the primitive preference for amino
acid replacements. Generally, site-specific amino acid preferences appear to remain
conserved throughout evolutionary history despite local sequence divergence. We
show such preference conservation to be readily understandable in molecular terms
and we provide crystallographic evidence for an intriguing structural-switch mechanism:
Energetic preference for an ancestral amino acid in a modern protein can be linked
to reorganization upon mutation to the ancestral local structure around the mutated
site. Finally, we point out that site-specific preference conservation naturally
leads to one plausible evolutionary explanation for the existence of intragenic
global suppressor mutations.'
author:
- first_name: Valeria
full_name: Risso, Valeria
last_name: Risso
- first_name: Fadia
full_name: Manssour Triedo, Fadia
last_name: Manssour Triedo
- first_name: Asuncion
full_name: Delgado Delgado, Asuncion
last_name: Delgado Delgado
- first_name: Rocio
full_name: Arco, Rocio
last_name: Arco
- first_name: Alicia
full_name: Barroso Deljesús, Alicia
last_name: Barroso Deljesús
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Raquel
full_name: Godoy Ruiz, Raquel
last_name: Godoy Ruiz
- first_name: Josè
full_name: Gavira, Josè
last_name: Gavira
- first_name: Eric
full_name: Gaucher, Eric
last_name: Gaucher
- first_name: Beatriz
full_name: Ibarra Molero, Beatriz
last_name: Ibarra Molero
- first_name: Jose
full_name: Sánchez Ruiz, Jose
last_name: Sánchez Ruiz
citation:
ama: Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on
resurrected ancestral proteins reveal conservation of site-specific amino acid
preferences throughout evolutionary history. Molecular Biology and Evolution.
2014;32(2):440-455. doi:10.1093/molbev/msu312
apa: Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús,
A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected
ancestral proteins reveal conservation of site-specific amino acid preferences
throughout evolutionary history. Molecular Biology and Evolution. Oxford
University Press. https://doi.org/10.1093/molbev/msu312
chicago: Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio
Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al.
“Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific
Amino Acid Preferences throughout Evolutionary History.” Molecular Biology
and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312.
ieee: V. Risso et al., “Mutational studies on resurrected ancestral proteins
reveal conservation of site-specific amino acid preferences throughout evolutionary
history,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University
Press, pp. 440–455, 2014.
ista: Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A,
Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz
J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation
of site-specific amino acid preferences throughout evolutionary history. Molecular
Biology and Evolution. 32(2), 440–455.
mla: Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins
Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary
History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University
Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312.
short: V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús,
Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez
Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.
date_created: 2018-12-11T11:54:19Z
date_published: 2014-11-12T00:00:00Z
date_updated: 2021-01-12T06:53:34Z
day: '12'
ddc:
- '571'
department:
- _id: HaJa
doi: 10.1093/molbev/msu312
file:
- access_level: open_access
checksum: 06215318e66be8f3e0c33abb07e9d3da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:56Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5247'
file_name: IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf
file_size: 1545246
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 32'
issue: '2'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 440 - 455
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5257'
pubrep_id: '430'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutational studies on resurrected ancestral proteins reveal conservation of
site-specific amino acid preferences throughout evolutionary history
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2014'
...
---
_id: '1852'
abstract:
- lang: eng
text: To control morphogenesis, molecular regulatory networks have to interfere
with the mechanical properties of the individual cells of developing organs and
tissues, but how this is achieved is not well known. We study this issue here
in the shoot meristem of higher plants, a group of undifferentiated cells where
complex changes in growth rates and directions lead to the continuous formation
of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important
role in this process via a dual, local effect on the extracellular matrix, the
cell wall, which determines cell shape. Our study reveals that auxin not only
causes a limited reduction in wall stiffness but also directly interferes with
wall anisotropy via the regulation of cortical microtubule dynamics. We further
show that to induce growth isotropy and organ outgrowth, auxin somehow interferes
with the cortical microtubule-ordering activity of a network of proteins, including
AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate
that the induced isotropy is sufficient to amplify the effects of the relatively
minor changes in wall stiffness to promote organogenesis and the establishment
of new growth axes in a robust manner.
acknowledgement: 'This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). '
author:
- first_name: Massimiliano
full_name: Sassi, Massimiliano
last_name: Sassi
- first_name: Olivier
full_name: Ali, Olivier
last_name: Ali
- first_name: Frédéric
full_name: Boudon, Frédéric
last_name: Boudon
- first_name: Gladys
full_name: Cloarec, Gladys
last_name: Cloarec
- first_name: Ursula
full_name: Abad, Ursula
last_name: Abad
- first_name: Coralie
full_name: Cellier, Coralie
last_name: Cellier
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Benjamin
full_name: Gilles, Benjamin
last_name: Gilles
- first_name: Pascale
full_name: Milani, Pascale
last_name: Milani
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Teva
full_name: Vernoux, Teva
last_name: Vernoux
- first_name: Christophe
full_name: Godin, Christophe
last_name: Godin
- first_name: Olivier
full_name: Hamant, Olivier
last_name: Hamant
- first_name: Jan
full_name: Traas, Jan
last_name: Traas
citation:
ama: Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy
promotes organ formation at the shoot meristem in Arabidopsis. Current Biology.
