---
_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'
...
---
_id: '1888'
abstract:
- lang: ger
text: 'Im Rahmen meiner Arbeit mit der kollektiven Krankheitsabwehr in Ameisengesellschaften
interessiert mich vor allem, wie sich die Kolonien als Ganzes gegen Krankheiten
wehren können. Warum ist dieses Thema der Krankheitsdynamik in Gruppen so wichtig?
Ein Vergleich von solitär lebenden Individuen mit Individuen, die in sozialen
Gruppen zusammenleben, zeigt die Kosten und die Vorteile des Gruppenlebens: Einerseits
haben Individuen in sozialen Gruppen aufgrund der hohen Dichte, in der die Tiere
zusammenleben, den hohen Interaktionsraten, die sie miteinander haben, und der
engen Verwandtschaft, die sie verbindet, ein höheres Ansteckungsrisiko. Andererseits
kann die individuelle Krankheitsabwehr durch die kollektive Abwehr in den Gruppen
ergänzt werden.'
alternative_title:
- Rundgespräche der Kommission für Ökologie
article_processing_charge: No
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. Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische
Akademie der Wissenschaften. In: Soziale Insekten in Einer Sich Wandelnden
Welt. Vol 43. Verlag Dr. Friedrich Pfeil; 2014:65-72.'
apa: 'Cremer, S. (2014). Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt
Bayerische Akademie der Wissenschaften. In Soziale Insekten in einer sich wandelnden
Welt (Vol. 43, pp. 65–72). Verlag Dr. Friedrich Pfeil.'
chicago: 'Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene
Wehrt Bayerische Akademie Der Wissenschaften.” In Soziale Insekten in Einer
Sich Wandelnden Welt, 43:65–72. Verlag Dr. Friedrich Pfeil, 2014.'
ieee: 'S. Cremer, “Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt
Bayerische Akademie der Wissenschaften,” in Soziale Insekten in einer sich
wandelnden Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.'
ista: 'Cremer S. 2014.Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt
Bayerische Akademie der Wissenschaften. In: Soziale Insekten in einer sich wandelnden
Welt. Rundgespräche der Kommission für Ökologie, vol. 43, 65–72.'
mla: 'Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt
Bayerische Akademie Der Wissenschaften.” Soziale Insekten in Einer Sich Wandelnden
Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.'
short: S. Cremer, in:, Soziale Insekten in Einer Sich Wandelnden Welt, Verlag Dr.
Friedrich Pfeil, 2014, pp. 65–72.
date_created: 2018-12-11T11:54:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-10-17T12:28:45Z
day: '01'
department:
- _id: SyCr
intvolume: ' 43'
language:
- iso: eng
month: '01'
oa_version: None
page: 65 - 72
publication: Soziale Insekten in einer sich wandelnden Welt
publication_identifier:
issn:
- 2366-2875
publication_status: published
publisher: Verlag Dr. Friedrich Pfeil
publist_id: '5207'
quality_controlled: '1'
status: public
title: 'Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie
der Wissenschaften'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2014'
...
---
_id: '1889'
abstract:
- lang: eng
text: We study translation-invariant quasi-free states for a system of fermions
with two-particle interactions. The associated energy functional is similar to
the BCS functional but also includes direct and exchange energies. We show that
for suitable short-range interactions, these latter terms only lead to a renormalization
of the chemical potential, with the usual properties of the BCS functional left
unchanged. Our analysis thus represents a rigorous justification of part of the
BCS approximation. We give bounds on the critical temperature below which the
system displays superfluidity.
acknowledgement: We would like to thank Max Lein and Andreas Deuchert for valuable
suggestions and remarks. Partial financial support by the NSERC (R.S.) is gratefully
acknowledged.
article_number: '1450012'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gerhard
full_name: Bräunlich, Gerhard
last_name: Bräunlich
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states
for fermionic systems and the BCS approximation. Reviews in Mathematical Physics.
2014;26(7). doi:10.1142/S0129055X14500123
apa: Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). Translation-invariant
quasi-free states for fermionic systems and the BCS approximation. Reviews
in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X14500123
chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant
Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews
in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X14500123.
ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free
states for fermionic systems and the BCS approximation,” Reviews in Mathematical
Physics, vol. 26, no. 7. World Scientific Publishing, 2014.
ista: Bräunlich G, Hainzl C, Seiringer R. 2014. Translation-invariant quasi-free
states for fermionic systems and the BCS approximation. Reviews in Mathematical
Physics. 26(7), 1450012.
mla: Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic
Systems and the BCS Approximation.” Reviews in Mathematical Physics, vol.
26, no. 7, 1450012, World Scientific Publishing, 2014, doi:10.1142/S0129055X14500123.
short: G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26
(2014).
date_created: 2018-12-11T11:54:33Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2022-06-07T09:03:09Z
day: '01'
department:
- _id: RoSe
doi: 10.1142/S0129055X14500123
external_id:
arxiv:
- '1305.5135'
intvolume: ' 26'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1305.5135
month: '08'
oa: 1
oa_version: Submitted Version
publication: Reviews in Mathematical Physics
publication_status: published
publisher: World Scientific Publishing
publist_id: '5206'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Translation-invariant quasi-free states for fermionic systems and the BCS approximation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2014'
...
---
_id: '1890'
abstract:
- lang: eng
text: To search for a target in a complex environment is an everyday behavior that
ends with finding the target. When we search for two identical targets, however,
we must continue the search after finding the first target and memorize its location.
We used fixation-related potentials to investigate the neural correlates of different
stages of the search, that is, before and after finding the first target. Having
found the first target influenced subsequent distractor processing. Compared to
distractor fixations before the first target fixation, a negative shift was observed
for three subsequent distractor fixations. These results suggest that processing
a target in continued search modulates the brain's response, either transiently
by reflecting temporary working memory processes or permanently by reflecting
working memory retention.
acknowledgement: 'Funded by Austrian Science Fund (FWF) Grant Number: P 22189-B18;
European Union within the 6th Framework Programme Grant Number: 517590; State government
of Styria Grant Number: PN 4055'
author:
- first_name: Christof
full_name: Körner, Christof
last_name: Körner
- first_name: Verena
full_name: Braunstein, Verena
last_name: Braunstein
- first_name: Matthias
full_name: Stangl, Matthias
last_name: Stangl
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Christa
full_name: Neuper, Christa
last_name: Neuper
- first_name: Anja
full_name: Ischebeck, Anja
last_name: Ischebeck
citation:
ama: 'Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. Sequential
effects in continued visual search: Using fixation-related potentials to compare
distractor processing before and after target detection. Psychophysiology.
2014;51(4):385-395. doi:10.1111/psyp.12062'
apa: 'Körner, C., Braunstein, V., Stangl, M., Schlögl, A., Neuper, C., & Ischebeck,
A. (2014). Sequential effects in continued visual search: Using fixation-related
potentials to compare distractor processing before and after target detection.
Psychophysiology. Wiley-Blackwell. https://doi.org/10.1111/psyp.12062'
chicago: 'Körner, Christof, Verena Braunstein, Matthias Stangl, Alois Schlögl, Christa
Neuper, and Anja Ischebeck. “Sequential Effects in Continued Visual Search: Using
Fixation-Related Potentials to Compare Distractor Processing before and after
Target Detection.” Psychophysiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/psyp.12062.'
ieee: 'C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, and A. Ischebeck,
“Sequential effects in continued visual search: Using fixation-related potentials
to compare distractor processing before and after target detection,” Psychophysiology,
vol. 51, no. 4. Wiley-Blackwell, pp. 385–395, 2014.'
ista: 'Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. 2014.
Sequential effects in continued visual search: Using fixation-related potentials
to compare distractor processing before and after target detection. Psychophysiology.
51(4), 385–395.'
mla: 'Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using
Fixation-Related Potentials to Compare Distractor Processing before and after
Target Detection.” Psychophysiology, vol. 51, no. 4, Wiley-Blackwell, 2014,
pp. 385–95, doi:10.1111/psyp.12062.'
short: C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, A. Ischebeck,
Psychophysiology 51 (2014) 385–395.
date_created: 2018-12-11T11:54:34Z
date_published: 2014-02-11T00:00:00Z
date_updated: 2021-01-12T06:53:52Z
day: '11'
ddc:
- '000'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.1111/psyp.12062
file:
- access_level: open_access
checksum: 4255b6185e774acce1d99f8e195c564d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:44Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5233'
file_name: IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf
file_size: 543243
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 51'
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 385 - 395
publication: Psychophysiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5205'
pubrep_id: '442'
scopus_import: 1
status: public
title: 'Sequential effects in continued visual search: Using fixation-related potentials
to compare distractor processing before and after target detection'
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
volume: 51
year: '2014'
...
