---
_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: '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: '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: 2022-05-23T08:26:44Z
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: '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: '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
license: https://creativecommons.org/licenses/by/4.0/
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: '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
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: '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: '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: '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: '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: '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: '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
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: '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'
...
---
_id: '1895'
abstract:
- lang: eng
text: Major histocompatibility complex class I (MHCI) molecules were recently identified
as novel regulators of synaptic plasticity. These molecules are expressed in various
brain areas, especially in regions undergoing activity-dependent synaptic plasticity,
but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated
the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin,
which causes lack of cell surface expression of MHCI. First, we confirmed that
MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed
electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin
knock-out mice lacking cell surface expression of MHCI. We found that low frequency
stimulation induced long-term depression in wild-type but not knock-out mice,
whereas high frequency stimulation induced long-term potentiation in both genotypes,
with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out
mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related
behavior. Using this model, we analyzed the density of total AMPA receptors and
their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture
replica labeling. After repeated cocaine exposure, the density of GluR1 was increased,
but there was no change in total AMPA receptors and GluR2 levels in wildtype mice.
In contrast, following repeated cocaine exposure, increased densities of total
AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results
indicate that functional deficiency of MHCI enhances synaptic potentiation, induced
by electrical and pharmacological stimulation.
acknowledgement: This work was supported in part by a Grant-in-Aid for Scientific
Research on Innovative Areas (Comprehensive Brain Science Network) and (B) 17330153,
from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
article_number: e107099
author:
- first_name: Mitsuhiro
full_name: Edamura, Mitsuhiro
last_name: Edamura
- first_name: Gen
full_name: Murakami, Gen
last_name: Murakami
- first_name: Hongrui
full_name: Meng, Hongrui
last_name: Meng
- first_name: Makoto
full_name: Itakura, Makoto
last_name: Itakura
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Atsuo
full_name: Fukuda, Atsuo
last_name: Fukuda
- first_name: Daiichiro
full_name: Nakahara, Daiichiro
last_name: Nakahara
citation:
ama: Edamura M, Murakami G, Meng H, et al. Functional deficiency of MHC class i
enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One.
2014;9(9). doi:10.1371/journal.pone.0107099
apa: Edamura, M., Murakami, G., Meng, H., Itakura, M., Shigemoto, R., Fukuda, A.,
& Nakahara, D. (2014). Functional deficiency of MHC class i enhances LTP and
abolishes LTD in the nucleus accumbens of mice. PLoS One. Public Library
of Science. https://doi.org/10.1371/journal.pone.0107099
chicago: Edamura, Mitsuhiro, Gen Murakami, Hongrui Meng, Makoto Itakura, Ryuichi
Shigemoto, Atsuo Fukuda, and Daiichiro Nakahara. “Functional Deficiency of MHC
Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS
One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107099.
ieee: M. Edamura et al., “Functional deficiency of MHC class i enhances LTP
and abolishes LTD in the nucleus accumbens of mice,” PLoS One, vol. 9,
no. 9. Public Library of Science, 2014.
ista: Edamura M, Murakami G, Meng H, Itakura M, Shigemoto R, Fukuda A, Nakahara
D. 2014. Functional deficiency of MHC class i enhances LTP and abolishes LTD in
the nucleus accumbens of mice. PLoS One. 9(9), e107099.
mla: Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP
and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One, vol. 9,
no. 9, e107099, Public Library of Science, 2014, doi:10.1371/journal.pone.0107099.
short: M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D.
Nakahara, PLoS One 9 (2014).
date_created: 2018-12-11T11:54:35Z
date_published: 2014-09-30T00:00:00Z
date_updated: 2021-01-12T06:53:54Z
day: '30'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1371/journal.pone.0107099
file:
- access_level: open_access
checksum: 1f3be936be93114596d61ba44cacee69
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:01Z
date_updated: 2020-07-14T12:45:20Z
file_id: '4724'
file_name: IST-2016-439-v1+1_journal.pone.0107099.pdf
file_size: 6262085
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: '5200'
pubrep_id: '439'
scopus_import: 1
status: public
title: Functional deficiency of MHC class i enhances LTP and abolishes LTD in the
nucleus accumbens of mice
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'
...
---
_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: '1896'
abstract:
- lang: eng
text: 'Biopolymer length regulation is a complex process that involves a large number
of biological, chemical, and physical subprocesses acting simultaneously across
multiple spatial and temporal scales. An illustrative example important for genomic
stability is the length regulation of telomeres - nucleoprotein structures at
the ends of linear chromosomes consisting of tandemly repeated DNA sequences and
a specialized set of proteins. Maintenance of telomeres is often facilitated by
the enzyme telomerase but, particularly in telomerase-free systems, the maintenance
of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms
mediated by recombination. Various linear and circular DNA structures were identified
to participate in ALT, however, dynamics of the whole process is still poorly
understood. We propose a chemical kinetics model of ALT with kinetic rates systematically
derived from the biophysics of DNA diffusion and looping. The reaction system
is reduced to a coagulation-fragmentation system by quasi-steady-state approximation.
The detailed treatment of kinetic rates yields explicit formulas for expected
size distributions of telomeres that demonstrate the key role played by the J
factor, a quantitative measure of bending of polymers. The results are in agreement
with experimental data and point out interesting phenomena: an appearance of very
long telomeric circles if the total telomere density exceeds a critical value
(excess mass) and a nonlinear response of the telomere size distributions to the
amount of telomeric DNA in the system. The results can be of general importance
for understanding dynamics of telomeres in telomerase-independent systems as this
mode of telomere maintenance is similar to the situation in tumor cells lacking
telomerase activity. Furthermore, due to its universality, the model may also
serve as a prototype of an interaction between linear and circular DNA structures
in various settings.'
acknowledgement: The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and
K.B.).
article_number: '032701'
article_processing_charge: No
author:
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Jozef
full_name: Nosek, Jozef
last_name: Nosek
- first_name: Ľubomír
full_name: Tomáška, Ľubomír
last_name: Tomáška
citation:
ama: Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism
of telomere length maintenance. Physical Review E Statistical Nonlinear and
Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701
apa: Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model
of alternative mechanism of telomere length maintenance. Physical Review E
Statistical Nonlinear and Soft Matter Physics. American Institute of Physics.
https://doi.org/10.1103/PhysRevE.89.032701
chicago: Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical
Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review
E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics,
2014. https://doi.org/10.1103/PhysRevE.89.032701.
ieee: R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative
mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014.
ista: Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative
mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear
and Soft Matter Physics. 89(3), 032701.
mla: Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere
Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter
Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.
short: R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical
Nonlinear and Soft Matter Physics 89 (2014).
date_created: 2018-12-11T11:54:35Z
date_published: 2014-03-04T00:00:00Z
date_updated: 2022-08-01T10:50:10Z
day: '04'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.89.032701
intvolume: ' 89'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.0430
month: '03'
oa: 1
oa_version: Submitted Version
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5198'
scopus_import: '1'
status: public
title: Mathematical model of alternative mechanism of telomere length maintenance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '1897'
abstract:
- lang: eng
text: GNOM is one of the most characterized membrane trafficking regulators in plants,
with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange
factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor)
class to mediate vesicle budding at endomembranes. The crucial role of GNOM in
recycling of PIN auxin transporters and other proteins to the plasma membrane
was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM,
the most prominent regulator of recycling in plants, has been proposed to act
and localize at so far elusive recycling endosomes. Here, we report the GNOM localization
in context of its cellular function in Arabidopsis thaliana. State-of-the-art
imaging, pharmacological interference, and ultrastructure analysis show that GNOM
predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging
microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains
on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus,
whereas prolonged exposures results in GNOM translocation to trans-Golgi network
(TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role
for GNOM in maintaining TGN/EE function. Our results redefine the subcellular
action of GNOM and reevaluate the identity and function of recycling endosomes
in plants.
acknowledgement: This work was supported by the Odysseus Program of the Research Foundation-Flanders
(J.F.).
author:
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Marisa
full_name: Otegui, Marisa
last_name: Otegui
- first_name: Natsumaro
full_name: Kutsuna, Natsumaro
last_name: Kutsuna
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Tomoko
full_name: Dainobu, Tomoko
last_name: Dainobu
- first_name: Michael
full_name: Karampelias, Michael
last_name: Karampelias
- first_name: Masaru
full_name: Fujimoto, Masaru
last_name: Fujimoto
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Daisuke
full_name: Miki, Daisuke
last_name: Miki
- first_name: Hiroo
full_name: Fukuda, Hiroo
last_name: Fukuda
- first_name: Akihiko
full_name: Nakano, Akihiko
last_name: Nakano
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and
function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus
in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880
apa: Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias,
M., … Friml, J. (2014). Insights into the localization and function of the membrane
trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant
Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880
chicago: Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko
Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization
and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus
in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014.
https://doi.org/10.1105/tpc.114.125880.
ieee: S. Naramoto et al., “Insights into the localization and function of
the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,”
Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076,
2014.
ista: Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto
M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization
and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus
in Arabidopsis. Plant Cell. 26(7), 3062–3076.
mla: Naramoto, Satoshi, et al. “Insights into the Localization and Function of the
Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.”
Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014,
pp. 3062–76, doi:10.1105/tpc.114.125880.
short: S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias,
M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26
(2014) 3062–3076.
date_created: 2018-12-11T11:54:36Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:55Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.114.125880
intvolume: ' 26'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/
month: '07'
oa: 1
oa_version: Submitted Version
page: 3062 - 3076
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5199'
scopus_import: 1
status: public
title: Insights into the localization and function of the membrane trafficking regulator
GNOM ARF-GEF at the Golgi apparatus in Arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2014'
...
---
_id: '1899'
abstract:
- lang: eng
text: Asymmetric cell divisions allow stem cells to balance proliferation and differentiation.
During embryogenesis, murine epidermis expands rapidly from a single layer of
unspecified basal layer progenitors to a stratified, differentiated epithelium.
Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation
protein LGN, but little is known about how the apical localization of LGN is regulated.
Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to
explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas
loss of each gene alone leads to randomized division angles, combined loss of
Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of
LGN. These findings lend experimental support for the hitherto untested model
that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular
divisions. Finally, we uncover a developmental switch between delamination-driven
early stratification and spindle-orientation-dependent differentiation that occurs
around E15, revealing a two-step mechanism underlying epidermal maturation.
article_processing_charge: No
article_type: original
author:
- first_name: Scott
full_name: Williams, Scott
last_name: Williams
- first_name: Lyndsay
full_name: Ratliff, Lyndsay
last_name: Ratliff
- first_name: Maria P
full_name: Postiglione, Maria P
id: 2C67902A-F248-11E8-B48F-1D18A9856A87
last_name: Postiglione
- first_name: Juergen
full_name: Knoblich, Juergen
last_name: Knoblich
- first_name: Elaine
full_name: Fuchs, Elaine
last_name: Fuchs
citation:
ama: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and
Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature
Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001
apa: Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E.
(2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions
through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001
chicago: Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich,
and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal
Cell Divisions through LGN.” Nature Cell Biology. Nature Publishing Group,
2014. https://doi.org/10.1038/ncb3001.
ieee: S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc
and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,”
Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769,
2014.
ista: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc
and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN.
Nature Cell Biology. 16(8), 758–769.
mla: Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented
Epidermal Cell Divisions through LGN.” Nature Cell Biology, vol. 16, no.
8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001.
short: S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature
Cell Biology 16 (2014) 758–769.
date_created: 2018-12-11T11:54:36Z
date_published: 2014-07-13T00:00:00Z
date_updated: 2021-01-12T06:53:55Z
day: '13'
department:
- _id: SiHi
doi: 10.1038/ncb3001
external_id:
pmid:
- '25016959'
intvolume: ' 16'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/
month: '07'
oa: 1
oa_version: Submitted Version
page: 758 - 769
pmid: 1
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5196'
quality_controlled: '1'
scopus_import: 1
status: public
title: Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions
through LGN
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2014'
...
---
_id: '1898'
abstract:
- lang: eng
text: Fast synaptic transmission is important for rapid information processing.
To explore the maximal rate of neuronal signaling and to analyze the presynaptic
mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally
high action potential (AP) frequencies have been reported invivo. With paired
recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic
granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic
APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels
mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic
efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic
Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore,
a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles
are rapidly recruited to the release site. These data reveal mechanisms of presynaptic
AP generation and transmitter release underlying neuronal kHz signaling.
author:
- first_name: Andreas
full_name: Ritzau Jost, Andreas
last_name: Ritzau Jost
- first_name: Igor
full_name: Delvendahl, Igor
last_name: Delvendahl
- first_name: Annika
full_name: Rings, Annika
last_name: Rings
- first_name: Niklas
full_name: Byczkowicz, Niklas
last_name: Byczkowicz
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Johannes
full_name: Hirrlinger, Johannes
last_name: Hirrlinger
- first_name: Jens
full_name: Eilers, Jens
last_name: Eilers
- first_name: Stefan
full_name: Hallermann, Stefan
last_name: Hallermann
citation:
ama: Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate
kilohertz signaling at a central synapse. Neuron. 2014;84(1):152-163. doi:10.1016/j.neuron.2014.08.036
apa: Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto,
R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling
at a central synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.08.036
chicago: Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz,
Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan
Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central
Synapse.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.08.036.
ieee: A. Ritzau Jost et al., “Ultrafast action potentials mediate kilohertz
signaling at a central synapse,” Neuron, vol. 84, no. 1. Elsevier, pp.