2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036
apa: Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas,
J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation
at the shoot meristem in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036
chicago: Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula
Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth
Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current
Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036.
ieee: M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes
organ formation at the shoot meristem in Arabidopsis,” Current Biology,
vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.
ista: Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B,
Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated
shift toward growth isotropy promotes organ formation at the shoot meristem in
Arabidopsis. Current Biology. 24(19), 2335–2342.
mla: Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy
Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology,
vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036.
short: M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B.
Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current
Biology 24 (2014) 2335–2342.
date_created: 2018-12-11T11:54:22Z
date_published: 2014-10-06T00:00:00Z
date_updated: 2021-01-12T06:53:37Z
day: '06'
department:
- _id: JiFr
doi: 10.1016/j.cub.2014.08.036
intvolume: ' 24'
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01074821
month: '10'
oa: 1
oa_version: Submitted Version
page: 2335 - 2342
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5248'
quality_controlled: '1'
scopus_import: 1
status: public
title: An auxin-mediated shift toward growth isotropy promotes organ formation at
the shoot meristem in Arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2014'
...
---
_id: '1853'
abstract:
- lang: eng
text: Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes
are expected to form the backbone of future intelligent networks for a broad range
of civil, industrial and military applications. These sensor nodes are often deployed
through random spreading, and function in dynamic environments. Many applications
of WSNs such as pollution tracking, forest fire detection, and military surveillance
require knowledge of the location of constituent nodes. But the use of technologies
such as GPS on all nodes is prohibitive due to power and cost constraints. So,
the sensor nodes need to autonomously determine their locations. Most localization
techniques use anchor nodes with known locations to determine the position of
remaining nodes. Localization techniques have two conflicting requirements. On
one hand, an ideal localization technique should be computationally simple and
on the other hand, it must be resistant to attacks that compromise anchor nodes.
In this paper, we propose a computationally light-weight game theoretic secure
localization technique and demonstrate its effectiveness in comparison to existing
techniques.
author:
- first_name: Susmit
full_name: Jha, Susmit
last_name: Jha
- first_name: Stavros
full_name: Tripakis, Stavros
last_name: Tripakis
- first_name: Sanjit
full_name: Seshia, Sanjit
last_name: Seshia
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization
in wireless sensor networks. In: IEEE; 2014:85-90. doi:10.1109/IOT.2014.7030120'
apa: 'Jha, S., Tripakis, S., Seshia, S., & Chatterjee, K. (2014). Game theoretic
secure localization in wireless sensor networks (pp. 85–90). Presented at the
IOT: Internet of Things, Cambridge, USA: IEEE. https://doi.org/10.1109/IOT.2014.7030120'
chicago: Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee.
“Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE,
2014. https://doi.org/10.1109/IOT.2014.7030120.
ieee: 'S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure
localization in wireless sensor networks,” presented at the IOT: Internet of Things,
Cambridge, USA, 2014, pp. 85–90.'
ista: 'Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization
in wireless sensor networks. IOT: Internet of Things, 85–90.'
mla: Jha, Susmit, et al. Game Theoretic Secure Localization in Wireless Sensor
Networks. IEEE, 2014, pp. 85–90, doi:10.1109/IOT.2014.7030120.
short: S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.
conference:
end_date: 2014-10-08
location: Cambridge, USA
name: 'IOT: Internet of Things'
start_date: 2014-10-06
date_created: 2018-12-11T11:54:22Z
date_published: 2014-02-03T00:00:00Z
date_updated: 2021-01-12T06:53:38Z
day: '03'
department:
- _id: KrCh
doi: 10.1109/IOT.2014.7030120
language:
- iso: eng
month: '02'
oa_version: None
page: 85 - 90
publication_status: published
publisher: IEEE
publist_id: '5247'
quality_controlled: '1'
status: public
title: Game theoretic secure localization in wireless sensor networks
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1854'
abstract:
- lang: eng
text: In this paper, we present a method for non-rigid, partial shape matching in
vector graphics. Given a user-specified query region in a 2D shape, similar regions
are found, even if they are non-linearly distorted. Furthermore, a non-linear
mapping is established between the query regions and these matches, which allows
the automatic transfer of editing operations such as texturing. This is achieved
by a two-step approach. First, pointwise correspondences between the query region
and the whole shape are established. The transformation parameters of these correspondences
are registered in an appropriate transformation space. For transformations between
similar regions, these parameters form surfaces in transformation space, which
are extracted in the second step of our method. The extracted regions may be related
to the query region by a non-rigid transform, enabling non-rigid shape matching.
