---
_id: '2844'
abstract:
- lang: eng
text: As soon as a seed germinates, plant growth relates to gravity to ensure that
the root penetrates the soil and the shoot expands aerially. Whereas mechanisms
of positive and negative orthogravitropism of primary roots and shoots are relatively
well understood [1-3], lateral organs often show more complex growth behavior
[4]. Lateral roots (LRs) seemingly suppress positive gravitropic growth and show
a defined gravitropic set-point angle (GSA) that allows radial expansion of the
root system (plagiotropism) [3, 4]. Despite its eminent importance for root architecture,
it so far remains completely unknown how lateral organs partially suppress positive
orthogravitropism. Here we show that the phytohormone auxin steers GSA formation
and limits positive orthogravitropism in LR. Low and high auxin levels/signaling
lead to radial or axial root systems, respectively. At a cellular level, it is
the auxin transport-dependent regulation of asymmetric growth in the elongation
zone that determines GSA. Our data suggest that strong repression of PIN4/PIN7
and transient PIN3 expression limit auxin redistribution in young LR columella
cells. We conclude that PIN activity, by temporally limiting the asymmetric auxin
fluxes in the tip of LRs, induces transient, differential growth responses in
the elongation zone and, consequently, controls root architecture.
article_processing_charge: No
author:
- first_name: Michel
full_name: Rosquete, Michel
last_name: Rosquete
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Ernst
full_name: Stelzer, Ernst
last_name: Stelzer
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Alexis
full_name: Maizel, Alexis
last_name: Maizel
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
citation:
ama: Rosquete M, von Wangenheim D, Marhavý P, et al. An auxin transport mechanism
restricts positive orthogravitropism in lateral roots. Current Biology.
2013;23(9):817-822. doi:10.1016/j.cub.2013.03.064
apa: Rosquete, M., von Wangenheim, D., Marhavý, P., Barbez, E., Stelzer, E., Benková,
E., … Kleine Vehn, J. (2013). An auxin transport mechanism restricts positive
orthogravitropism in lateral roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.03.064
chicago: Rosquete, Michel, Daniel von Wangenheim, Peter Marhavý, Elke Barbez, Ernst
Stelzer, Eva Benková, Alexis Maizel, and Jürgen Kleine Vehn. “An Auxin Transport
Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” Current Biology.
Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.03.064.
ieee: M. Rosquete et al., “An auxin transport mechanism restricts positive
orthogravitropism in lateral roots,” Current Biology, vol. 23, no. 9. Cell
Press, pp. 817–822, 2013.
ista: Rosquete M, von Wangenheim D, Marhavý P, Barbez E, Stelzer E, Benková E, Maizel
A, Kleine Vehn J. 2013. An auxin transport mechanism restricts positive orthogravitropism
in lateral roots. Current Biology. 23(9), 817–822.
mla: Rosquete, Michel, et al. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism
in Lateral Roots.” Current Biology, vol. 23, no. 9, Cell Press, 2013, pp.
817–22, doi:10.1016/j.cub.2013.03.064.
short: M. Rosquete, D. von Wangenheim, P. Marhavý, E. Barbez, E. Stelzer, E. Benková,
A. Maizel, J. Kleine Vehn, Current Biology 23 (2013) 817–822.
date_created: 2018-12-11T11:59:53Z
date_published: 2013-05-06T00:00:00Z
date_updated: 2025-09-29T13:43:30Z
day: '06'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1016/j.cub.2013.03.064
ec_funded: 1
external_id:
isi:
- '000318750900035'
intvolume: ' 23'
isi: 1
issue: '9'
language:
- iso: eng
month: '05'
oa_version: None
page: 817 - 822
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3950'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An auxin transport mechanism restricts positive orthogravitropism in lateral
roots
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 23
year: '2013'
...
---
_id: '2845'
abstract:
- lang: eng
text: At synapses formed between dissociated neurons, about half of all synaptic
vesicles are refractory to evoked release, forming the so-called "resting
pool." Here, we use optical measurements of vesicular pH to study developmental
changes in pool partitioning and vesicle cycling in cultured hippocampal slices.