152–163, 2014.
ista: Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R,
Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate
kilohertz signaling at a central synapse. Neuron. 84(1), 152–163.
mla: Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz
Signaling at a Central Synapse.” Neuron, vol. 84, no. 1, Elsevier, 2014,
pp. 152–63, doi:10.1016/j.neuron.2014.08.036.
short: A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto,
J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163.
date_created: 2018-12-11T11:54:36Z
date_published: 2014-10-01T00:00:00Z
date_updated: 2021-01-12T06:53:55Z
day: '01'
department:
- _id: RySh
doi: 10.1016/j.neuron.2014.08.036
intvolume: ' 84'
issue: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 152 - 163
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5197'
quality_controlled: '1'
scopus_import: 1
status: public
title: Ultrafast action potentials mediate kilohertz signaling at a central synapse
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2014'
...
---
_id: '1906'
abstract:
- lang: eng
text: In this paper, we introduce a novel scene representation for the visualization
of large-scale point clouds accompanied by a set of high-resolution photographs.
Many real-world applications deal with very densely sampled point-cloud data,
which are augmented with photographs that often reveal lighting variations and
inaccuracies in registration. Consequently, the high-quality representation of
the captured data, i.e., both point clouds and photographs together, is a challenging
and time-consuming task. We propose a two-phase approach, in which the first (preprocessing)
phase generates multiple overlapping surface patches and handles the problem of
seamless texture generation locally for each patch. The second phase stitches
these patches at render-time to produce a high-quality visualization of the data.
As a result of the proposed localization of the global texturing problem, our
algorithm is more than an order of magnitude faster than equivalent mesh-based
texturing techniques. Furthermore, since our preprocessing phase requires only
a minor fraction of the whole data set at once, we provide maximum flexibility
when dealing with growing data sets.
acknowledgement: This research was supported by the Austrian Research Promotion Agency
(FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567).
author:
- first_name: Murat
full_name: Arikan, Murat
last_name: Arikan
- first_name: Reinhold
full_name: Preiner, Reinhold
last_name: Preiner
- first_name: Claus
full_name: Scheiblauer, Claus
last_name: Scheiblauer
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
citation:
ama: Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud
visualization through localized textured surface reconstruction. IEEE Transactions
on Visualization and Computer Graphics. 2014;20(9):1280-1292. doi:10.1109/TVCG.2014.2312011
apa: Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., & Wimmer, M. (2014).
Large-scale point-cloud visualization through localized textured surface reconstruction.
IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2312011
chicago: Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and
Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured
Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics.
IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2312011.
ieee: M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale
point-cloud visualization through localized textured surface reconstruction,”
IEEE Transactions on Visualization and Computer Graphics, vol. 20, no.
9. IEEE, pp. 1280–1292, 2014.
ista: Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale
point-cloud visualization through localized textured surface reconstruction. IEEE
Transactions on Visualization and Computer Graphics. 20(9), 1280–1292.
mla: Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized
Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer
Graphics, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:10.1109/TVCG.2014.2312011.
short: M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions
on Visualization and Computer Graphics 20 (2014) 1280–1292.
date_created: 2018-12-11T11:54:39Z
date_published: 2014-09-09T00:00:00Z
date_updated: 2021-01-12T06:53:59Z
day: '09'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1109/TVCG.2014.2312011
file:
- access_level: open_access
checksum: 5bf58942d2eb20adf03c7f9ea2e68124
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:41Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5297'
file_name: IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf
file_size: 13594598
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 20'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 1280 - 1292
project:
- _id: 25357BD2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 24352-N23
name: 'Deep Pictures: Creating Visual and Haptic Vector Images'
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '5189'
pubrep_id: '573'
scopus_import: 1
status: public
title: Large-scale point-cloud visualization through localized textured surface reconstruction
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2014'
...
---
_id: '1905'
abstract:
- lang: eng
text: The unprecedented polymorphism in the major histocompatibility complex (MHC)
genes is thought to be maintained by balancing selection from parasites. However,
do parasites also drive divergence at MHC loci between host populations, or do
the effects of balancing selection maintain similarities among populations? We
examined MHC variation in populations of the livebearing fish Poecilia mexicana
and characterized their parasite communities. Poecilia mexicana populations in
the Cueva del Azufre system are locally adapted to darkness and the presence of
toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species.
Parasite communities differed significantly across populations, and populations
with higher parasite loads had higher levels of diversity at class II MHC genes.
However, despite different parasite communities, marked divergence in adaptive
traits and in neutral genetic markers, we found MHC alleles to be remarkably similar
among host populations. Our findings indicate that balancing selection from parasites
maintains immunogenetic diversity of hosts, but this process does not promote
MHC divergence in this system. On the contrary, we suggest that balancing selection
on immunogenetic loci may outweigh divergent selection causing divergence, thereby
hindering host divergence and speciation. Our findings support the hypothesis
that balancing selection maintains MHC similarities among lineages during and
after speciation (trans-species evolution).
acknowledgement: This study was funded by grants from the National Science Foundation
(NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation
(DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer
Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Tobler, Michael
last_name: Tobler
- first_name: Martin
full_name: Plath, Martin
last_name: Plath
- first_name: Rüdiger
full_name: Riesch, Rüdiger
last_name: Riesch
- first_name: Ingo
full_name: Schlupp, Ingo
last_name: Schlupp
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Gopi
full_name: Munimanda, Gopi
last_name: Munimanda
- first_name: C
full_name: Setzer, C
last_name: Setzer
- first_name: Dustin
full_name: Penn, Dustin
last_name: Penn
- first_name: Yoshan
full_name: Moodley, Yoshan
last_name: Moodley
citation:
ama: Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic
diversity but not divergence among locally adapted host populations. Journal
of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370
apa: Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G.,
… Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity
but not divergence among locally adapted host populations. Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.12370
chicago: Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse,
Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites
Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host
Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370.
ieee: M. Tobler et al., “Selection from parasites favours immunogenetic diversity
but not divergence among locally adapted host populations,” Journal of Evolutionary
Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014.
ista: Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C,
Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity
but not divergence among locally adapted host populations. Journal of Evolutionary
Biology. 27(5), 960–974.
mla: Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity
but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary
Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370.
short: M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C.
Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974.
date_created: 2018-12-11T11:54:38Z
date_published: 2014-04-12T00:00:00Z
date_updated: 2022-06-07T09:22:20Z
day: '12'
department:
- _id: SyCr
doi: 10.1111/jeb.12370
external_id:
pmid:
- '24725091'
intvolume: ' 27'
issue: '5'
language:
- iso: eng
month: '04'
oa_version: None
page: 960 - 974
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
publist_id: '5190'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection from parasites favours immunogenetic diversity but not divergence
among locally adapted host populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2014'
...
---
_id: '1902'
abstract:
- lang: eng
text: In the 1960s-1980s, determination of bacterial growth rates was an important
tool in microbial genetics, biochemistry, molecular biology, and microbial physiology.
The exciting technical developments of the 1990s and the 2000s eclipsed that tool;
as a result, many investigators today lack experience with growth rate measurements.
Recently, investigators in a number of areas have started to use measurements
of bacterial growth rates for a variety of purposes. Those measurements have been
greatly facilitated by the availability of microwell plate readers that permit
the simultaneous measurements on up to 384 different cultures. Only the exponential
(logarithmic) portions of the resulting growth curves are useful for determining
growth rates, and manual determination of that portion and calculation of growth
rates can be tedious for high-throughput purposes. Here, we introduce the program
GrowthRates that uses plate reader output files to automatically determine the
exponential portion of the curve and to automatically calculate the growth rate,
the maximum culture density, and the duration of the growth lag phase. GrowthRates
is freely available for Macintosh, Windows, and Linux.We discuss the effects of
culture volume, the classical bacterial growth curve, and the differences between
determinations in rich media and minimal (mineral salts) media. This protocol
covers calibration of the plate reader, growth of culture inocula for both rich
and minimal media, and experimental setup. As a guide to reliability, we report
typical day-to-day variation in growth rates and variation within experiments
with respect to position of wells within the plates.
article_processing_charge: No
article_type: original
author:
- first_name: Barry
full_name: Hall, Barry
last_name: Hall
- first_name: Hande
full_name: Acar, Hande
id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
last_name: Acar
orcid: 0000-0003-1986-9753
- first_name: Anna
full_name: Nandipati, Anna
last_name: Nandipati
- first_name: Miriam
full_name: Barlow, Miriam
last_name: Barlow
citation:
ama: Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular
Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187
apa: Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made
easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187
chicago: Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates
Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014.
https://doi.org/10.1093/molbev/mst187.
ieee: B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular
Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238,
2014.
ista: Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular
Biology and Evolution. 31(1), 232–238.
mla: Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution,
vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187.
short: B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution
31 (2014) 232–238.
date_created: 2018-12-11T11:54:37Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2022-06-07T11:08:13Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/molbev/mst187
external_id:
pmid:
- '24170494'
intvolume: ' 31'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 232 - 238
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '5193'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Growth rates made easy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2014'
...
---
_id: '1901'
abstract:
- lang: eng
text: In plants, the patterning of stem cell-enriched meristems requires a graded
auxin response maximum that emerges from the concerted action of polar auxin transport,
auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However,
mechanisms underlying this auxin response maximum-mediated root stem cell maintenance
are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED
HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic
genes in the quiescent center (QC) of the root and thus provides a robust mechanism
for the maintenance of auxin response maximum in the root tip. This WOX5 action
is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response
repressor. Our combined genetic, cell biology, and computational modeling studies
revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin
production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback
circuit further assures the maintenance of auxin response maximum in the root
tip and thereby contributes to the maintenance of distal stem cell (DSC) populations.
Our experimental studies and in silico computer simulations both demonstrate that
the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient
in the root tip and the auxin-mediated root DSC differentiation.
acknowledgement: "This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043
and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology)
and the Odysseus program of the Research Foundation-Flanders to J.F\r\n"
author:
- first_name: Huiyu
full_name: Tian, Huiyu
last_name: Tian
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
last_name: Wabnik
- first_name: Tiantian
full_name: Niu, Tiantian
last_name: Niu
- first_name: Hongjiang
full_name: Li, Hongjiang
last_name: Li
- first_name: Qianqian
full_name: Yu, Qianqian
last_name: Yu
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Willy
full_name: Govaerts, Willy
last_name: Govaerts
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
citation:
ama: Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular
auxin response is crucial for the patterning of root stem cell niches in arabidopsis.
Molecular Plant. 2014;7(2):277-289. doi:10.1093/mp/sst118
apa: Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z.
(2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial
for the patterning of root stem cell niches in arabidopsis. Molecular Plant.
Oxford University Press. https://doi.org/10.1093/mp/sst118
chicago: Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu,
Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated
Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches
in Arabidopsis.” Molecular Plant. Oxford University Press, 2014. https://doi.org/10.1093/mp/sst118.
ieee: H. Tian et al., “WOX5-IAA17 feedback circuit-mediated cellular auxin
response is crucial for the patterning of root stem cell niches in arabidopsis,”
Molecular Plant, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014.
ista: Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W,
Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated
cellular auxin response is crucial for the patterning of root stem cell niches
in arabidopsis. Molecular Plant. 7(2), 277–289.
mla: Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response
Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular
Plant, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:10.1093/mp/sst118.
short: H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W.
Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289.
date_created: 2018-12-11T11:54:37Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:53:57Z
day: '01'
department:
- _id: JiFr
doi: 10.1093/mp/sst118
intvolume: ' 7'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 277 - 289
publication: Molecular Plant
publication_status: published
publisher: Oxford University Press
publist_id: '5194'
scopus_import: 1
status: public
title: WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for
the patterning of root stem cell niches in arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2014'
...
---
_id: '1904'
abstract:
- lang: eng
text: We prove a Strichartz inequality for a system of orthonormal functions, with
an optimal behavior of the constant in the limit of a large number of functions.
The estimate generalizes the usual Strichartz inequality, in the same fashion
as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application,
we consider the Schrödinger equation with a time-dependent potential and we show
the existence of the wave operator in Schatten spaces.
author:
- first_name: Rupert
full_name: Frank, Rupert
last_name: Frank
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Élliott
full_name: Lieb, Élliott
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Frank R, Lewin M, Lieb É, Seiringer R. Strichartz inequality for orthonormal
functions. Journal of the European Mathematical Society. 2014;16(7):1507-1526.
doi:10.4171/JEMS/467
apa: Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2014). Strichartz inequality
for orthonormal functions. Journal of the European Mathematical Society.