In this paper, we present a method for non-rigid, partial shape matching in vector
graphics. Given a user-specified query region in a 2D shape, similar regions are
found, even if they are non-linearly distorted. Furthermore, a non-linear mapping
is established between the query regions and these matches, which allows the automatic
transfer of editing operations such as texturing. This is achieved by a two-step
approach. First, pointwise correspondences between the query region and the whole
shape are established. The transformation parameters of these correspondences
are registered in an appropriate transformation space. For transformations between
similar regions, these parameters form surfaces in transformation space, which
are extracted in the second step of our method. The extracted regions may be related
to the query region by a non-rigid transform, enabling non-rigid shape matching.
author:
- first_name: Paul
full_name: Guerrero, Paul
last_name: Guerrero
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
citation:
ama: Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation
parameter similarity. Computer Graphics Forum. 2014;34(1):239-252. doi:10.1111/cgf.12509
apa: Guerrero, P., Auzinger, T., Wimmer, M., & Jeschke, S. (2014). Partial shape
matching using transformation parameter similarity. Computer Graphics Forum.
Wiley. https://doi.org/10.1111/cgf.12509
chicago: Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial
Shape Matching Using Transformation Parameter Similarity.” Computer Graphics
Forum. Wiley, 2014. https://doi.org/10.1111/cgf.12509.
ieee: P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching
using transformation parameter similarity,” Computer Graphics Forum, vol.
34, no. 1. Wiley, pp. 239–252, 2014.
ista: Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching
using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252.
mla: Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter
Similarity.” Computer Graphics Forum, vol. 34, no. 1, Wiley, 2014, pp.
239–52, doi:10.1111/cgf.12509.
short: P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum
34 (2014) 239–252.
date_created: 2018-12-11T11:54:22Z
date_published: 2014-11-05T00:00:00Z
date_updated: 2021-01-12T06:53:38Z
day: '05'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/cgf.12509
file:
- access_level: open_access
checksum: 91946bfc509c77f5fd3151a3ff2b2c8f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:58Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5182'
file_name: IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf
file_size: 24817484
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 239 - 252
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley
publist_id: '5246'
pubrep_id: '574'
quality_controlled: '1'
scopus_import: 1
status: public
title: Partial shape matching using transformation parameter similarity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2014'
...
---
_id: '1862'
abstract:
- lang: eng
text: The prominent and evolutionarily ancient role of the plant hormone auxin is
the regulation of cell expansion. Cell expansion requires ordered arrangement
of the cytoskeleton but molecular mechanisms underlying its regulation by signalling
molecules including auxin are unknown. Here we show in the model plant Arabidopsis
thaliana that in elongating cells exogenous application of auxin or redistribution
of endogenous auxin induces very rapid microtubule re-orientation from transverse
to longitudinal, coherent with the inhibition of cell expansion. This fast auxin
effect requires auxin binding protein 1 (ABP1) and involves a contribution of
downstream signalling components such as ROP6 GTPase, ROP-interactive protein
RIC1 and the microtubule-severing protein katanin. These components are required
for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell
elongation in roots and dark-grown hypocotyls as well as asymmetric growth during
gravitropic responses.
acknowledgement: We thank R. Dixit for performing complementary experiments, D. W.
Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively,
E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J.
Leung for text optimization. This work was supported by the European Research Council
(project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007,
to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT)
(to H.R.). This work benefited from the facilities and expertise of the Imagif Cell
Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil
Général de l’Essonne.
article_processing_charge: No
article_type: original
author:
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Laurie
full_name: Grandont, Laurie
last_name: Grandont
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Sébastien
full_name: Paque, Sébastien
last_name: Paque
- first_name: Anas
full_name: Abuzeineh, Anas
last_name: Abuzeineh
- first_name: Hana
full_name: Rakusova, Hana
id: 4CAAA450-78D2-11EA-8E57-B40A396E08BA
last_name: Rakusova
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Catherine
full_name: Perrot Rechenmann, Catherine
last_name: Perrot Rechenmann
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated
auxin effect on microtubules. Nature. 2014;516(729):90-93. doi:10.1038/nature13889
apa: Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., …
Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect
on microtubules. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13889
chicago: Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque,
Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří
Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.”
Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13889.
ieee: X. Chen et al., “Inhibition of cell expansion by rapid ABP1-mediated
auxin effect on microtubules,” Nature, vol. 516, no. 729. Nature Publishing
Group, pp. 90–93, 2014.
ista: Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková
E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated
auxin effect on microtubules. Nature. 516(729), 90–93.
mla: Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin
Effect on Microtubules.” Nature, vol. 516, no. 729, Nature Publishing Group,
2014, pp. 90–93, doi:10.1038/nature13889.
short: X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova,
E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93.
date_created: 2018-12-11T11:54:25Z
date_published: 2014-12-04T00:00:00Z
date_updated: 2025-05-07T11:12:31Z
day: '04'
department:
- _id: JiFr
- _id: Bio
- _id: EvBe
doi: 10.1038/nature13889
ec_funded: 1
external_id:
pmid:
- '25409144'
intvolume: ' 516'
issue: '729'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/
month: '12'
oa: 1
oa_version: Submitted Version
page: 90 - 93
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Nature Publishing Group
publist_id: '5237'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 516
year: '2014'
...
---
_id: '1869'
abstract:
- lang: eng
text: Boolean controllers for systems with complex datapaths are often very difficult
to implement correctly, in particular when concurrency is involved. Yet, in many
instances it is easy to formally specify correctness. For example, the specification
for the controller of a pipelined processor only has to state that the pipelined
processor gives the same results as a non-pipelined reference design. This makes
such controllers a good target for automated synthesis. However, an efficient
abstraction for the complex datapath elements is needed, as a bit-precise description
is often infeasible. We present Suraq, the first controller synthesis tool which
uses uninterpreted functions for the abstraction. Quantified firstorder formulas
(with specific quantifier structure) serve as the specification language from
which Suraq synthesizes Boolean controllers. Suraq transforms the specification
into an unsatisfiable SMT formula, and uses Craig interpolation to compute its
results. Using Suraq, we were able to synthesize a controller (consisting of two
Boolean signals) for a five-stage pipelined DLX processor in roughly one hour
and 15 minutes.
acknowledgement: The work presented in this paper was supported in part by the European
Research Council (ERC) under grant agreement QUAINT (I774-N23)
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Hofferek, Georg
last_name: Hofferek
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
citation:
ama: 'Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted
functions. In: Yahav E, ed. HVC 2014. Vol 8855. Springer; 2014:68-74. doi:10.1007/978-3-319-13338-6_6'
apa: 'Hofferek, G., & Gupta, A. (2014). Suraq - a controller synthesis tool
using uninterpreted functions. In E. Yahav (Ed.), HVC 2014 (Vol. 8855,
pp. 68–74). Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-13338-6_6'
chicago: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool
Using Uninterpreted Functions.” In HVC 2014, edited by Eran Yahav, 8855:68–74.
Springer, 2014. https://doi.org/10.1007/978-3-319-13338-6_6.
ieee: G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted
functions,” in HVC 2014, Haifa, Israel, 2014, vol. 8855, pp. 68–74.
ista: 'Hofferek G, Gupta A. 2014. Suraq - a controller synthesis tool using uninterpreted
functions. HVC 2014. HVC: Haifa Verification Conference, LNCS, vol. 8855, 68–74.'
mla: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using
Uninterpreted Functions.” HVC 2014, edited by Eran Yahav, vol. 8855, Springer,
2014, pp. 68–74, doi:10.1007/978-3-319-13338-6_6.
short: G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp.
68–74.
conference:
end_date: 2014-11-20
location: Haifa, Israel
name: 'HVC: Haifa Verification Conference'
start_date: 2014-11-18
date_created: 2018-12-11T11:54:27Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:44Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-13338-6_6
ec_funded: 1
editor:
- first_name: Eran
full_name: Yahav, Eran
last_name: Yahav
intvolume: ' 8855'
language:
- iso: eng
month: '01'
oa_version: None
page: 68 - 74
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: HVC 2014
publication_status: published
publisher: Springer
publist_id: '5228'
quality_controlled: '1'
status: public
title: Suraq - a controller synthesis tool using uninterpreted functions
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8855
year: '2014'
...