Two-photon imaging of a genetically encoded two-color release sensor (ratio-sypHy)
allowed us to perform calibrated measurements at individual Schaffer collateral
boutons. Mature boutons released a large fraction of their vesicles during simulated
place field activity, and vesicle retrieval rates were 7-fold higher compared
to immature boutons. Saturating stimulation mobilized essentially all vesicles
at mature synapses. Resting pool formation and a concomitant reduction in evoked
release was induced by chronic depolarization but not by acute inhibition of the
protein phosphatase calcineurin. We conclude that synapses in CA1 undergo a prominent
refinement of vesicle use during early postnatal development that is not recapitulated
in dissociated neuronal culture.
article_processing_charge: No
author:
- first_name: Tobias
full_name: Rose, Tobias
last_name: Rose
- first_name: Philipp
full_name: Schönenberger, Philipp
id: 3B9D816C-F248-11E8-B48F-1D18A9856A87
last_name: Schönenberger
- first_name: Karel
full_name: Jezek, Karel
last_name: Jezek
- first_name: Thomas
full_name: Oertner, Thomas
last_name: Oertner
citation:
ama: Rose T, Schönenberger P, Jezek K, Oertner T. Developmental refinement of vesicle
cycling at Schaffer collateral synapses. Neuron. 2013;77(6):1109-1121.
doi:10.1016/j.neuron.2013.01.021
apa: Rose, T., Schönenberger, P., Jezek, K., & Oertner, T. (2013). Developmental
refinement of vesicle cycling at Schaffer collateral synapses. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2013.01.021
chicago: Rose, Tobias, Philipp Schönenberger, Karel Jezek, and Thomas Oertner. “Developmental
Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” Neuron.
Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.01.021.
ieee: T. Rose, P. Schönenberger, K. Jezek, and T. Oertner, “Developmental refinement
of vesicle cycling at Schaffer collateral synapses,” Neuron, vol. 77, no.
6. Elsevier, pp. 1109–1121, 2013.
ista: Rose T, Schönenberger P, Jezek K, Oertner T. 2013. Developmental refinement
of vesicle cycling at Schaffer collateral synapses. Neuron. 77(6), 1109–1121.
mla: Rose, Tobias, et al. “Developmental Refinement of Vesicle Cycling at Schaffer
Collateral Synapses.” Neuron, vol. 77, no. 6, Elsevier, 2013, pp. 1109–21,
doi:10.1016/j.neuron.2013.01.021.
short: T. Rose, P. Schönenberger, K. Jezek, T. Oertner, Neuron 77 (2013) 1109–1121.
date_created: 2018-12-11T11:59:54Z
date_published: 2013-03-20T00:00:00Z
date_updated: 2025-09-29T13:42:59Z
day: '20'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2013.01.021
external_id:
isi:
- '000316645000012'
intvolume: ' 77'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 1109 - 1121
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '3949'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Developmental refinement of vesicle cycling at Schaffer collateral synapses
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 77
year: '2013'
...
---
_id: '2846'
abstract:
- lang: eng
text: The Red Queen hypothesis proposes that coevolving parasites select for outcrossing
in the host. Outcrossing relies on males, which often show lower immune investment
due to, for example, sexual selection. Here, we demonstrate that such sex differences
in immunity interfere with parasite-mediated selection for outcrossing. Two independent
coevolution experiments with Caenorhabditis elegans and its microparasite Bacillus
thuringiensis produced decreased yet stable frequencies of outcrossing male hosts.
A subsequent systematic analysis verified that male C. elegans suffered from a
direct selective disadvantage under parasite pressure (i.e. lower resistance,
decreased sexual activity, increased escape behaviour), which can reduce outcrossing
and thus male frequencies. At the same time, males offered an indirect selective
benefit, because male-mediated outcrossing increased offspring resistance, thus
favouring male persistence in the evolving populations. As sex differences in
immunity are widespread, such interference of opposing selective constraints is
likely of central importance during host adaptation to a coevolving parasite.