European Mathematical Society. https://doi.org/10.4171/JEMS/467
chicago: Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Strichartz
Inequality for Orthonormal Functions.” Journal of the European Mathematical
Society. European Mathematical Society, 2014. https://doi.org/10.4171/JEMS/467.
ieee: R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Strichartz inequality for
orthonormal functions,” Journal of the European Mathematical Society, vol.
16, no. 7. European Mathematical Society, pp. 1507–1526, 2014.
ista: Frank R, Lewin M, Lieb É, Seiringer R. 2014. Strichartz inequality for orthonormal
functions. Journal of the European Mathematical Society. 16(7), 1507–1526.
mla: Frank, Rupert, et al. “Strichartz Inequality for Orthonormal Functions.” Journal
of the European Mathematical Society, vol. 16, no. 7, European Mathematical
Society, 2014, pp. 1507–26, doi:10.4171/JEMS/467.
short: R. Frank, M. Lewin, É. Lieb, R. Seiringer, Journal of the European Mathematical
Society 16 (2014) 1507–1526.
date_created: 2018-12-11T11:54:38Z
date_published: 2014-08-23T00:00:00Z
date_updated: 2021-01-12T06:53:58Z
day: '23'
department:
- _id: RoSe
doi: 10.4171/JEMS/467
intvolume: ' 16'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1306.1309
month: '08'
oa: 1
oa_version: Submitted Version
page: 1507 - 1526
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Journal of the European Mathematical Society
publication_status: published
publisher: European Mathematical Society
publist_id: '5191'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strichartz inequality for orthonormal functions
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2014'
...
---
_id: '1900'
abstract:
- lang: eng
text: Epithelial cell layers need to be tightly regulated to maintain their integrity
and correct function. Cell integration into epithelial sheets is now shown to
depend on the N-WASP-regulated stabilization of cortical F-actin, which generates
distinct patterns of apical-lateral contractility at E-cadherin-based cell-cell
junctions.
author:
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Behrndt M, Heisenberg C-PJ. Lateral junction dynamics lead the way out. Nature
Cell Biology. 2014;16(2):127-129. doi:10.1038/ncb2913
apa: Behrndt, M., & Heisenberg, C.-P. J. (2014). Lateral junction dynamics lead
the way out. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2913
chicago: Behrndt, Martin, and Carl-Philipp J Heisenberg. “Lateral Junction Dynamics
Lead the Way Out.” Nature Cell Biology. Nature Publishing Group, 2014.
https://doi.org/10.1038/ncb2913.
ieee: M. Behrndt and C.-P. J. Heisenberg, “Lateral junction dynamics lead the way
out,” Nature Cell Biology, vol. 16, no. 2. Nature Publishing Group, pp.
127–129, 2014.
ista: Behrndt M, Heisenberg C-PJ. 2014. Lateral junction dynamics lead the way out.
Nature Cell Biology. 16(2), 127–129.
mla: Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Lateral Junction Dynamics
Lead the Way Out.” Nature Cell Biology, vol. 16, no. 2, Nature Publishing
Group, 2014, pp. 127–29, doi:10.1038/ncb2913.
short: M. Behrndt, C.-P.J. Heisenberg, Nature Cell Biology 16 (2014) 127–129.
date_created: 2018-12-11T11:54:37Z
date_published: 2014-01-31T00:00:00Z
date_updated: 2021-01-12T06:53:56Z
day: '31'
department:
- _id: CaHe
doi: 10.1038/ncb2913
intvolume: ' 16'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 127 - 129
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5195'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lateral junction dynamics lead the way out
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2014'
...
---
_id: '1909'
abstract:
- lang: eng
text: 'Summary: Phenotypes are often environmentally dependent, which requires organisms
to track environmental change. The challenge for organisms is to construct phenotypes
using the most accurate environmental cue. Here, we use a quantitative genetic
model of adaptation by additive genetic variance, within- and transgenerational
plasticity via linear reaction norms and indirect genetic effects respectively.
We show how the relative influence on the eventual phenotype of these components
depends on the predictability of environmental change (fast or slow, sinusoidal
or stochastic) and the developmental lag τ between when the environment is perceived
and when selection acts. We then decompose expected mean fitness into three components
(variance load, adaptation and fluctuation load) to study the fitness costs of
within- and transgenerational plasticity. A strongly negative maternal effect
coefficient m minimizes the variance load, but a strongly positive m minimises
the fluctuation load. The adaptation term is maximized closer to zero, with positive
or negative m preferred under different environmental scenarios. Phenotypic plasticity
is higher when τ is shorter and when the environment changes frequently between
seasonal extremes. Expected mean population fitness is highest away from highest
observed levels of phenotypic plasticity. Within- and transgenerational plasticity
act in concert to deliver well-adapted phenotypes, which emphasizes the need to
study both simultaneously when investigating phenotypic evolution.'
acknowledgement: 'Engineering and Physical Sciences Research Council. Grant Number:
EP/H031928/1'
author:
- first_name: Thomas
full_name: Ezard, Thomas
last_name: Ezard
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Rebecca
full_name: Hoyle, Rebecca
last_name: Hoyle
citation:
ama: Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic
plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701.
doi:10.1111/1365-2435.12207
apa: Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation
via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell.
https://doi.org/10.1111/1365-2435.12207
chicago: Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of
Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology.
Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.
ieee: T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic
plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell,
pp. 693–701, 2014.
ista: Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic
plasticity and maternal effects. Functional Ecology. 28(3), 693–701.
mla: Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity
and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell,
2014, pp. 693–701, doi:10.1111/1365-2435.12207.
short: T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.
date_created: 2018-12-11T11:54:40Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T06:54:00Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1111/1365-2435.12207
file:
- access_level: open_access
checksum: 3cbe8623174709a8ceec2103246f8fe0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:45Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5167'
file_name: IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf
file_size: 536154
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 28'
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 693 - 701
publication: Functional Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5186'
pubrep_id: '419'
scopus_import: 1
status: public
title: The fitness costs of adaptation via phenotypic plasticity and maternal effects
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: 28
year: '2014'
...
---
_id: '1910'
abstract:
- lang: eng
text: angerhans cells (LCs) are a unique subset of dendritic cells (DCs) that express
epithelial adhesion molecules, allowing them to form contacts with epithelial
cells and reside in epidermal/epithelial tissues. The dynamic regulation of epithelial
adhesion plays a decisive role in the life cycle of LCs. It controls whether LCs
remain immature and sessile within the epidermis or mature and egress to initiate
immune responses. So far, the molecular machinery regulating epithelial adhesion
molecules during LC maturation remains elusive. Here, we generated pure populations
of immature human LCs in vitro to systematically probe for gene-expression changes
during LC maturation. LCs down-regulate a set of epithelial genes including E-cadherin,
while they upregulate the mesenchymal marker N-cadherin known to facilitate cell
migration. In addition, N-cadherin is constitutively expressed by monocyte-derived
DCs known to exhibit characteristics of both inflammatory-type and interstitial/dermal
DCs. Moreover, the transcription factors ZEB1 and ZEB2 (ZEB is zinc-finger E-box-binding
homeobox) are upregulated in migratory LCs. ZEB1 and ZEB2 have been shown to induce
epithelial-to-mesenchymal transition (EMT) and invasive behavior in cancer cells
undergoing metastasis. Our results provide the first hint that the molecular EMT
machinery might facilitate LC mobilization. Moreover, our study suggests that
N-cadherin plays a role during DC migration.
acknowledgement: 'FWF. Grant Number: P22058-B20'
author:
- first_name: Sabine
full_name: Konradi, Sabine
last_name: Konradi
- first_name: Nighat
full_name: Yasmin, Nighat
last_name: Yasmin
- first_name: Denise
full_name: Haslwanter, Denise
last_name: Haslwanter
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- first_name: Bernd
full_name: Gesslbauer, Bernd
last_name: Gesslbauer
- 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: Herbert
full_name: Strobl, Herbert
last_name: Strobl
citation:
ama: Konradi S, Yasmin N, Haslwanter D, et al. Langerhans cell maturation is accompanied
by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal
transition ZEB1/2. European Journal of Immunology. 2014;44(2):553-560.
doi:10.1002/eji.201343681
apa: Konradi, S., Yasmin, N., Haslwanter, D., Weber, M., Gesslbauer, B., Sixt, M.
K., & Strobl, H. (2014). Langerhans cell maturation is accompanied by induction
of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition
ZEB1/2. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201343681
chicago: Konradi, Sabine, Nighat Yasmin, Denise Haslwanter, Michele Weber, Bernd
Gesslbauer, Michael K Sixt, and Herbert Strobl. “Langerhans Cell Maturation Is
Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal
Transition ZEB1/2.” European Journal of Immunology. Wiley-Blackwell, 2014.
https://doi.org/10.1002/eji.201343681.
ieee: S. Konradi et al., “Langerhans cell maturation is accompanied by induction
of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition
ZEB1/2,” European Journal of Immunology, vol. 44, no. 2. Wiley-Blackwell,
pp. 553–560, 2014.
ista: Konradi S, Yasmin N, Haslwanter D, Weber M, Gesslbauer B, Sixt MK, Strobl
H. 2014. Langerhans cell maturation is accompanied by induction of N-cadherin
and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2.
European Journal of Immunology. 44(2), 553–560.
mla: Konradi, Sabine, et al. “Langerhans Cell Maturation Is Accompanied by Induction
of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition
ZEB1/2.” European Journal of Immunology, vol. 44, no. 2, Wiley-Blackwell,
2014, pp. 553–60, doi:10.1002/eji.201343681.
short: S. Konradi, N. Yasmin, D. Haslwanter, M. Weber, B. Gesslbauer, M.K. Sixt,
H. Strobl, European Journal of Immunology 44 (2014) 553–560.
date_created: 2018-12-11T11:54:40Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:54:01Z
day: '01'
department:
- _id: MiSi
doi: 10.1002/eji.201343681
intvolume: ' 44'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 553 - 560
publication: European Journal of Immunology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5185'
scopus_import: 1
status: public
title: Langerhans cell maturation is accompanied by induction of N-cadherin and the
transcriptional regulators of epithelial-mesenchymal transition ZEB1/2
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2014'
...
---
_id: '1907'
abstract:
- lang: eng
text: 'Most cryptographic security proofs require showing that two systems are indistinguishable.
A central tool in such proofs is that of a game, where winning the game means
provoking a certain condition, and it is shown that the two systems considered
cannot be distinguished unless this condition is provoked. Upper bounding the
probability of winning such a game, i.e., provoking this condition, for an arbitrary
strategy is usually hard, except in the special case where the best strategy for
winning such a game is known to be non-adaptive. A sufficient criterion for ensuring
the optimality of non-adaptive strategies is that of conditional equivalence to
a system, a notion introduced in [1]. In this paper, we show that this criterion
is not necessary to ensure the optimality of non-adaptive strategies by giving
two results of independent interest: 1) the optimality of non-adaptive strategies
is not preserved under parallel composition; 2) in contrast, conditional equivalence
is preserved under parallel composition.'
article_number: '6875125'
author:
- first_name: Grégory
full_name: Demay, Grégory
last_name: Demay
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Ueli
full_name: Maurer, Ueli
last_name: Maurer
- first_name: Björn
full_name: Tackmann, Björn
last_name: Tackmann
citation:
ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Optimality of non-adaptive strategies:
The case of parallel games. In: IEEE International Symposium on Information
Theory. IEEE; 2014. doi:10.1109/ISIT.2014.6875125'
apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2014). Optimality of
non-adaptive strategies: The case of parallel games. In IEEE International
Symposium on Information Theory. Honolulu, USA: IEEE. https://doi.org/10.1109/ISIT.2014.6875125'
chicago: 'Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Optimality
of Non-Adaptive Strategies: The Case of Parallel Games.” In IEEE International
Symposium on Information Theory. IEEE, 2014. https://doi.org/10.1109/ISIT.2014.6875125.'
ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Optimality of non-adaptive
strategies: The case of parallel games,” in IEEE International Symposium on
Information Theory, Honolulu, USA, 2014.'
ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2014. Optimality of non-adaptive strategies:
The case of parallel games. IEEE International Symposium on Information Theory.
IEEE International Symposium on Information Theory Proceedings, 6875125.'
mla: 'Demay, Grégory, et al. “Optimality of Non-Adaptive Strategies: The Case of
Parallel Games.” IEEE International Symposium on Information Theory, 6875125,
IEEE, 2014, doi:10.1109/ISIT.2014.6875125.'
short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, IEEE International Symposium
on Information Theory, IEEE, 2014.
conference:
end_date: 2014-07-04
location: Honolulu, USA
name: IEEE International Symposium on Information Theory Proceedings
start_date: 2014-06-29
date_created: 2018-12-11T11:54:39Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:59Z
day: '01'
department:
- _id: KrPi
doi: 10.1109/ISIT.2014.6875125
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2014/299
month: '01'
oa: 1
oa_version: Submitted Version
publication: IEEE International Symposium on Information Theory
publication_status: published
publisher: IEEE
publist_id: '5188'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Optimality of non-adaptive strategies: The case of parallel games'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1908'
abstract:
- lang: eng
text: In large populations, multiple beneficial mutations may be simultaneously
spreading. In asexual populations, these mutations must either arise on the same
background or compete against each other. In sexual populations, recombination
can bring together beneficial alleles from different backgrounds, but tightly
linked alleles may still greatly interfere with each other. We show for well-mixed
populations that when this interference is strong, the genome can be seen as consisting
of many effectively asexual stretches linked together. The rate at which beneficial
alleles fix is thus roughly proportional to the rate of recombination and depends
only logarithmically on the mutation supply and the strength of selection. Our
scaling arguments also allow us to predict, with reasonable accuracy, the fitness
distribution of fixed mutations when the mutational effect sizes are broad. We
focus on the regime in which crossovers occur more frequently than beneficial
mutations, as is likely to be the case for many natural populations.