---
_id: '1870'
abstract:
- lang: eng
text: We investigate the problem of checking if a finite-state transducer is robust
to uncertainty in its input. Our notion of robustness is based on the analytic
notion of Lipschitz continuity - a transducer is K-(Lipschitz) robust if the perturbation
in its output is at most K times the perturbation in its input. We quantify input
and output perturbation using similarity functions. We show that K-robustness
is undecidable even for deterministic transducers. We identify a class of functional
transducers, which admits a polynomial time automata-theoretic decision procedure
for K-robustness. This class includes Mealy machines and functional letter-to-letter
transducers. We also study K-robustness of nondeterministic transducers. Since
a nondeterministic transducer generates a set of output words for each input word,
we quantify output perturbation using setsimilarity functions. We show that K-robustness
of nondeterministic transducers is undecidable, even for letter-to-letter transducers.
We identify a class of set-similarity functions which admit decidable K-robustness
of letter-to-letter transducers.
alternative_title:
- LIPIcs
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
citation:
ama: 'Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers.
In: Leibniz International Proceedings in Informatics, LIPIcs. Vol 29. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:10.4230/LIPIcs.FSTTCS.2014.431'
apa: 'Henzinger, T. A., Otop, J., & Samanta, R. (2014). Lipschitz robustness
of finite-state transducers. In Leibniz International Proceedings in Informatics,
LIPIcs (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431'
chicago: Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness
of Finite-State Transducers.” In Leibniz International Proceedings in Informatics,
LIPIcs, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014.
https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431.
ieee: T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of finite-state
transducers,” in Leibniz International Proceedings in Informatics, LIPIcs,
Delhi, India, 2014, vol. 29, pp. 431–443.
ista: 'Henzinger TA, Otop J, Samanta R. 2014. Lipschitz robustness of finite-state
transducers. Leibniz International Proceedings in Informatics, LIPIcs. FSTTCS:
Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol.
29, 431–443.'
mla: Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.”
Leibniz International Proceedings in Informatics, LIPIcs, vol. 29, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:10.4230/LIPIcs.FSTTCS.2014.431.
short: T.A. Henzinger, J. Otop, R. Samanta, in:, Leibniz International Proceedings
in Informatics, LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014,
pp. 431–443.
conference:
end_date: 2014-12-17
location: Delhi, India
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
start_date: 2014-12-15
date_created: 2018-12-11T11:54:27Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-01-12T06:53:45Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.FSTTCS.2014.431
file:
- access_level: open_access
checksum: 7b1aff1710a8bffb7080ec07f62d9a17
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:11Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4734'
file_name: IST-2017-804-v1+1_37.pdf
file_size: 562151
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 29'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 431 - 443
publication: Leibniz International Proceedings in Informatics, LIPIcs
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5227'
pubrep_id: '804'
quality_controlled: '1'
status: public
title: Lipschitz robustness of finite-state transducers
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: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2014'
...
---
_id: '1872'
abstract:
- lang: eng
text: Extensionality axioms are common when reasoning about data collections, such
as arrays and functions in program analysis, or sets in mathematics. An extensionality
axiom asserts that two collections are equal if they consist of the same elements
at the same indices. Using extensionality is often required to show that two collections
are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly,
while humans have no problem with proving such set identities using extensionality,
they are very hard for superposition theorem provers because of the calculi they
use. In this paper we show how addition of a new inference rule, called extensionality
resolution, allows first-order theorem provers to easily solve problems no modern
first-order theorem prover can solve. We illustrate this by running the VAMPIRE
theorem prover with extensionality resolution on a number of set theory and array
problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP
library of first-order problems that were never solved before by any prover.
acknowledgement: This research was supported in part by the Austrian National Research
Network RiSE (S11410-N23).
alternative_title:
- LNCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
citation:
ama: 'Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity.
In: Cassez F, Raskin J-F, eds. ATVA 2014. Vol 8837. Springer; 2014:185-200.
doi:10.1007/978-3-319-11936-6_14'
apa: 'Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis
and proving identity. In F. Cassez & J.-F. Raskin (Eds.), ATVA 2014
(Vol. 8837, pp. 185–200). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_14'
chicago: Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional
Crisis and Proving Identity.” In ATVA 2014, edited by Franck Cassez and
Jean-François Raskin, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14.
ieee: A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving
identity,” in ATVA 2014, Sydney, Australia, 2014, vol. 8837, pp. 185–200.
ista: 'Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving
identity. ATVA 2014. ATVA: Automated Technology for Verification and Analysis,
LNCS, vol. 8837, 185–200.'
mla: Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” ATVA
2014, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer,
2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14.
short: A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin
(Eds.), ATVA 2014, Springer, 2014, pp. 185–200.
conference:
end_date: 2014-11-07
location: Sydney, Australia
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2014-11-03
date_created: 2018-12-11T11:54:28Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:45Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-11936-6_14
ec_funded: 1
editor:
- first_name: Franck
full_name: Cassez, Franck
last_name: Cassez
- first_name: Jean-François
full_name: Raskin, Jean-François
last_name: Raskin
file:
- access_level: open_access
checksum: af4bd3fc1f4c93075e4dc5cbf625fe7b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:15Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4801'
file_name: IST-2016-641-v1+1_atva2014.pdf
file_size: 244294
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 8837'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 185 - 200
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: ATVA 2014
publication_status: published
publisher: Springer
publist_id: '5226'
pubrep_id: '641'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extensional crisis and proving identity
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8837
year: '2014'
...