article_processing_charge: No
author:
- first_name: Leila
full_name: El Masri, Leila
id: 349A6E66-F248-11E8-B48F-1D18A9856A87
last_name: El Masri
- first_name: Rebecca
full_name: Schulte, Rebecca
last_name: Schulte
- first_name: Nadine
full_name: Timmermeyer, Nadine
last_name: Timmermeyer
- first_name: Stefanie
full_name: Thanisch, Stefanie
last_name: Thanisch
- first_name: Lena
full_name: Crummenerl, Lena
last_name: Crummenerl
- first_name: Gunther
full_name: Jansen, Gunther
last_name: Jansen
- first_name: Nico
full_name: Michiels, Nico
last_name: Michiels
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: El Masri L, Schulte R, Timmermeyer N, et al. Sex differences in host defence
interfere with parasite-mediated selection for outcrossing during host-parasite
coevolution. Ecology Letters. 2013;16(4):461-468. doi:10.1111/ele.12068
apa: El Masri, L., Schulte, R., Timmermeyer, N., Thanisch, S., Crummenerl, L., Jansen,
G., … Schulenburg, H. (2013). Sex differences in host defence interfere with parasite-mediated
selection for outcrossing during host-parasite coevolution. Ecology Letters.
Wiley-Blackwell. https://doi.org/10.1111/ele.12068
chicago: El Masri, Leila, Rebecca Schulte, Nadine Timmermeyer, Stefanie Thanisch,
Lena Crummenerl, Gunther Jansen, Nico Michiels, and Hinrich Schulenburg. “Sex
Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing
during Host-Parasite Coevolution.” Ecology Letters. Wiley-Blackwell, 2013.
https://doi.org/10.1111/ele.12068.
ieee: L. El Masri et al., “Sex differences in host defence interfere with
parasite-mediated selection for outcrossing during host-parasite coevolution,”
Ecology Letters, vol. 16, no. 4. Wiley-Blackwell, pp. 461–468, 2013.
ista: El Masri L, Schulte R, Timmermeyer N, Thanisch S, Crummenerl L, Jansen G,
Michiels N, Schulenburg H. 2013. Sex differences in host defence interfere with
parasite-mediated selection for outcrossing during host-parasite coevolution.
Ecology Letters. 16(4), 461–468.
mla: El Masri, Leila, et al. “Sex Differences in Host Defence Interfere with Parasite-Mediated
Selection for Outcrossing during Host-Parasite Coevolution.” Ecology Letters,
vol. 16, no. 4, Wiley-Blackwell, 2013, pp. 461–68, doi:10.1111/ele.12068.
short: L. El Masri, R. Schulte, N. Timmermeyer, S. Thanisch, L. Crummenerl, G. Jansen,
N. Michiels, H. Schulenburg, Ecology Letters 16 (2013) 461–468.
date_created: 2018-12-11T11:59:54Z
date_published: 2013-04-04T00:00:00Z
date_updated: 2022-08-25T14:51:57Z
day: '04'
ddc:
- '570'
doi: 10.1111/ele.12068
extern: '1'
file:
- access_level: open_access
checksum: aa7db788f7da7d7f102539a249ebce50
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:52Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5176'
file_name: IST-2016-404-v1+1_ele12068.pdf
file_size: 763731
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 461 - 468
publication: Ecology Letters
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3948'
pubrep_id: '404'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sex differences in host defence interfere with parasite-mediated selection
for outcrossing during host-parasite coevolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2013'
...
---
_id: '2847'
abstract:
- lang: eng
text: Depth-Bounded Systems form an expressive class of well-structured transition
systems. They can model a wide range of concurrent infinite-state systems including
those with dynamic thread creation, dynamically changing communication topology,
and complex shared heap structures. We present the first method to automatically
prove fair termination of depth-bounded systems. Our method uses a numerical abstraction
of the system, which we obtain by systematically augmenting an over-approximation
of the system’s reachable states with a finite set of counters. This numerical
abstraction can be analyzed with existing termination provers. What makes our
approach unique is the way in which it exploits the well-structuredness of the
analyzed system. We have implemented our work in a prototype tool and used it
to automatically prove liveness properties of complex concurrent systems, including
nonblocking algorithms such as Treiber’s stack and several distributed processes.