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Oskar
full_name: Hallatschek, Oskar
last_name: Hallatschek
citation:
ama: Weissman D, Hallatschek O. The rate of adaptation in large sexual populations
with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705
apa: Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large
sexual populations with linear chromosomes. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.113.160705
chicago: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large
Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society
of America, 2014. https://doi.org/10.1534/genetics.113.160705.
ieee: D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations
with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of
America, pp. 1167–1183, 2014.
ista: Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations
with linear chromosomes. Genetics. 196(4), 1167–1183.
mla: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual
Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics
Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705.
short: D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.
date_created: 2018-12-11T11:54:39Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:59Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.113.160705
ec_funded: 1
intvolume: ' 196'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.0737
month: '04'
oa: 1
oa_version: Submitted Version
page: 1167 - 1183
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5187'
quality_controlled: '1'
scopus_import: 1
status: public
title: The rate of adaptation in large sexual populations with linear chromosomes
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 196
year: '2014'
...
---
_id: '1911'
abstract:
- lang: eng
text: The topological Tverberg theorem has been generalized in several directions
by setting extra restrictions on the Tverberg partitions. Restricted Tverberg
partitions, defined by the idea that certain points cannot be in the same part,
are encoded with graphs. When two points are adjacent in the graph, they are not
in the same part. If the restrictions are too harsh, then the topological Tverberg
theorem fails. The colored Tverberg theorem corresponds to graphs constructed
as disjoint unions of small complete graphs. Hell studied the case of paths and
cycles. In graph theory these partitions are usually viewed as graph colorings.
As explored by Aharoni, Haxell, Meshulam and others there are fundamental connections
between several notions of graph colorings and topological combinatorics. For
ordinary graph colorings it is enough to require that the number of colors q satisfy
q>Δ, where Δ is the maximal degree of the graph. It was proven by the first
author using equivariant topology that if q>Δ 2 then the topological Tverberg
theorem still works. It is conjectured that q>KΔ is also enough for some constant
K, and in this paper we prove a fixed-parameter version of that conjecture. The
required topological connectivity results are proven with shellability, which
also strengthens some previous partial results where the topological connectivity
was proven with the nerve lemma.
acknowledgement: Patrik Norén gratefully acknowledges support from the Wallenberg
foundation
author:
- first_name: Alexander
full_name: Engström, Alexander
last_name: Engström
- first_name: Patrik
full_name: Noren, Patrik
id: 46870C74-F248-11E8-B48F-1D18A9856A87
last_name: Noren
citation:
ama: Engström A, Noren P. Tverberg’s Theorem and Graph Coloring. Discrete &
Computational Geometry. 2014;51(1):207-220. doi:10.1007/s00454-013-9556-3
apa: Engström, A., & Noren, P. (2014). Tverberg’s Theorem and Graph Coloring.
Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9556-3
chicago: Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.”
Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-013-9556-3.
ieee: A. Engström and P. Noren, “Tverberg’s Theorem and Graph Coloring,” Discrete
& Computational Geometry, vol. 51, no. 1. Springer, pp. 207–220, 2014.
ista: Engström A, Noren P. 2014. Tverberg’s Theorem and Graph Coloring. Discrete
& Computational Geometry. 51(1), 207–220.
mla: Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.”
Discrete & Computational Geometry, vol. 51, no. 1, Springer, 2014,
pp. 207–20, doi:10.1007/s00454-013-9556-3.
short: A. Engström, P. Noren, Discrete & Computational Geometry 51 (2014) 207–220.
date_created: 2018-12-11T11:54:40Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:01Z
day: '01'
department:
- _id: CaUh
doi: 10.1007/s00454-013-9556-3
intvolume: ' 51'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 207 - 220
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '5183'
scopus_import: 1
status: public
title: Tverberg's Theorem and Graph Coloring
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2014'
...
---
_id: '1916'
abstract:
- lang: eng
text: Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases
characterized by progressive age-dependent loss of corticospinal motor tract function.
Although the genetic basis is partly understood, only a fraction of cases can
receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome
sequencing in combination with network analysis, we identified 18 previously unknown
putative HSP genes and validated nearly all of these genes functionally or genetically.
The pathways highlighted by these mutations link HSP to cellular transport, nucleotide
metabolism, and synapse and axon development. Network analysis revealed a host
of further candidate genes, of which three were mutated in our cohort. Our analysis
links HSP to other neurodegenerative disorders and can facilitate gene discovery
and mechanistic understanding of disease.
acknowledgement: Supported by the Deutsche Forschungsgemeinschaft (G.N.)
article_processing_charge: No
article_type: original
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Ali
full_name: Fenstermaker, Ali
last_name: Fenstermaker
- first_name: Maha
full_name: Zaki, Maha
last_name: Zaki
- first_name: Matan
full_name: Hofree, Matan
last_name: Hofree
- first_name: Jennifer
full_name: Silhavy, Jennifer
last_name: Silhavy
- first_name: Andrew
full_name: Heiberg, Andrew
last_name: Heiberg
- first_name: Mostafa
full_name: Abdellateef, Mostafa
last_name: Abdellateef
- first_name: Başak
full_name: Rosti, Başak
last_name: Rosti
- first_name: Eric
full_name: Scott, Eric
last_name: Scott
- first_name: Lobna
full_name: Mansour, Lobna
last_name: Mansour
- first_name: Amira
full_name: Masri, Amira
last_name: Masri
- first_name: Hülya
full_name: Kayserili, Hülya
last_name: Kayserili
- first_name: Jumana
full_name: Al Aama, Jumana
last_name: Al Aama
- first_name: Ghada
full_name: Abdel Salam, Ghada
last_name: Abdel Salam
- first_name: Ariana
full_name: Karminejad, Ariana
last_name: Karminejad
- first_name: Majdi
full_name: Kara, Majdi
last_name: Kara
- first_name: Bülent
full_name: Kara, Bülent
last_name: Kara
- first_name: Bita
full_name: Bozorgmehri, Bita
last_name: Bozorgmehri
- first_name: Tawfeg
full_name: Ben Omran, Tawfeg
last_name: Ben Omran
- first_name: Faezeh
full_name: Mojahedi, Faezeh
last_name: Mojahedi
- first_name: Iman
full_name: Mahmoud, Iman
last_name: Mahmoud
- first_name: Naïma
full_name: Bouslam, Naïma
last_name: Bouslam
- first_name: Ahmed
full_name: Bouhouche, Ahmed
last_name: Bouhouche
- first_name: Ali
full_name: Benomar, Ali
last_name: Benomar
- first_name: Sylvain
full_name: Hanein, Sylvain
last_name: Hanein
- first_name: Laure
full_name: Raymond, Laure
last_name: Raymond
- first_name: Sylvie
full_name: Forlani, Sylvie
last_name: Forlani
- first_name: Massimo
full_name: Mascaro, Massimo
last_name: Mascaro
- first_name: Laila
full_name: Selim, Laila
last_name: Selim
- first_name: Nabil
full_name: Shehata, Nabil
last_name: Shehata
- first_name: Nasir
full_name: Al Allawi, Nasir
last_name: Al Allawi
- first_name: Parayil
full_name: Bindu, Parayil
last_name: Bindu
- first_name: Matloob
full_name: Azam, Matloob
last_name: Azam
- first_name: Murat
full_name: Günel, Murat
last_name: Günel
- first_name: Ahmet
full_name: Caglayan, Ahmet
last_name: Caglayan
- first_name: Kaya
full_name: Bilgüvar, Kaya
last_name: Bilgüvar
- first_name: Aslihan
full_name: Tolun, Aslihan
last_name: Tolun
- first_name: Mahmoud
full_name: Issa, Mahmoud
last_name: Issa
- first_name: Jana
full_name: Schroth, Jana
last_name: Schroth
- first_name: Emily
full_name: Spencer, Emily
last_name: Spencer
- first_name: Rasim
full_name: Rosti, Rasim
last_name: Rosti
- first_name: Naiara
full_name: Akizu, Naiara
last_name: Akizu
- first_name: Keith
full_name: Vaux, Keith
last_name: Vaux
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Alice
full_name: Koh, Alice
last_name: Koh
- first_name: Hisham
full_name: Megahed, Hisham
last_name: Megahed
- first_name: Alexandra
full_name: Dürr, Alexandra
last_name: Dürr
- first_name: Alexis
full_name: Brice, Alexis
last_name: Brice
- first_name: Giovanni
full_name: Stévanin, Giovanni
last_name: Stévanin
- first_name: Stacy
full_name: Gabriel, Stacy
last_name: Gabriel
- first_name: Trey
full_name: Ideker, Trey
last_name: Ideker
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Novarino G, Fenstermaker A, Zaki M, et al. Exome sequencing links corticospinal
motor neuron disease to common neurodegenerative disorders. Science. 2014;343(6170):506-511.
doi:10.1126/science.1247363
apa: Novarino, G., Fenstermaker, A., Zaki, M., Hofree, M., Silhavy, J., Heiberg,
A., … Gleeson, J. (2014). Exome sequencing links corticospinal motor neuron disease
to common neurodegenerative disorders. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.1247363
chicago: Novarino, Gaia, Ali Fenstermaker, Maha Zaki, Matan Hofree, Jennifer Silhavy,
Andrew Heiberg, Mostafa Abdellateef, et al. “Exome Sequencing Links Corticospinal
Motor Neuron Disease to Common Neurodegenerative Disorders.” Science. American
Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1247363.
ieee: G. Novarino et al., “Exome sequencing links corticospinal motor neuron
disease to common neurodegenerative disorders,” Science, vol. 343, no.
6170. American Association for the Advancement of Science, pp. 506–511, 2014.
ista: Novarino G, Fenstermaker A, Zaki M, Hofree M, Silhavy J, Heiberg A, Abdellateef
M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al Aama J, Abdel Salam G,
Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben Omran T, Mojahedi F, Mahmoud
I, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro
M, Selim L, Shehata N, Al Allawi N, Bindu P, Azam M, Günel M, Caglayan A, Bilgüvar
K, Tolun A, Issa M, Schroth J, Spencer E, Rosti R, Akizu N, Vaux K, Johansen A,
Koh A, Megahed H, Dürr A, Brice A, Stévanin G, Gabriel S, Ideker T, Gleeson J.
2014. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative
disorders. Science. 343(6170), 506–511.
mla: Novarino, Gaia, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease
to Common Neurodegenerative Disorders.” Science, vol. 343, no. 6170, American
Association for the Advancement of Science, 2014, pp. 506–11, doi:10.1126/science.1247363.
short: G. Novarino, A. Fenstermaker, M. Zaki, M. Hofree, J. Silhavy, A. Heiberg,
M. Abdellateef, B. Rosti, E. Scott, L. Mansour, A. Masri, H. Kayserili, J. Al
Aama, G. Abdel Salam, A. Karminejad, M. Kara, B. Kara, B. Bozorgmehri, T. Ben
Omran, F. Mojahedi, I. Mahmoud, N. Bouslam, A. Bouhouche, A. Benomar, S. Hanein,
L. Raymond, S. Forlani, M. Mascaro, L. Selim, N. Shehata, N. Al Allawi, P. Bindu,
M. Azam, M. Günel, A. Caglayan, K. Bilgüvar, A. Tolun, M. Issa, J. Schroth, E.
Spencer, R. Rosti, N. Akizu, K. Vaux, A. Johansen, A. Koh, H. Megahed, A. Dürr,
A. Brice, G. Stévanin, S. Gabriel, T. Ideker, J. Gleeson, Science 343 (2014) 506–511.
date_created: 2018-12-11T11:54:42Z
date_published: 2014-01-31T00:00:00Z
date_updated: 2021-01-12T06:54:03Z
day: '31'
department:
- _id: GaNo
doi: 10.1126/science.1247363
external_id:
pmid:
- '24482476'
intvolume: ' 343'
issue: '6170'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/
month: '01'
oa: 1
oa_version: Submitted Version
page: 506 - 511
pmid: 1
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5178'
quality_controlled: '1'
scopus_import: 1
status: public
title: Exome sequencing links corticospinal motor neuron disease to common neurodegenerative
disorders
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 343
year: '2014'
...