---
_id: '1891'
abstract:
- lang: eng
text: We provide theoretical tests of a novel experimental technique to determine
mechanostability of proteins based on stretching a mechanically protected protein
by single-molecule force spectroscopy. This technique involves stretching a homogeneous
or heterogeneous chain of reference proteins (single-molecule markers) in which
one of them acts as host to the guest protein under study. The guest protein is
grafted into the host through genetic engineering. It is expected that unraveling
of the host precedes the unraveling of the guest removing ambiguities in the reading
of the force-extension patterns of the guest protein. We study examples of such
systems within a coarse-grained structure-based model. We consider systems with
various ratios of mechanostability for the host and guest molecules and compare
them to experimental results involving cohesin I as the guest molecule. For a
comparison, we also study the force-displacement patterns in proteins that are
linked in a serial fashion. We find that the mechanostability of the guest is
similar to that of the isolated or serially linked protein. We also demonstrate
that the ideal configuration of this strategy would be one in which the host is
much more mechanostable than the single-molecule markers. We finally show that
it is troublesome to use the highly stable cystine knot proteins as a host to
graft a guest in stretching studies because this would involve a cleaving procedure.
acknowledgement: Grant Nr. 2011/01/N/ST3/02475
author:
- first_name: Mateusz
full_name: Chwastyk, Mateusz
last_name: Chwastyk
- first_name: Albert
full_name: Galera Prat, Albert
last_name: Galera Prat
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
citation:
ama: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M,
Cieplak M. Theoretical tests of the mechanical protection strategy in protein
nanomechanics. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726.
doi:10.1002/prot.24436'
apa: 'Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez,
M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy
in protein nanomechanics. Proteins: Structure, Function and Bioinformatics.
Wiley-Blackwell. https://doi.org/10.1002/prot.24436'
chicago: 'Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia,
Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical
Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function
and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.'
ieee: 'M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez,
and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein
nanomechanics,” Proteins: Structure, Function and Bioinformatics, vol.
82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.'
ista: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M,
Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein
nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726.'
mla: 'Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection
Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics,
vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436.'
short: 'M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez,
M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.'
date_created: 2018-12-11T11:54:34Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-01-12T06:53:52Z
day: '01'
department:
- _id: CaHe
doi: 10.1002/prot.24436
intvolume: ' 82'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 717 - 726
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5204'
scopus_import: 1
status: public
title: Theoretical tests of the mechanical protection strategy in protein nanomechanics
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2014'
...
---
_id: '1892'
abstract:
- lang: eng
text: Behavioural variation among conspecifics is typically contingent on individual
state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic
because they lack conditionality, and genes causing adaptive trait variation in
one sex may reduce Darwinian fitness in the other. One way to avoid such genetic
antagonism is to control sex-specific traits by inheritance via sex chromosomes.
Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish
a single locus, two-allele polymorphism located on a sex-linked chromosome of
heterogametic males generates an extreme reproductive dimorphism. Both natural
and sexual selection are responsible for exceptionally large body size of bourgeois
males, creating a niche for a miniature male phenotype to evolve. This extreme
intrasexual dimorphism results from selection on opposite size thresholds caused
by a single ecological factor, empty snail shells used as breeding substrate.
Paternity analyses reveal that in the field parasitic dwarf males sire the majority
of offspring in direct sperm competition with large nest owners exceeding their
size more than 40 times. Apparently, use of empty snail shells as breeding substrate
and single locus sex-linked inheritance of growth are the major ecological and
genetic mechanisms responsible for the extreme intrasexual diversity observed
in Lamprologus callipterus.
acknowledgement: "This research was supported by grants of the Swiss National Science
Foundation to M.T.\r\nWe thank Tetsu Sato for providing field samples, Olivier Goffinet
for field assistance, Dolores Schütz for vital help in the field and with the manuscript,
David Lank, Barbara Taborsky, Suzanne Alonzo and two anonymous referees for comments
on earlier manuscript versions, and the Fisheries Department, Ministry of Agriculture
and Livestock of Zambia, for permission and support."