---
_id: '1875'
abstract:
- lang: eng
text: We present a formal framework for repairing infinite-state, imperative, sequential
programs, with (possibly recursive) procedures and multiple assertions; the framework
can generate repaired programs by modifying the original erroneous program in
multiple program locations, and can ensure the readability of the repaired program
using user-defined expression templates; the framework also generates a set of
inductive assertions that serve as a proof of correctness of the repaired program.
As a step toward integrating programmer intent and intuition in automated program
repair, we present a cost-aware formulation - given a cost function associated
with permissible statement modifications, the goal is to ensure that the total
program modification cost does not exceed a given repair budget. As part of our
predicate abstractionbased solution framework, we present a sound and complete
algorithm for repair of Boolean programs. We have developed a prototype tool based
on SMT solving and used it successfully to repair diverse errors in benchmark
C programs.
alternative_title:
- LNCS
author:
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Oswaldo
full_name: Olivo, Oswaldo
last_name: Olivo
- first_name: Emerson
full_name: Allen, Emerson
last_name: Allen
citation:
ama: 'Samanta R, Olivo O, Allen E. Cost-aware automatic program repair. In: Müller-Olm
M, Seidl H, eds. Vol 8723. Springer; 2014:268-284. doi:10.1007/978-3-319-10936-7_17'
apa: 'Samanta, R., Olivo, O., & Allen, E. (2014). Cost-aware automatic program
repair. In M. Müller-Olm & H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented
at the SAS: Static Analysis Symposium, Munich, Germany: Springer. https://doi.org/10.1007/978-3-319-10936-7_17'
chicago: Samanta, Roopsha, Oswaldo Olivo, and Emerson Allen. “Cost-Aware Automatic
Program Repair.” edited by Markus Müller-Olm and Helmut Seidl, 8723:268–84. Springer,
2014. https://doi.org/10.1007/978-3-319-10936-7_17.
ieee: 'R. Samanta, O. Olivo, and E. Allen, “Cost-aware automatic program repair,”
presented at the SAS: Static Analysis Symposium, Munich, Germany, 2014, vol. 8723,
pp. 268–284.'
ista: 'Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS:
Static Analysis Symposium, LNCS, vol. 8723, 268–284.'
mla: Samanta, Roopsha, et al. Cost-Aware Automatic Program Repair. Edited
by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84,
doi:10.1007/978-3-319-10936-7_17.
short: R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer,
2014, pp. 268–284.
conference:
end_date: 2014-09-14
location: Munich, Germany
name: 'SAS: Static Analysis Symposium'
start_date: 2014-09-11
date_created: 2018-12-11T11:54:29Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2021-01-12T06:53:46Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-10936-7_17
editor:
- first_name: Markus
full_name: Müller-Olm, Markus
last_name: Müller-Olm
- first_name: Helmut
full_name: Seidl, Helmut
last_name: Seidl
file:
- access_level: open_access
checksum: 78ec4ea1bdecc676cd3e8cad35c6182c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:51Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4650'
file_name: IST-2014-313-v1+1_SOE.SAS14.pdf
file_size: 409485
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 8723'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 268 - 284
publication_status: published
publisher: Springer
publist_id: '5221'
pubrep_id: '313'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cost-aware automatic program repair
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8723
year: '2014'
...
---
_id: '1876'
abstract:
- lang: eng
text: We study densities of functionals over uniformly bounded triangulations of
a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay
triangulation if this is the case for finite sets.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nikolai
full_name: Dolbilin, Nikolai
last_name: Dolbilin
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Alexey
full_name: Glazyrin, Alexey
last_name: Glazyrin
- first_name: Oleg
full_name: Musin, Oleg
last_name: Musin
citation:
ama: Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations
of delaunay sets. Moscow Mathematical Journal. 2014;14(3):491-504. doi:10.17323/1609-4514-2014-14-3-491-504
apa: Dolbilin, N., Edelsbrunner, H., Glazyrin, A., & Musin, O. (2014). Functionals
on triangulations of delaunay sets. Moscow Mathematical Journal. Independent
University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-3-491-504
chicago: Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin.
“Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal.
Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-3-491-504.
ieee: N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations
of delaunay sets,” Moscow Mathematical Journal, vol. 14, no. 3. Independent
University of Moscow, pp. 491–504, 2014.
ista: Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. 2014. Functionals on triangulations
of delaunay sets. Moscow Mathematical Journal. 14(3), 491–504.
mla: Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.”
Moscow Mathematical Journal, vol. 14, no. 3, Independent University of
Moscow, 2014, pp. 491–504, doi:10.17323/1609-4514-2014-14-3-491-504.
short: N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical
Journal 14 (2014) 491–504.
date_created: 2018-12-11T11:54:29Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2022-03-03T11:47:09Z
day: '01'
department:
- _id: HeEd
doi: 10.17323/1609-4514-2014-14-3-491-504
external_id:
arxiv:
- '1211.7053'
intvolume: ' 14'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1211.7053
month: '07'
oa: 1
oa_version: Submitted Version
page: 491 - 504
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- '16093321'
publication_status: published
publisher: Independent University of Moscow
publist_id: '5220'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Functionals on triangulations of delaunay sets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '1877'
abstract:
- lang: eng
text: During inflammation, lymph nodes swell with an influx of immune cells. New
findings identify a signalling pathway that induces relaxation in the contractile
cells that give structure to these organs.
article_type: letter_note
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
citation:
ama: 'Sixt MK, Vaahtomeri K. Physiology: Relax and come in. Nature. 2014;514(7523):441-442.
doi:10.1038/514441a'
apa: 'Sixt, M. K., & Vaahtomeri, K. (2014). Physiology: Relax and come in. Nature.
Springer Nature. https://doi.org/10.1038/514441a'
chicago: 'Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.”
Nature. Springer Nature, 2014. https://doi.org/10.1038/514441a.'
ieee: 'M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” Nature,
vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.'
ista: 'Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523),
441–442.'
mla: 'Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature,
vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:10.1038/514441a.'
short: M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442.
date_created: 2018-12-11T11:54:30Z
date_published: 2014-10-23T00:00:00Z
date_updated: 2021-01-12T06:53:47Z
day: '23'
department:
- _id: MiSi
doi: 10.1038/514441a
intvolume: ' 514'
issue: '7523'
language:
- iso: eng
month: '10'
oa_version: None
page: 441 - 442
publication: Nature
publication_status: published
publisher: Springer Nature
publist_id: '5219'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Physiology: Relax and come in'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 514
year: '2014'
...
---
_id: '1884'
abstract:
- lang: eng
text: Unbiased high-throughput massively parallel sequencing methods have transformed
the process of discovery of novel putative driver gene mutations in cancer. In
chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected
findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis,
utilizing down-sampling of existing datasets, has shown that the discovery process
of putative drivers is far from complete across cancer. In CLL, while driver gene
mutations affecting >10% of patients were efficiently discovered with previously
published CLL cohorts of up to 160 samples subjected to whole exome sequencing
(WES), this sample size has only 0.78 power to detect drivers affecting 5% of
patients, and only 0.12 power for drivers affecting 2% of patients. These calculations
emphasize the need to apply unbiased WES to larger patient cohorts.
author:
- first_name: Dan
full_name: Landau, Dan
last_name: Landau
- first_name: Chip
full_name: Stewart, Chip
last_name: Stewart
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Michael
full_name: Lawrence, Michael
last_name: Lawrence
- first_name: Carrie
full_name: Sougnez, Carrie
last_name: Sougnez
- first_name: Jennifer
full_name: Brown, Jennifer
last_name: Brown
- first_name: Armando
full_name: Lopez Guillermo, Armando
last_name: Lopez Guillermo
- first_name: Stacey
full_name: Gabriel, Stacey
last_name: Gabriel
- first_name: Eric
full_name: Lander, Eric
last_name: Lander
- first_name: Donna
full_name: Neuberg, Donna
last_name: Neuberg
- first_name: Carlos
full_name: López Otín, Carlos
last_name: López Otín
- first_name: Elias
full_name: Campo, Elias
last_name: Campo
- first_name: Gad
full_name: Getz, Gad
last_name: Getz
- first_name: Catherine
full_name: Wu, Catherine
last_name: Wu
citation:
ama: 'Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations
in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole
exome sequencing of 262 primary CLL aamples. Blood. 2014;124(21):1952-1952.'
apa: 'Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J.,
… Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia
(CLL): results from a combined analysis of whole exome sequencing of 262 primary
CLL aamples. Blood. American Society of Hematology.'
chicago: 'Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez,
Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations
in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole
Exome Sequencing of 262 Primary CLL Aamples.” Blood. American Society of
Hematology, 2014.'
ieee: 'D. Landau et al., “Novel putative driver gene mutations in chronic
lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing
of 262 primary CLL aamples,” Blood, vol. 124, no. 21. American Society
of Hematology, pp. 1952–1952, 2014.'
ista: 'Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo
A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014.
Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results
from a combined analysis of whole exome sequencing of 262 primary CLL aamples.
Blood. 124(21), 1952–1952.'
mla: 'Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic
Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of
262 Primary CLL Aamples.” Blood, vol. 124, no. 21, American Society of
Hematology, 2014, pp. 1952–1952.'
short: D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez
Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz,
C. Wu, Blood 124 (2014) 1952–1952.
date_created: 2018-12-11T11:54:32Z
date_published: 2014-12-04T00:00:00Z
date_updated: 2021-01-12T06:53:50Z
day: '04'
department:
- _id: KrCh
intvolume: ' 124'
issue: '21'
language:
- iso: eng
main_file_link:
- url: http://www.bloodjournal.org/content/124/21/1952?sso-checked=true
month: '12'
oa_version: None
page: 1952 - 1952
publication: Blood
publication_status: published
publisher: American Society of Hematology
publist_id: '5211'
status: public
title: 'Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL):
results from a combined analysis of whole exome sequencing of 262 primary CLL aamples'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 124
year: '2014'
...
---
_id: '1886'
abstract:
- lang: eng
text: 'Information processing in the sensory periphery is shaped by natural stimulus
statistics. In the periphery, a transmission bottleneck constrains performance;
thus efficient coding implies that natural signal components with a predictably
wider range should be compressed. In a different regime—when sampling limitations
constrain performance—efficient coding implies that more resources should be allocated
to informative features that are more variable. We propose that this regime is
relevant for sensory cortex when it extracts complex features from limited numbers
of sensory samples. To test this prediction, we use central visual processing
as a model: we show that visual sensitivity for local multi-point spatial correlations,
described by dozens of independently-measured parameters, can be quantitatively
predicted from the structure of natural images. This suggests that efficient coding
applies centrally, where it extends to higher-order sensory features and operates
in a regime in which sensitivity increases with feature variability.'
article_number: e03722
author:
- first_name: Ann
full_name: Hermundstad, Ann
last_name: Hermundstad
- first_name: John
full_name: Briguglio, John
last_name: Briguglio
- first_name: Mary
full_name: Conte, Mary
last_name: Conte
- first_name: Jonathan
full_name: Victor, Jonathan
last_name: Victor
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G.
Variance predicts salience in central sensory processing. eLife. 2014;(November).
doi:10.7554/eLife.03722
apa: Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V.,
& Tkačik, G. (2014). Variance predicts salience in central sensory processing.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722
chicago: Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian,
and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.”
ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.03722.
ieee: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and
G. Tkačik, “Variance predicts salience in central sensory processing,” eLife,
no. November. eLife Sciences Publications, 2014.
ista: Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G.
2014. Variance predicts salience in central sensory processing. eLife. (November),
e03722.
mla: Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.”
ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.
short: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G.
Tkačik, ELife (2014).
date_created: 2018-12-11T11:54:32Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2021-01-12T06:53:50Z
day: '14'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.7554/eLife.03722
file:
- access_level: open_access
checksum: 766ac8999ac6e3364f10065a06024b8f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:04Z
date_updated: 2020-07-14T12:45:20Z
file_id: '4922'
file_name: IST-2016-420-v1+1_e03722.full.pdf
file_size: 5117086
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
issue: November
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '5209'
pubrep_id: '420'
quality_controlled: '1'
scopus_import: 1
status: public
title: Variance predicts salience in central sensory processing
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
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1887'
article_processing_charge: No
article_type: original
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie.
2014:23-30.
apa: Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie.
Deutsche Zoologische Gesellschaft.
chicago: Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.”
Zoologie. Deutsche Zoologische Gesellschaft, 2014.
ieee: S. Cremer, “Gemeinsame Krankheitsabwehr in Ameisengesellschaften,” Zoologie.
Deutsche Zoologische Gesellschaft, pp. 23–30, 2014.
ista: Cremer S. 2014. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie.,
23–30.
mla: Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” Zoologie,
Deutsche Zoologische Gesellschaft, 2014, pp. 23–30.
short: S. Cremer, Zoologie (2014) 23–30.
date_created: 2018-12-11T11:54:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-10-17T07:54:57Z
day: '01'
department:
- _id: SyCr
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 23 - 30
publication: Zoologie
publication_status: published
publisher: Deutsche Zoologische Gesellschaft
publist_id: '5208'
quality_controlled: '1'
status: public
title: Gemeinsame Krankheitsabwehr in Ameisengesellschaften
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...