---
_id: '1917'
abstract:
- lang: eng
text: Auxin-binding protein 1 (ABP1) was discovered nearly 40 years ago and was
shown to be essential for plant development and morphogenesis, but its mode of
action remains unclear. Here, we report that the plasma membrane-localized transmembrane
kinase (TMK) receptor-like kinases interact with ABP1 and transduce auxin signal
to activate plasma membrane-associated ROPs [Rho-like guanosine triphosphatases
(GTPase) from plants], leading to changes in the cytoskeleton and the shape of
leaf pavement cells in Arabidopsis. The interaction between ABP1 and TMK at the
cell surface is induced by auxin and requires ABP1 sensing of auxin. These findings
show that TMK proteins and ABP1 form a cell surface auxin perception complex that
activates ROP signaling pathways, regulating nontranscriptional cytoplasmic responses
and associated fundamental processes.
acknowledgement: Supported by the intramural research program of the National Institute
of Arthritis and Musculoskeletal and Skin Diseases and by its Laboratory Animal
Care and Use Section and Flow Cytometry Group, Office of Science and Technology
article_processing_charge: No
article_type: original
author:
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Ning
full_name: Dai, Ning
last_name: Dai
- first_name: Jisheng
full_name: Chen, Jisheng
last_name: Chen
- first_name: Shingo
full_name: Nagawa, Shingo
last_name: Nagawa
- first_name: Min
full_name: Cao, Min
last_name: Cao
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Zimin
full_name: Zhou, Zimin
last_name: Zhou
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Wen
full_name: Wang, Wen
last_name: Wang
- first_name: Alan
full_name: Jones, Alan
last_name: Jones
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Sara
full_name: Patterson, Sara
last_name: Patterson
- first_name: Anthony
full_name: Bleecker, Anthony
last_name: Bleecker
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Xu T, Dai N, Chen J, et al. Cell surface ABP1-TMK auxin sensing complex activates
ROP GTPase signaling. Science. 2014;343(6174):1025-1028. doi:10.1126/science.1245125
apa: Xu, T., Dai, N., Chen, J., Nagawa, S., Cao, M., Li, H., … Yang, Z. (2014).
Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1245125
chicago: Xu, Tongda, Ning Dai, Jisheng Chen, Shingo Nagawa, Min Cao, Hongjiang Li,
Zimin Zhou, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP
GTPase Signaling.” Science. American Association for the Advancement of
Science, 2014. https://doi.org/10.1126/science.1245125.
ieee: T. Xu et al., “Cell surface ABP1-TMK auxin sensing complex activates
ROP GTPase signaling,” Science, vol. 343, no. 6174. American Association
for the Advancement of Science, pp. 1025–1028, 2014.
ista: Xu T, Dai N, Chen J, Nagawa S, Cao M, Li H, Zhou Z, Chen X, De Rycke R, Rakusová
H, Wang W, Jones A, Friml J, Patterson S, Bleecker A, Yang Z. 2014. Cell surface
ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 343(6174),
1025–1028.
mla: Xu, Tongda, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP
GTPase Signaling.” Science, vol. 343, no. 6174, American Association for
the Advancement of Science, 2014, pp. 1025–28, doi:10.1126/science.1245125.
short: T. Xu, N. Dai, J. Chen, S. Nagawa, M. Cao, H. Li, Z. Zhou, X. Chen, R. De
Rycke, H. Rakusová, W. Wang, A. Jones, J. Friml, S. Patterson, A. Bleecker, Z.
Yang, Science 343 (2014) 1025–1028.
date_created: 2018-12-11T11:54:42Z
date_published: 2014-02-28T00:00:00Z
date_updated: 2021-01-12T06:54:03Z
day: '28'
department:
- _id: JiFr
doi: 10.1126/science.1245125
external_id:
pmid:
- '24578577'
intvolume: ' 343'
issue: '6174'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166562/
month: '02'
oa: 1
oa_version: Submitted Version
page: 1025 - 1028
pmid: 1
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5177'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 343
year: '2014'
...
---
_id: '1920'
abstract:
- lang: eng
text: Cerebellar motor learning is suggested to be caused by long-term plasticity
of excitatory parallel fiber-Purkinje cell (PF-PC) synapses associated with changes
in the number of synaptic AMPA-type glutamate receptors (AMPARs). However, whether
the AMPARs decrease or increase in individual PF-PC synapses occurs in physiological
motor learning and accounts for memory that lasts over days remains elusive. We
combined quantitative SDS-digested freeze-fracture replica labeling for AMPAR
and physical dissector electron microscopy with a simple model of cerebellar motor
learning, adaptation of horizontal optokinetic response (HOKR) in mouse. After
1-h training of HOKR, short-term adaptation (STA) was accompanied with transient
decrease in AMPARs by 28% in target PF-PC synapses. STA was well correlated with
AMPAR decrease in individual animals and both STA and AMPAR decrease recovered
to basal levels within 24 h. Surprisingly, long-termadaptation (LTA) after five
consecutive daily trainings of 1-h HOKR did not alter the number of AMPARs in
PF-PC synapses but caused gradual and persistent synapse elimination by 45%, with
corresponding PC spine loss by the fifth training day. Furthermore, recovery of
LTA after 2 wk was well correlated with increase of PF-PC synapses to the control
level. Our findings indicate that the AMPARs decrease in PF-PC synapses and the
elimination of these synapses are in vivo engrams in short- and long-term motor
learning, respectively, showing a unique type of synaptic plasticity that may
contribute to memory consolidation.
acknowledgement: This work was supported by Solution-Oriented Research for Science
and Technology from the Japan Science and Technology Agency; Ministry of Education,
Culture, Sports, Science and Technology of Japan Grant 16300114 (to R.S.).
author:
- first_name: Wen
full_name: Wang, Wen
last_name: Wang
- first_name: Kazuhiko
full_name: Nakadate, Kazuhiko
last_name: Nakadate
- first_name: Miwako
full_name: Masugi Tokita, Miwako
last_name: Masugi Tokita
- first_name: Fumihiro
full_name: Shutoh, Fumihiro
last_name: Shutoh
- first_name: Wajeeha
full_name: Aziz, Wajeeha
last_name: Aziz
- first_name: Etsuko
full_name: Tarusawa, Etsuko
last_name: Tarusawa
- first_name: Andrea
full_name: Lörincz, Andrea
last_name: Lörincz
- first_name: Elek
full_name: Molnár, Elek
last_name: Molnár
- first_name: Sebnem
full_name: Kesaf, Sebnem
id: 401AB46C-F248-11E8-B48F-1D18A9856A87
last_name: Kesaf
- first_name: Yunqing
full_name: Li, Yunqing
last_name: Li
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Soichi
full_name: Nagao, Soichi
last_name: Nagao
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Wang W, Nakadate K, Masugi Tokita M, et al. Distinct cerebellar engrams in
short-term and long-term motor learning. PNAS. 2014;111(1):E188-E193. doi:10.1073/pnas.1315541111
apa: Wang, W., Nakadate, K., Masugi Tokita, M., Shutoh, F., Aziz, W., Tarusawa,
E., … Shigemoto, R. (2014). Distinct cerebellar engrams in short-term and long-term
motor learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315541111
chicago: Wang, Wen, Kazuhiko Nakadate, Miwako Masugi Tokita, Fumihiro Shutoh, Wajeeha
Aziz, Etsuko Tarusawa, Andrea Lörincz, et al. “Distinct Cerebellar Engrams in
Short-Term and Long-Term Motor Learning.” PNAS. National Academy of Sciences,
2014. https://doi.org/10.1073/pnas.1315541111.
ieee: W. Wang et al., “Distinct cerebellar engrams in short-term and long-term
motor learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp.
E188–E193, 2014.
ista: Wang W, Nakadate K, Masugi Tokita M, Shutoh F, Aziz W, Tarusawa E, Lörincz
A, Molnár E, Kesaf S, Li Y, Fukazawa Y, Nagao S, Shigemoto R. 2014. Distinct cerebellar
engrams in short-term and long-term motor learning. PNAS. 111(1), E188–E193.
mla: Wang, Wen, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term
Motor Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014,
pp. E188–93, doi:10.1073/pnas.1315541111.
short: W. Wang, K. Nakadate, M. Masugi Tokita, F. Shutoh, W. Aziz, E. Tarusawa,
A. Lörincz, E. Molnár, S. Kesaf, Y. Li, Y. Fukazawa, S. Nagao, R. Shigemoto, PNAS
111 (2014) E188–E193.
date_created: 2018-12-11T11:54:43Z
date_published: 2014-01-07T00:00:00Z
date_updated: 2021-01-12T06:54:05Z
day: '07'
department:
- _id: RySh
doi: 10.1073/pnas.1315541111
intvolume: ' 111'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890858/
month: '01'
oa: 1
oa_version: Submitted Version
page: E188 - E193
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5174'
scopus_import: 1
status: public
title: Distinct cerebellar engrams in short-term and long-term motor learning
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '1915'
abstract:
- lang: eng
text: ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small
GTPases that function as essential molecular switches to control diverse cellular
processes including cytoskeleton organization, cell polarization, cytokinesis,
cell differentiation and vesicle trafficking. Although the machineries of vesicle
trafficking and cell polarity in plants have been individually well addressed,
how ROPs co-ordinate those processes is still largely unclear. Recent progress
has been made towards an understanding of the coordination of ROP signalling and
trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both
root and leaf pavement cells. PIN transporters constantly shuttle between the
endosomal compartments and the polar plasma membrane domains, therefore the modulation
of PIN-dependent auxin transport between cells is a main developmental output
of ROP-regulated vesicle trafficking. The present review focuses on these cellular
mechanisms, especially the integration of ROP-based vesicle trafficking and plant
cell polarity.
acknowledgement: This work was supported by the European Research Council [project
ERC-2011-StG-20101109-PSDP], Central European Institute of Technology (CEITEC) [grant
number CZ.1.05/1.1.00/02.0068], European Social Fund [grant number CZ.1.07/2.3.00/20.0043]
and the Czec
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: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity.
Biochemical Society Transactions. 2014;42(1):212-218. doi:10.1042/BST20130269
apa: Chen, X., & Friml, J. (2014). Rho-GTPase-regulated vesicle trafficking
in plant cell polarity. Biochemical Society Transactions. Portland Press.
https://doi.org/10.1042/BST20130269
chicago: Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in
Plant Cell Polarity.” Biochemical Society Transactions. Portland Press,
2014. https://doi.org/10.1042/BST20130269.
ieee: X. Chen and J. Friml, “Rho-GTPase-regulated vesicle trafficking in plant cell
polarity,” Biochemical Society Transactions, vol. 42, no. 1. Portland Press,
pp. 212–218, 2014.
ista: Chen X, Friml J. 2014. Rho-GTPase-regulated vesicle trafficking in plant cell
polarity. Biochemical Society Transactions. 42(1), 212–218.
mla: Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant
Cell Polarity.” Biochemical Society Transactions, vol. 42, no. 1, Portland
Press, 2014, pp. 212–18, doi:10.1042/BST20130269.
short: X. Chen, J. Friml, Biochemical Society Transactions 42 (2014) 212–218.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2022-06-07T11:20:56Z
day: '01'
department:
- _id: JiFr
doi: 10.1042/BST20130269
ec_funded: 1
external_id:
pmid:
- '24450654'
intvolume: ' 42'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 212 - 218
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Biochemical Society Transactions
publication_identifier:
eissn:
- 1470-8752
issn:
- 0300-5127
publication_status: published
publisher: Portland Press
publist_id: '5179'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rho-GTPase-regulated vesicle trafficking in plant cell polarity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2014'
...
---
_id: '1919'
abstract:
- lang: eng
text: Long-lasting memories are formed when the stimulus is temporally distributed
(spacing effect). However, the synaptic mechanisms underlying this robust phenomenon
and the precise time course of the synaptic modifications that occur during learning
remain unclear. Here we examined the adaptation of horizontal optokinetic response
in mice that underwent 1 h of massed and spaced training at varying intervals.