article_number: '20140253'
article_processing_charge: No
article_type: original
author:
- first_name: Sabine
full_name: Ocana, Sabine
last_name: Ocana
- first_name: Patrick
full_name: Meidl, Patrick
id: 4709BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Meidl
- first_name: Danielle
full_name: Bonfils, Danielle
last_name: Bonfils
- first_name: Michael
full_name: Taborsky, Michael
last_name: Taborsky
citation:
ama: Ocana S, Meidl P, Bonfils D, Taborsky M. Y-linked Mendelian inheritance of
giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the
Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.0253
apa: Ocana, S., Meidl, P., Bonfils, D., & Taborsky, M. (2014). Y-linked Mendelian
inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings
of the Royal Society of London Series B Biological Sciences. The Royal Society.
https://doi.org/10.1098/rspb.2014.0253
chicago: Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “Y-Linked
Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.”
Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society, 2014. https://doi.org/10.1098/rspb.2014.0253.
ieee: S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “Y-linked Mendelian inheritance
of giant and dwarf male morphs in shell-brooding cichlids,” Proceedings of
the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794.
The Royal Society, 2014.
ista: Ocana S, Meidl P, Bonfils D, Taborsky M. 2014. Y-linked Mendelian inheritance
of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the
Royal Society of London Series B Biological Sciences. 281(1794), 20140253.
mla: Ocana, Sabine, et al. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male
Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 281, no. 1794, 20140253, The Royal Society,
2014, doi:10.1098/rspb.2014.0253.
short: S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society
of London Series B Biological Sciences 281 (2014).
date_created: 2018-12-11T11:54:34Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2022-06-07T09:12:32Z
day: '07'
department:
- _id: CampIT
doi: 10.1098/rspb.2014.0253
external_id:
pmid:
- '25232141'
intvolume: ' 281'
issue: '1794'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/
month: '11'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: The Royal Society
publist_id: '5203'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding
cichlids
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2014'
...
---
_id: '1893'
abstract:
- lang: eng
text: Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated
into various lipid signaling molecules, designated polyphosphoinositides (PPIs).
The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol
is performed by a set of organelle-specific kinases and phosphatases, and the
characteristic head groups make these molecules ideal for regulating biological
processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2
play crucial roles in trafficking toward the lytic compartments, whereas the role
in plants is not yet fully understood. Here we identified the role of a land plant-specific
subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during
vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize
to the tonoplast along with PtdIns3P, the presumable product of their activity.
In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates
and bisphosphates were changed, with opposite effects on the morphology of storage
and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover,
multiple sac knockout mutants had an increased number of smaller storage and lytic
vacuoles, whereas extralarge vacuoles were observed in the overexpression lines,
correlating with various growth and developmental defects. The fragmented vacuolar
phenotype of sac mutants could be mimicked by treating wild-type seedlings with
PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology.
Taken together, these results provide evidence that PPIs, together with their
metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar
morphology and function in plants.
acknowledgement: This work was supported by grants from the Research Foundation-Flanders
(Odysseus).
author:
- first_name: Petra
full_name: Nováková, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Nováková
- first_name: Sibylle
full_name: Hirsch, Sibylle
last_name: Hirsch
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Ringo
full_name: Van Wijk, Ringo
last_name: Van Wijk
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Mareike
full_name: Heilmann, Mareike
last_name: Heilmann
- first_name: Jennifer
full_name: Lerche, Jennifer
last_name: Lerche
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Mugurel
full_name: Feraru, Mugurel
last_name: Feraru
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Marc
full_name: Van Montagu, Marc
last_name: Van Montagu
- first_name: Ingo
full_name: Heilmann, Ingo
last_name: Heilmann
- first_name: Teun
full_name: Munnik, Teun
last_name: Munnik
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at
the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823.
doi:10.1073/pnas.1324264111
apa: Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., …
Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar
function in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111
chicago: Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van
Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases
at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS. National
Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111.
ieee: P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast
mediate vacuolar function in Arabidopsis,” PNAS, vol. 111, no. 7. National
Academy of Sciences, pp. 2818–2823, 2014.
ista: Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M,
Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T,
Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar
function in Arabidopsis. PNAS. 111(7), 2818–2823.
mla: Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast
Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National
Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111.
short: P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann,
J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T.