Despite similar acquisition by all training protocols, 1 h of spacing produced
the highest memory retention at 24 h, which lasted for 1 mo. The distinct kinetics
of memory are strongly correlated with the reduction of floccular parallel fiber-Purkinje
cell synapses but not with AMPA receptor (AMPAR) number and synapse size. After
the spaced training, we observed 25%, 23%, and 12% reduction in AMPAR density,
synapse size, and synapse number, respectively. Four hours after the spaced training,
half of the synapses and Purkinje cell spines had been eliminated, whereas AMPAR
density and synapse size were recovered in remaining synapses. Surprisingly, massed
training also produced long-term memory and halving of synapses; however, this
occurred slowly over days, and the memory lasted for only 1 wk. This distinct
kinetics of structural plasticity may serve as a basis for unique temporal profiles
in the formation and decay of memory with or without intervals.
acknowledgement: his work was supported by Solution Oriented Research for Science
and Technology (R.S.), Core Research for Evolutional Science and Technology, Japan
Science and Technology Agency (Y.F.), and Grants-in-Aid for Scientific Research
on Priority Areas-Molecular Brain Sciences 16300114 (to R.S.) and 18022043 (to Y.F.).
author:
- first_name: Wajeeha
full_name: Aziz, Wajeeha
last_name: Aziz
- first_name: Wen
full_name: Wang, Wen
last_name: Wang
- first_name: Sebnem
full_name: Kesaf, Sebnem
id: 401AB46C-F248-11E8-B48F-1D18A9856A87
last_name: Kesaf
- first_name: Alsayed
full_name: Mohamed, Alsayed
last_name: Mohamed
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. Distinct kinetics
of synaptic structural plasticity, memory formation, and memory decay in massed
and spaced learning. PNAS. 2014;111(1):E194-E202. doi:10.1073/pnas.1303317110
apa: Aziz, W., Wang, W., Kesaf, S., Mohamed, A., Fukazawa, Y., & Shigemoto,
R. (2014). Distinct kinetics of synaptic structural plasticity, memory formation,
and memory decay in massed and spaced learning. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1303317110
chicago: Aziz, Wajeeha, Wen Wang, Sebnem Kesaf, Alsayed Mohamed, Yugo Fukazawa,
and Ryuichi Shigemoto. “Distinct Kinetics of Synaptic Structural Plasticity, Memory
Formation, and Memory Decay in Massed and Spaced Learning.” PNAS. National
Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1303317110.
ieee: W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, and R. Shigemoto, “Distinct
kinetics of synaptic structural plasticity, memory formation, and memory decay
in massed and spaced learning,” PNAS, vol. 111, no. 1. National Academy
of Sciences, pp. E194–E202, 2014.
ista: Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. 2014. Distinct
kinetics of synaptic structural plasticity, memory formation, and memory decay
in massed and spaced learning. PNAS. 111(1), E194–E202.
mla: Aziz, Wajeeha, et al. “Distinct Kinetics of Synaptic Structural Plasticity,
Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS,
vol. 111, no. 1, National Academy of Sciences, 2014, pp. E194–202, doi:10.1073/pnas.1303317110.
short: W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, R. Shigemoto, PNAS 111
(2014) E194–E202.
date_created: 2018-12-11T11:54:43Z
date_published: 2014-01-07T00:00:00Z
date_updated: 2021-01-12T06:54:04Z
day: '07'
department:
- _id: RySh
doi: 10.1073/pnas.1303317110
intvolume: ' 111'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890840/
month: '01'
oa: 1
oa_version: Submitted Version
page: E194 - E202
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5175'
scopus_import: 1
status: public
title: Distinct kinetics of synaptic structural plasticity, memory formation, and
memory decay in massed and spaced learning
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '1918'
abstract:
- lang: eng
text: As the nuclear charge Z is continuously decreased an N-electron atom undergoes
a binding-unbinding transition. We investigate whether the electrons remain bound
and whether the radius of the system stays finite as the critical value Zc is
approached. Existence of a ground state at Zc is shown under the condition Zc
< N-K, where K is the maximal number of electrons that can be removed at Zc
without changing the energy.
article_number: '1350021'
author:
- first_name: Jacopo
full_name: Bellazzini, Jacopo
last_name: Bellazzini
- first_name: Rupert
full_name: Frank, Rupert
last_name: Frank
- first_name: Élliott
full_name: Lieb, Élliott
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Bellazzini J, Frank R, Lieb É, Seiringer R. Existence of ground states for
negative ions at the binding threshold. Reviews in Mathematical Physics.
2014;26(1). doi:10.1142/S0129055X13500219
apa: Bellazzini, J., Frank, R., Lieb, É., & Seiringer, R. (2014). Existence
of ground states for negative ions at the binding threshold. Reviews in Mathematical
Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X13500219
chicago: Bellazzini, Jacopo, Rupert Frank, Élliott Lieb, and Robert Seiringer. “Existence
of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical
Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X13500219.
ieee: J. Bellazzini, R. Frank, É. Lieb, and R. Seiringer, “Existence of ground states
for negative ions at the binding threshold,” Reviews in Mathematical Physics,
vol. 26, no. 1. World Scientific Publishing, 2014.
ista: Bellazzini J, Frank R, Lieb É, Seiringer R. 2014. Existence of ground states
for negative ions at the binding threshold. Reviews in Mathematical Physics. 26(1),
1350021.
mla: Bellazzini, Jacopo, et al. “Existence of Ground States for Negative Ions at
the Binding Threshold.” Reviews in Mathematical Physics, vol. 26, no. 1,
1350021, World Scientific Publishing, 2014, doi:10.1142/S0129055X13500219.
short: J. Bellazzini, R. Frank, É. Lieb, R. Seiringer, Reviews in Mathematical Physics
26 (2014).
date_created: 2018-12-11T11:54:42Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:54:04Z
day: '01'
department:
- _id: RoSe
doi: 10.1142/S0129055X13500219
intvolume: ' 26'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1301.5370
month: '02'
oa: 1
oa_version: Submitted Version
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Reviews in Mathematical Physics
publication_status: published
publisher: World Scientific Publishing
publist_id: '5176'
quality_controlled: '1'
scopus_import: 1
status: public
title: Existence of ground states for negative ions at the binding threshold
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2014'
...
---
_id: '1914'
abstract:
- lang: eng
text: Targeting membrane proteins for degradation requires the sequential action
of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally
conserved among kingdoms, plants lack the essential ESCRT-0 components. A new
report closes this gap by identifying a novel protein family that substitutes
for ESCRT-0 function in plants.
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Sauer M, Friml J. Plant biology: Gatekeepers of the road to protein perdition.
Current Biology. 2014;24(1):R27-R29. doi:10.1016/j.cub.2013.11.019'
apa: 'Sauer, M., & Friml, J. (2014). Plant biology: Gatekeepers of the road
to protein perdition. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.11.019'
chicago: 'Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road
to Protein Perdition.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2013.11.019.'
ieee: 'M. Sauer and J. Friml, “Plant biology: Gatekeepers of the road to protein
perdition,” Current Biology, vol. 24, no. 1. Cell Press, pp. R27–R29, 2014.'
ista: 'Sauer M, Friml J. 2014. Plant biology: Gatekeepers of the road to protein
perdition. Current Biology. 24(1), R27–R29.'
mla: 'Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to
Protein Perdition.” Current Biology, vol. 24, no. 1, Cell Press, 2014,
pp. R27–29, doi:10.1016/j.cub.2013.11.019.'
short: M. Sauer, J. Friml, Current Biology 24 (2014) R27–R29.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-01-06T00:00:00Z
date_updated: 2021-01-12T06:54:02Z
day: '06'
department:
- _id: JiFr
doi: 10.1016/j.cub.2013.11.019
intvolume: ' 24'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: R27 - R29
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5180'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Plant biology: Gatekeepers of the road to protein perdition'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2014'
...
---
_id: '1925'
abstract:
- lang: eng
text: In the past decade carbon nanotubes (CNTs) have been widely studied as a potential
drug-delivery system, especially with functionality for cellular targeting. Yet,
little is known about the actual process of docking to cell receptors and transport
dynamics after internalization. Here we performed single-particle studies of folic
acid (FA) mediated CNT binding to human carcinoma cells and their transport inside
the cytosol. In particular, we employed molecular recognition force spectroscopy,
an atomic force microscopy based method, to visualize and quantify docking of
FA functionalized CNTs to FA binding receptors in terms of binding probability
and binding force. We then traced individual fluorescently labeled, FA functionalized
CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed
trajectories of directed diffusion and areas of nanotube confinement in the cytosol.
Our results demonstrate the potential of a single-molecule approach for investigation
of drug-delivery vehicles and their targeting capacity.
acknowledgement: "This work was supported by EC grant Marie Curie RTN-CT-2006-035616,
CARBIO 'Carbon nanotubes for biomedical applications' and Austrian FFG grant mnt-era.net
823980, 'IntelliTip'.\r\n"
article_number: '125704'
article_processing_charge: No
article_type: original
author:
- first_name: Constanze
full_name: Lamprecht, Constanze
last_name: Lamprecht
- first_name: Birgit
full_name: Plochberger, Birgit
last_name: Plochberger
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Christian
full_name: Rankl, Christian
last_name: Rankl
- first_name: Elena
full_name: Heister, Elena
last_name: Heister
- first_name: Barbara
full_name: Unterauer, Barbara
last_name: Unterauer
- first_name: Mario
full_name: Brameshuber, Mario
last_name: Brameshuber
- first_name: Jürgen
full_name: Danzberger, Jürgen
last_name: Danzberger
- first_name: Petar
full_name: Lukanov, Petar
last_name: Lukanov
- first_name: Emmanuel
full_name: Flahaut, Emmanuel
last_name: Flahaut
- first_name: Gerhard
full_name: Schütz, Gerhard
last_name: Schütz
- first_name: Peter
full_name: Hinterdorfer, Peter
last_name: Hinterdorfer
- first_name: Andreas
full_name: Ebner, Andreas
last_name: Ebner
citation:
ama: Lamprecht C, Plochberger B, Ruprecht V, et al. A single-molecule approach to
explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology.
2014;25(12). doi:10.1088/0957-4484/25/12/125704
apa: Lamprecht, C., Plochberger, B., Ruprecht, V., Wieser, S., Rankl, C., Heister,
E., … Ebner, A. (2014). A single-molecule approach to explore binding uptake and
transport of cancer cell targeting nanotubes. Nanotechnology. IOP Publishing.
https://doi.org/10.1088/0957-4484/25/12/125704
chicago: Lamprecht, Constanze, Birgit Plochberger, Verena Ruprecht, Stefan Wieser,
Christian Rankl, Elena Heister, Barbara Unterauer, et al. “A Single-Molecule Approach
to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology.
IOP Publishing, 2014. https://doi.org/10.1088/0957-4484/25/12/125704.
ieee: C. Lamprecht et al., “A single-molecule approach to explore binding
uptake and transport of cancer cell targeting nanotubes,” Nanotechnology,
vol. 25, no. 12. IOP Publishing, 2014.
ista: Lamprecht C, Plochberger B, Ruprecht V, Wieser S, Rankl C, Heister E, Unterauer
B, Brameshuber M, Danzberger J, Lukanov P, Flahaut E, Schütz G, Hinterdorfer P,
Ebner A. 2014. A single-molecule approach to explore binding uptake and transport
of cancer cell targeting nanotubes. Nanotechnology. 25(12), 125704.
mla: Lamprecht, Constanze, et al. “A Single-Molecule Approach to Explore Binding
Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology,
vol. 25, no. 12, 125704, IOP Publishing, 2014, doi:10.1088/0957-4484/25/12/125704.
short: C. Lamprecht, B. Plochberger, V. Ruprecht, S. Wieser, C. Rankl, E. Heister,
B. Unterauer, M. Brameshuber, J. Danzberger, P. Lukanov, E. Flahaut, G. Schütz,
P. Hinterdorfer, A. Ebner, Nanotechnology 25 (2014).
date_created: 2018-12-11T11:54:45Z
date_published: 2014-03-28T00:00:00Z
date_updated: 2021-01-12T06:54:07Z
day: '28'
ddc:
- '570'
department:
- _id: CaHe
- _id: MiSi
doi: 10.1088/0957-4484/25/12/125704
file:
- access_level: open_access
checksum: df4e03d225a19179e7790f6d87a12332
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T09:21:19Z
date_updated: 2020-07-14T12:45:21Z
file_id: '7856'
file_name: 2014_Nanotechnology_Lamprecht.pdf
file_size: 3804152
relation: main_file
file_date_updated: 2020-07-14T12:45:21Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '12'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
publication: Nanotechnology
publication_status: published
publisher: IOP Publishing
publist_id: '5169'
scopus_import: 1
status: public
title: A single-molecule approach to explore binding uptake and transport of cancer
cell targeting nanotubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2014'
...
---
_id: '1923'
abstract:
- lang: eng
text: We derive the equations for a thin, axisymmetric elastic shell subjected to
an internal active stress giving rise to active tension and moments within the
shell. We discuss the stability of a cylindrical elastic shell and its response
to a localized change in internal active stress. This description is relevant
to describe the cellular actomyosin cortex, a thin shell at the cell surface behaving
elastically at a short timescale and subjected to active internal forces arising
from myosin molecular motor activity. We show that the recent observations of
cell deformation following detachment of adherent cells (Maître J-L et al 2012
Science 338 253-6) are well accounted for by this mechanical description. The
actin cortex elastic and bending moduli can be obtained from a quantitative analysis
of cell shapes observed in these experiments. Our approach thus provides a non-invasive,
imaging-based method for the extraction of cellular physical parameters.
article_number: '065005'
author:
- first_name: Hélène
full_name: Berthoumieux, Hélène
last_name: Berthoumieux
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
citation:
ama: Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux
G. Active elastic thin shell theory for cellular deformations. New Journal
of Physics. 2014;16. doi:10.1088/1367-2630/16/6/065005
apa: Berthoumieux, H., Maître, J.-L., Heisenberg, C.-P. J., Paluch, E., Julicher,
F., & Salbreux, G. (2014). Active elastic thin shell theory for cellular deformations.
New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/16/6/065005
chicago: Berthoumieux, Hélène, Jean-Léon Maître, Carl-Philipp J Heisenberg, Ewa
Paluch, Frank Julicher, and Guillaume Salbreux. “Active Elastic Thin Shell Theory
for Cellular Deformations.” New Journal of Physics. IOP Publishing Ltd.,
2014. https://doi.org/10.1088/1367-2630/16/6/065005.
ieee: H. Berthoumieux, J.-L. Maître, C.-P. J. Heisenberg, E. Paluch, F. Julicher,
and G. Salbreux, “Active elastic thin shell theory for cellular deformations,”
New Journal of Physics, vol. 16. IOP Publishing Ltd., 2014.
ista: Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux
G. 2014. Active elastic thin shell theory for cellular deformations. New Journal
of Physics. 16, 065005.
mla: Berthoumieux, Hélène, et al. “Active Elastic Thin Shell Theory for Cellular
Deformations.” New Journal of Physics, vol. 16, 065005, IOP Publishing
Ltd., 2014, doi:10.1088/1367-2630/16/6/065005.
short: H. Berthoumieux, J.-L. Maître, C.-P.J. Heisenberg, E. Paluch, F. Julicher,
G. Salbreux, New Journal of Physics 16 (2014).
date_created: 2018-12-11T11:54:44Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T06:54:06Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1088/1367-2630/16/6/065005
file:
- access_level: open_access
checksum: 8dbe81ec656bf1264d8889bda9b2b985
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:16Z
date_updated: 2020-07-14T12:45:21Z
file_id: '5202'
file_name: IST-2016-429-v1+1_document.pdf
file_size: 941387
relation: main_file
file_date_updated: 2020-07-14T12:45:21Z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5171'
pubrep_id: '429'
quality_controlled: '1'
scopus_import: 1
status: public
title: Active elastic thin shell theory for cellular deformations
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: 16
year: '2014'
...
---
_id: '1921'
abstract:
- lang: eng
text: Cell polarity manifested by asymmetric distribution of cargoes, such as receptors
and transporters, within the plasma membrane (PM) is crucial for essential functions
in multicellular organisms. In plants, cell polarity (re)establishment is intimately
linked to patterning processes. Despite the importance of cell polarity, its underlying
mechanisms are still largely unknown, including the definition and distinctiveness
of the polar domains within the PM. Here, we show in Arabidopsis thaliana that
the signaling membrane components, the phosphoinositides phosphatidylinositol
4-phosphate (PtdIns4P) and phosphatidylinositol 4, 5-bisphosphate [PtdIns(4, 5)P2]
as well as PtdIns4P 5-kinases mediating their interconversion, are specifically
enriched at apical and basal polar plasma membrane domains. The PtdIns4P 5-kinases
PIP5K1 and PIP5K2 are redundantly required for polar localization of specifically
apical and basal cargoes, such as PIN-FORMED transporters for the plant hormone
auxin. As a consequence of the polarity defects, instructive auxin gradients as
well as embryonic and postembryonic patterning are severely compromised. Furthermore,
auxin itself regulates PIP5K transcription and PtdIns4P and PtdIns(4, 5)P2 levels,
in particular their association with polar PM domains. Our results provide insight
into the polar domain-delineating mechanisms in plant cells that depend on apical
and basal distribution of membrane lipids and are essential for embryonic and
postembryonic patterning.
acknowledgement: This work was supported by grants from the Odysseus program of the
Research Foundation-Flanders (to J.F.).
author:
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: 'MiriamPalacios '
full_name: 'Palacios-Gomez, MiriamPalacios '
last_name: Palacios-Gomez
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Mareike
full_name: Heilmann, Mareike
last_name: Heilmann
- first_name: Ringo
full_name: Van Wijk, Ringo
last_name: Van Wijk
- first_name: Joop
full_name: Vermeer, Joop
last_name: Vermeer
- 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: Tejos R, Sauer M, Vanneste S, et al. Bipolar plasma membrane distribution of
phosphoinositides and their requirement for auxin-mediated cell polarity and patterning
in Arabidopsis. Plant Cell. 2014;26(5):2114-2128. doi:10.1105/tpc.114.126185
apa: Tejos, R., Sauer, M., Vanneste, S., Palacios-Gomez, M., Li, H., Heilmann, M.,
… Friml, J. (2014). Bipolar plasma membrane distribution of phosphoinositides
and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis.
Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.126185
chicago: Tejos, Ricardo, Michael Sauer, Steffen Vanneste, MiriamPalacios Palacios-Gomez,
Hongjiang Li, Mareike Heilmann, Ringo Van Wijk, et al. “Bipolar Plasma Membrane
Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell
Polarity and Patterning in Arabidopsis.” Plant Cell. American Society of
Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.126185.
ieee: R. Tejos et al., “Bipolar plasma membrane distribution of phosphoinositides
and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis,”
Plant Cell, vol. 26, no. 5. American Society of Plant Biologists, pp. 2114–2128,
2014.
ista: Tejos R, Sauer M, Vanneste S, Palacios-Gomez M, Li H, Heilmann M, Van Wijk
R, Vermeer J, Heilmann I, Munnik T, Friml J. 2014. Bipolar plasma membrane distribution
of phosphoinositides and their requirement for auxin-mediated cell polarity and
patterning in Arabidopsis. Plant Cell. 26(5), 2114–2128.
mla: Tejos, Ricardo, et al. “Bipolar Plasma Membrane Distribution of Phosphoinositides
and Their Requirement for Auxin-Mediated Cell Polarity and Patterning in Arabidopsis.”
Plant Cell, vol. 26, no. 5, American Society of Plant Biologists, 2014,
pp. 2114–28, doi:10.1105/tpc.114.126185.
short: R. Tejos, M. Sauer, S. Vanneste, M. Palacios-Gomez, H. Li, M. Heilmann, R.
Van Wijk, J. Vermeer, I. Heilmann, T. Munnik, J. Friml, Plant Cell 26 (2014) 2114–2128.
date_created: 2018-12-11T11:54:43Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-01-12T06:54:05Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.114.126185
ec_funded: 1
intvolume: ' 26'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079372/
month: '05'
oa: 1
oa_version: Submitted Version
page: 2114 - 2128
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5173'
scopus_import: 1
status: public
title: Bipolar plasma membrane distribution of phosphoinositides and their requirement
for auxin-mediated cell polarity and patterning in Arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2014'
...
---
_id: '1922'
abstract:
- lang: eng
text: Germination of Arabidopsis seeds in darkness induces apical hook development,
based on a tightly regulated differential growth coordinated by a multiple hormone
cross-talk. Here, we endeavoured to clarify the function of brassinosteroids (BRs)
and cross-talk with ethylene in hook development. An automated infrared imaging
system was developed to study the kinetics of hook development in etiolated Arabidopsis
seedlings. To ascertain the photomorphogenic control of hook opening, the system
was equipped with an automatic light dimmer. We demonstrate that ethylene and
BRs are indispensable for hook formation and maintenance. Ethylene regulation
of hook formation functions partly through BRs, with BR feedback inhibition of
ethylene action. Conversely, BR-mediated extension of hook maintenance functions
partly through ethylene. Furthermore, we revealed that a short light pulse is
sufficient to induce rapid hook opening. Our dynamic infrared imaging system allows
high-resolution, kinetic imaging of up to 112 seedlings in a single experimental
run. At this high throughput, it is ideally suited to rapidly gain insight in
pathway networks. We demonstrate that BRs and ethylene cooperatively regulate
apical hook development in a phase-dependent manner. Furthermore, we show that
light is a predominant regulator of hook opening, inhibiting ethylene- and BR-mediated
postponement of hook opening.
acknowledgement: 'Funded by Ghent University; Research Foundation Flanders Grant Number:
G065613N European Research Council Grant Number: CZ.1.07/2.3.00/20.0043'
author:
- first_name: Dajo
full_name: Smet, Dajo
last_name: Smet
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Filip
full_name: Vandenbussche, Filip
last_name: Vandenbussche
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
citation:
ama: 'Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. Dynamic
infrared imaging analysis of apical hook development in Arabidopsis: The case
of brassinosteroids. New Phytologist. 2014;202(4):1398-1411. doi:10.1111/nph.12751'
apa: 'Smet, D., Žádníková, P., Vandenbussche, F., Benková, E., & Van Der Straeten,
D. (2014). Dynamic infrared imaging analysis of apical hook development in Arabidopsis:
The case of brassinosteroids. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.12751'
chicago: 'Smet, Dajo, Petra Žádníková, Filip Vandenbussche, Eva Benková, and Dominique
Van Der Straeten. “Dynamic Infrared Imaging Analysis of Apical Hook Development
in Arabidopsis: The Case of Brassinosteroids.” New Phytologist. Wiley-Blackwell,
2014. https://doi.org/10.1111/nph.12751.'
ieee: 'D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, and D. Van Der Straeten,
“Dynamic infrared imaging analysis of apical hook development in Arabidopsis:
The case of brassinosteroids,” New Phytologist, vol. 202, no. 4. Wiley-Blackwell,
pp. 1398–1411, 2014.'
ista: 'Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. 2014.
Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The
case of brassinosteroids. New Phytologist. 202(4), 1398–1411.'
mla: 'Smet, Dajo, et al. “Dynamic Infrared Imaging Analysis of Apical Hook Development
in Arabidopsis: The Case of Brassinosteroids.” New Phytologist, vol. 202,
no. 4, Wiley-Blackwell, 2014, pp. 1398–411, doi:10.1111/nph.12751.'
short: D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, D. Van Der Straeten,
New Phytologist 202 (2014) 1398–1411.
date_created: 2018-12-11T11:54:44Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T06:54:05Z
day: '01'
department:
- _id: EvBe
doi: 10.1111/nph.12751
ec_funded: 1
intvolume: ' 202'
issue: '4'
language:
- iso: eng
month: '06'
oa_version: None
page: 1398 - 1411
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: New Phytologist
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5172'
scopus_import: 1
status: public
title: 'Dynamic infrared imaging analysis of apical hook development in Arabidopsis:
The case of brassinosteroids'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2014'
...
---
_id: '1927'
abstract:
- lang: eng
text: Constrained pseudorandom functions have recently been introduced independently
by Boneh and Waters (Asiacrypt’13), Kiayias et al. (CCS’13), and Boyle et al.
(PKC’14). In a standard pseudorandom function (PRF) a key k is used to evaluate
the PRF on all inputs in the domain. Constrained PRFs additionally offer the functionality
to delegate “constrained” keys kS which allow to evaluate the PRF only on a subset
S of the domain. The three above-mentioned papers all show that the classical
GGM construction (J.ACM’86) of a PRF from a pseudorandom generator (PRG) directly
yields a constrained PRF where one can compute constrained keys to evaluate the
PRF on all inputs with a given prefix. This constrained PRF has already found
many interesting applications. Unfortunately, the existing security proofs only
show selective security (by a reduction to the security of the underlying PRG).
To achieve full security, one has to use complexity leveraging, which loses an
exponential factor 2N in security, where N is the input length. The first contribution
of this paper is a new reduction that only loses a quasipolynomial factor qlog
N, where q is the number of adversarial queries. For this we develop a new proof
technique which constructs a distinguisher by interleaving simple guessing steps
and hybrid arguments a small number of times. This approach might be of interest
also in other contexts where currently the only technique to achieve full security
is complexity leveraging. Our second contribution is concerned with another constrained
PRF, due to Boneh and Waters, which allows for constrained keys for the more general
class of bit-fixing functions. Their security proof also suffers from a 2N loss,
which we show is inherent. We construct a meta-reduction which shows that any
“simple” reduction of full security from a noninteractive hardness assumption
must incur an exponential security loss.
acknowledgement: We are grateful to Mihir Bellare for his feedback on earlier versions
of this paper. We are indebted to Vanishree Rao for her generous assistance in preparing
this proceedings version.
author:
- first_name: Georg
full_name: Georg Fuchsbauer
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Momchil
full_name: Konstantinov, Momchil
last_name: Konstantinov
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Vanishree
full_name: Rao, Vanishree
last_name: Rao
citation:
ama: 'Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. Adaptive security of constrained
PRFs. In: Vol 8874. Springer; 2014:173-192. doi:10.1145/2591796.2591825'
apa: Fuchsbauer, G., Konstantinov, M., Pietrzak, K. Z., & Rao, V. (2014). Adaptive
security of constrained PRFs (Vol. 8874, pp. 173–192). Presented at the Lecture
Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), Springer. https://doi.org/10.1145/2591796.2591825
chicago: Fuchsbauer, Georg, Momchil Konstantinov, Krzysztof Z Pietrzak, and Vanishree
Rao. “Adaptive Security of Constrained PRFs,” 8874:173–92. Springer, 2014. https://doi.org/10.1145/2591796.2591825.
ieee: G. Fuchsbauer, M. Konstantinov, K. Z. Pietrzak, and V. Rao, “Adaptive security
of constrained PRFs,” presented at the Lecture Notes in Computer Science (including
subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
2014, vol. 8874, pp. 173–192.
ista: Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. 2014. Adaptive security
of constrained PRFs. Lecture Notes in Computer Science (including subseries Lecture
Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) vol. 8874,
173–192.
mla: Fuchsbauer, Georg, et al. Adaptive Security of Constrained PRFs. Vol.