Munnik, J. Friml, PNAS 111 (2014) 2818–2823.
date_created: 2018-12-11T11:54:34Z
date_published: 2014-02-18T00:00:00Z
date_updated: 2021-01-12T06:53:53Z
day: '18'
department:
- _id: JiFr
doi: 10.1073/pnas.1324264111
ec_funded: 1
intvolume: ' 111'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/
month: '02'
oa: 1
oa_version: Submitted Version
page: 2818 - 2823
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5202'
scopus_import: 1
status: public
title: SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function
in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '1894'
abstract:
- lang: eng
text: 'Background: Bacterial Dsb enzymes are involved in the oxidative folding of
many proteins, through the formation of disulfide bonds between their cysteine
residues. The Dsb protein network has been well characterized in cells of the
model microorganism Escherichia coli. To gain insight into the functioning of
the Dsb system in epsilon-Proteobacteria, where it plays an important role in
the colonization process, we studied two homologs of the main Escherichia coli
Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter
jejuni, the most frequently reported bacterial cause of human enteritis in the
world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer
of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria,
which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest
that the two C. jejuni DsbAs play different roles in bacterial cells and have
divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination
phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical
role in the oxidative folding that ensures the activity of alkaline phosphatase
CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA,
encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that
CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated
with bacterial spread and host colonization, as well as ensuring the oxidative
folding of particular protein substrates. In contrast, CjDsbA2 activity does not
affect the same processes and so far its oxidative folding activity has been demonstrated
for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation
between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not
exclusive and there is probably another protein to be identified in C. jejuni
cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute
the considerable insight to the Epsilonproteobacterial Dsb systems, which have
been poorly understood so far.'
article_number: e106247
author:
- first_name: Anna
full_name: Grabowska, Anna
last_name: Grabowska
- first_name: Ewa
full_name: Wywiał, Ewa
last_name: Wywiał
- first_name: Stanislaw
full_name: Dunin Horkawicz, Stanislaw
last_name: Dunin Horkawicz
- first_name: Anna
full_name: Łasica, Anna
last_name: Łasica
- first_name: Marc
full_name: Wösten, Marc
last_name: Wösten
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
- first_name: Renata
full_name: Godlewska, Renata
last_name: Godlewska
- first_name: Katarzyna
full_name: Bocian Ostrzycka, Katarzyna
last_name: Bocian Ostrzycka
- first_name: Katarzyna
full_name: Pieńkowska, Katarzyna
last_name: Pieńkowska
- first_name: Paweł
full_name: Łaniewski, Paweł
last_name: Łaniewski
- first_name: Janusz
full_name: Bujnicki, Janusz
last_name: Bujnicki
- first_name: Jos
full_name: Van Putten, Jos
last_name: Van Putten
- first_name: Elzbieta
full_name: Jagusztyn Krynicka, Elzbieta
last_name: Jagusztyn Krynicka
citation:
ama: Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics
analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase,
DsbA. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247
apa: Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron,
A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis
of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0106247
chicago: Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc
Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics
Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase,
DsbA.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0106247.
ieee: A. Grabowska et al., “Functional and bioinformatics analysis of two
Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS
One, vol. 9, no. 9. Public Library of Science, 2014.
ista: Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron
AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van
Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of
two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA.
PLoS One. 9(9), e106247.
mla: Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter
Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One,
vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:10.1371/journal.pone.0106247.
short: A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron,
R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J.
Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).
date_created: 2018-12-11T11:54:35Z
date_published: 2014-09-02T00:00:00Z
date_updated: 2021-01-12T06:53:54Z
day: '02'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.pone.0106247
file:
- access_level: open_access
checksum: 7d02c3da7f72b82bb5d7932d80c3251f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:19Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5205'
file_name: IST-2016-438-v1+1_journal.pone.0106247.pdf
file_size: 4248801
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5201'
pubrep_id: '438'
quality_controlled: '1'
scopus_import: 1
status: public
title: Functional and bioinformatics analysis of two Campylobacter jejuni homologs
of the thiol-disulfide oxidoreductase, DsbA
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
volume: 9
year: '2014'
...