8874, Springer, 2014, pp. 173–92, doi:10.1145/2591796.2591825.
short: G. Fuchsbauer, M. Konstantinov, K.Z. Pietrzak, V. Rao, in:, Springer, 2014,
pp. 173–192.
conference:
name: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics)
date_created: 2018-12-11T11:54:45Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:08Z
day: '01'
doi: 10.1145/2591796.2591825
extern: 1
intvolume: ' 8874'
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2014/416
month: '01'
oa: 1
page: 173 - 192
publication_status: published
publisher: Springer
publist_id: '5167'
quality_controlled: 0
status: public
title: Adaptive security of constrained PRFs
type: conference
volume: 8874
year: '2014'
...
---
_id: '1926'
abstract:
- lang: eng
text: We consider cross products of finite graphs with a class of trees that have
arbitrarily but finitely long line segments, such as the Fibonacci tree. Such
cross products are called tree-strips. We prove that for small disorder random
Schrödinger operators on such tree-strips have purely absolutely continuous spectrum
in a certain set.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Sadel, Christian
id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
last_name: Sadel
orcid: 0000-0001-8255-3968
citation:
ama: Sadel C. Absolutely continuous spectrum for random Schrödinger operators on
the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry.
2014;17(3-4):409-440. doi:10.1007/s11040-014-9163-4
apa: Sadel, C. (2014). Absolutely continuous spectrum for random Schrödinger operators
on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and
Geometry. Springer. https://doi.org/10.1007/s11040-014-9163-4
chicago: Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger
Operators on the Fibonacci and Similar Tree-Strips.” Mathematical Physics,
Analysis and Geometry. Springer, 2014. https://doi.org/10.1007/s11040-014-9163-4.
ieee: C. Sadel, “Absolutely continuous spectrum for random Schrödinger operators
on the Fibonacci and similar Tree-strips,” Mathematical Physics, Analysis and
Geometry, vol. 17, no. 3–4. Springer, pp. 409–440, 2014.
ista: Sadel C. 2014. Absolutely continuous spectrum for random Schrödinger operators
on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry.
17(3–4), 409–440.
mla: Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger Operators
on the Fibonacci and Similar Tree-Strips.” Mathematical Physics, Analysis and
Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 409–40, doi:10.1007/s11040-014-9163-4.
short: C. Sadel, Mathematical Physics, Analysis and Geometry 17 (2014) 409–440.
date_created: 2018-12-11T11:54:45Z
date_published: 2014-12-17T00:00:00Z
date_updated: 2021-01-12T06:54:07Z
day: '17'
department:
- _id: LaEr
doi: 10.1007/s11040-014-9163-4
ec_funded: 1
external_id:
arxiv:
- '1304.3862'
intvolume: ' 17'
issue: 3-4
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1304.3862
month: '12'
oa: 1
oa_version: Preprint
page: 409 - 440
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Mathematical Physics, Analysis and Geometry
publication_status: published
publisher: Springer
publist_id: '5168'
quality_controlled: '1'
scopus_import: 1
status: public
title: Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci
and similar Tree-strips
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2014'
...
---
_id: '1924'
abstract:
- lang: eng
text: Stomata are two-celled valves that control epidermal pores whose spacing optimizes
shoot-atmosphere gas exchange. They develop from protodermal cells after unequal
divisions followed by an equal division and differentiation. The concentration
of the hormone auxin, a master plant developmental regulator, is tightly controlled
in time and space, but its role, if any, in stomatal formation is obscure. Here
dynamic changes of auxin activity during stomatal development are monitored using
auxin input (DII-VENUS) and output (DR5:VENUS) markers by time-lapse imaging.
A decrease in auxin levels in the smaller daughter cell after unequal division
presages the acquisition of a guard mother cell fate whose equal division produces
the two guard cells. Thus, stomatal patterning requires auxin pathway control
of stem cell compartment size, as well as auxin depletion that triggers a developmental
switch from unequal to equal division.
article_number: '3090'
author:
- first_name: Jie
full_name: Le, Jie
last_name: Le
- first_name: Xuguang
full_name: Liu, Xuguang
last_name: Liu
- first_name: Kezhen
full_name: Yang, Kezhen
last_name: Yang
- first_name: Xiaolan
full_name: Chen, Xiaolan
last_name: Chen
- first_name: Lingling
full_name: Zhu, Lingling
last_name: Zhu
- first_name: Hongzhe
full_name: Wang, Hongzhe
last_name: Wang
- first_name: Ming
full_name: Wang, Ming
last_name: Wang
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Miyo
full_name: Morita, Miyo
last_name: Morita
- first_name: Masao
full_name: Tasaka, Masao
last_name: Tasaka
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Fred
full_name: Sack, Fred
last_name: Sack
citation:
ama: Le J, Liu X, Yang K, et al. Auxin transport and activity regulate stomatal
patterning and development. Nature Communications. 2014;5. doi:10.1038/ncomms4090
apa: Le, J., Liu, X., Yang, K., Chen, X., Zhu, L., Wang, H., … Sack, F. (2014).
Auxin transport and activity regulate stomatal patterning and development. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4090
chicago: Le, Jie, Xuguang Liu, Kezhen Yang, Xiaolan Chen, Lingling Zhu, Hongzhe
Wang, Ming Wang, et al. “Auxin Transport and Activity Regulate Stomatal Patterning
and Development.” Nature Communications. Nature Publishing Group, 2014.
https://doi.org/10.1038/ncomms4090.
ieee: J. Le et al., “Auxin transport and activity regulate stomatal patterning
and development,” Nature Communications, vol. 5. Nature Publishing Group,
2014.
ista: Le J, Liu X, Yang K, Chen X, Zhu L, Wang H, Wang M, Vanneste S, Morita M,
Tasaka M, Ding Z, Friml J, Beeckman T, Sack F. 2014. Auxin transport and activity
regulate stomatal patterning and development. Nature Communications. 5, 3090.
mla: Le, Jie, et al. “Auxin Transport and Activity Regulate Stomatal Patterning
and Development.” Nature Communications, vol. 5, 3090, Nature Publishing
Group, 2014, doi:10.1038/ncomms4090.
short: J. Le, X. Liu, K. Yang, X. Chen, L. Zhu, H. Wang, M. Wang, S. Vanneste, M.
Morita, M. Tasaka, Z. Ding, J. Friml, T. Beeckman, F. Sack, Nature Communications
5 (2014).
date_created: 2018-12-11T11:54:44Z
date_published: 2014-01-27T00:00:00Z
date_updated: 2021-01-12T06:54:06Z
day: '27'
department:
- _id: JiFr
doi: 10.1038/ncomms4090
intvolume: ' 5'
language:
- iso: eng
month: '01'
oa_version: None
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5170'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin transport and activity regulate stomatal patterning and development
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '1928'
abstract:
- lang: eng
text: In infectious disease epidemiology the basic reproductive ratio, R0, is defined
as the average number of new infections caused by a single infected individual
in a fully susceptible population. Many models describing competition for hosts
between non-interacting pathogen strains in an infinite population lead to the
conclusion that selection favors invasion of new strains if and only if they have
higher R0 values than the resident. Here we demonstrate that this picture fails
in finite populations. Using a simple stochastic SIS model, we show that in general
there is no analogous optimization principle. We find that successive invasions
may in some cases lead to strains that infect a smaller fraction of the host population,
and that mutually invasible pathogen strains exist. In the limit of weak selection
we demonstrate that an optimization principle does exist, although it differs
from R0 maximization. For strains with very large R0, we derive an expression
for this local fitness function and use it to establish a lower bound for the
error caused by neglecting stochastic effects. Furthermore, we apply this weak
selection limit to investigate the selection dynamics in the presence of a trade-off
between the virulence and the transmission rate of a pathogen.
acknowledgement: J.H. received support from the Zdenek Bakala Foundation and the Mobility
Fund of Charles University in Prague.
author:
- first_name: Jan
full_name: Humplik, Jan
id: 2E9627A8-F248-11E8-B48F-1D18A9856A87
last_name: Humplik
- first_name: Alison
full_name: Hill, Alison
last_name: Hill
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in
finite populations. Journal of Theoretical Biology. 2014;360:149-162. doi:10.1016/j.jtbi.2014.06.039
apa: Humplik, J., Hill, A., & Nowak, M. (2014). Evolutionary dynamics of infectious
diseases in finite populations. Journal of Theoretical Biology. Elsevier.
https://doi.org/10.1016/j.jtbi.2014.06.039
chicago: Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of
Infectious Diseases in Finite Populations.” Journal of Theoretical Biology.
Elsevier, 2014. https://doi.org/10.1016/j.jtbi.2014.06.039.
ieee: J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases
in finite populations,” Journal of Theoretical Biology, vol. 360. Elsevier,
pp. 149–162, 2014.
ista: Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases
in finite populations. Journal of Theoretical Biology. 360, 149–162.
mla: Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite
Populations.” Journal of Theoretical Biology, vol. 360, Elsevier, 2014,
pp. 149–62, doi:10.1016/j.jtbi.2014.06.039.
short: J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014)
149–162.
date_created: 2018-12-11T11:54:46Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2021-01-12T06:54:08Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.jtbi.2014.06.039
intvolume: ' 360'
language:
- iso: eng
month: '11'
oa_version: None
page: 149 - 162
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '5166'
scopus_import: 1
status: public
title: Evolutionary dynamics of infectious diseases in finite populations
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 360
year: '2014'
...
---
_id: '1929'
abstract:
- lang: eng
text: We propose an algorithm for the generalization of cartographic objects that
can be used to represent maps on different scales.
acknowledgement: We would like to offer our special thanks to students of the Department
of Mathematics of Demidov Yaroslavl State University A. A. Gorokhov and V. N. Knyazev
for participation in developing the program and assistance in preparation of test
data. This work was supported by grant 11.G34.31.0053 from the government of the
Russian Federation.
article_processing_charge: No
article_type: original
author:
- first_name: V V
full_name: Alexeev, V V
last_name: Alexeev
- first_name: V G
full_name: Bogaevskaya, V G
last_name: Bogaevskaya
- first_name: M M
full_name: Preobrazhenskaya, M M
last_name: Preobrazhenskaya
- first_name: A Y
full_name: Ukhalov, A Y
last_name: Ukhalov
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Olga
full_name: Yakimova, Olga
last_name: Yakimova
citation:
ama: Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H,
Yakimova O. An algorithm for cartographic generalization that preserves global
topology. Journal of Mathematical Sciences. 2014;203(6):754-760. doi:10.1007/s10958-014-2165-8
apa: Alexeev, V. V., Bogaevskaya, V. G., Preobrazhenskaya, M. M., Ukhalov, A. Y.,
Edelsbrunner, H., & Yakimova, O. (2014). An algorithm for cartographic generalization
that preserves global topology. Journal of Mathematical Sciences. Springer.
https://doi.org/10.1007/s10958-014-2165-8
chicago: Alexeev, V V, V G Bogaevskaya, M M Preobrazhenskaya, A Y Ukhalov, Herbert
Edelsbrunner, and Olga Yakimova. “An Algorithm for Cartographic Generalization
That Preserves Global Topology.” Journal of Mathematical Sciences. Springer,
2014. https://doi.org/10.1007/s10958-014-2165-8.
ieee: V. V. Alexeev, V. G. Bogaevskaya, M. M. Preobrazhenskaya, A. Y. Ukhalov, H.
Edelsbrunner, and O. Yakimova, “An algorithm for cartographic generalization that
preserves global topology,” Journal of Mathematical Sciences, vol. 203,
no. 6. Springer, pp. 754–760, 2014.
ista: Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner
H, Yakimova O. 2014. An algorithm for cartographic generalization that preserves
global topology. Journal of Mathematical Sciences. 203(6), 754–760.
mla: Alexeev, V. V., et al. “An Algorithm for Cartographic Generalization That Preserves
Global Topology.” Journal of Mathematical Sciences, vol. 203, no. 6, Springer,
2014, pp. 754–60, doi:10.1007/s10958-014-2165-8.
short: V.V. Alexeev, V.G. Bogaevskaya, M.M. Preobrazhenskaya, A.Y. Ukhalov, H. Edelsbrunner,
O. Yakimova, Journal of Mathematical Sciences 203 (2014) 754–760.
date_created: 2018-12-11T11:54:46Z
date_published: 2014-11-16T00:00:00Z
date_updated: 2022-05-24T10:39:06Z
day: '16'
department:
- _id: HeEd
doi: 10.1007/s10958-014-2165-8
intvolume: ' 203'
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 754 - 760
publication: Journal of Mathematical Sciences
publication_identifier:
eissn:
- 1573-8795
issn:
- 1072-3374
publication_status: published
publisher: Springer
publist_id: '5165'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An algorithm for cartographic generalization that preserves global topology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 203
year: '2014'
...