Many of these examples are beyond the scope of termination analyses that are based
on traditional counter abstractions.
alternative_title:
- LNCS
author:
- first_name: Kshitij
full_name: Bansal, Kshitij
last_name: Bansal
- first_name: Eric
full_name: Koskinen, Eric
last_name: Koskinen
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: Bansal K, Koskinen E, Wies T, Zufferey D. Structural Counter Abstraction. Piterman
N, Smolka S, eds. 2013;7795:62-77. doi:10.1007/978-3-642-36742-7_5
apa: 'Bansal, K., Koskinen, E., Wies, T., & Zufferey, D. (2013). Structural
Counter Abstraction. (N. Piterman & S. Smolka, Eds.). Presented at the TACAS:
Tools and Algorithms for the Construction and Analysis of Systems, Rome, Italy:
Springer. https://doi.org/10.1007/978-3-642-36742-7_5'
chicago: Bansal, Kshitij, Eric Koskinen, Thomas Wies, and Damien Zufferey. “Structural
Counter Abstraction.” Edited by Nir Piterman and Scott Smolka. Lecture Notes in
Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36742-7_5.
ieee: K. Bansal, E. Koskinen, T. Wies, and D. Zufferey, “Structural Counter Abstraction,”
vol. 7795. Springer, pp. 62–77, 2013.
ista: Bansal K, Koskinen E, Wies T, Zufferey D. 2013. Structural Counter Abstraction
(eds. N. Piterman & S. Smolka). 7795, 62–77.
mla: Bansal, Kshitij, et al. Structural Counter Abstraction. Edited by Nir
Piterman and Scott Smolka, vol. 7795, Springer, 2013, pp. 62–77, doi:10.1007/978-3-642-36742-7_5.
short: K. Bansal, E. Koskinen, T. Wies, D. Zufferey, 7795 (2013) 62–77.
conference:
end_date: 2013-03-24
location: Rome, Italy
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2013-03-16
date_created: 2018-12-11T11:59:54Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2025-04-15T08:11:55Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-36742-7_5
ec_funded: 1
editor:
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
- first_name: Scott
full_name: Smolka, Scott
last_name: Smolka
intvolume: ' 7795'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arise.or.at/pubpdf/Structural_Counter_Abstraction.pdf
month: '03'
oa: 1
oa_version: Submitted Version
page: 62 - 77
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '3947'
quality_controlled: '1'
related_material:
record:
- id: '1405'
relation: dissertation_contains
status: public
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Structural Counter Abstraction
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7795
year: '2013'
...
---
_id: '2850'
abstract:
- lang: eng
text: "Recent work emphasizes that the maximum entropy principle provides a bridge
between statistical mechanics models for collective behavior in neural networks
and experiments on networks of real neurons. Most of this work has focused on
capturing the measured correlations among pairs of neurons. Here we suggest an
alternative, constructing models that are consistent with the distribution of
global network activity, i.e. the probability that K out of N cells in the network
generate action potentials in the same small time bin. The inverse problem that
we need to solve in constructing the model is analytically tractable, and provides
a natural 'thermodynamics' for the network in the limit of large N. We analyze
the responses of neurons in a small patch of the retina to naturalistic stimuli,
and find that the implied thermodynamics is very close to an unusual critical
point, in which the entropy (in proper units) is exactly equal to the energy.
© 2013 IOP Publishing Ltd and SISSA Medialab srl.\r\n"
acknowledgement: "his work was supported in part by NSF Grants IIS-0613435 and PHY-0957573,
by NIH Grants R01 EY14196 and P50 GM071508, by the Fannie and John Hertz Foundation,
by the Human Frontiers Science Program, by the Swartz Foundation, and by the WM
Keck Foundation.\r\n"
article_number: P03011
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
- first_name: Dario
full_name: Amodei, Dario
last_name: Amodei
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. The simplest maximum
entropy model for collective behavior in a neural network. Journal of Statistical
Mechanics Theory and Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03011
apa: Tkačik, G., Marre, O., Mora, T., Amodei, D., Berry, M., & Bialek, W. (2013).
The simplest maximum entropy model for collective behavior in a neural network.
Journal of Statistical Mechanics Theory and Experiment. IOP Publishing.
https://doi.org/10.1088/1742-5468/2013/03/P03011
chicago: Tkačik, Gašper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry,
and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior
in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing, 2013. https://doi.org/10.1088/1742-5468/2013/03/P03011.
ieee: G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest
maximum entropy model for collective behavior in a neural network,” Journal
of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3. IOP Publishing,
2013.
ista: Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. 2013. The simplest
maximum entropy model for collective behavior in a neural network. Journal of
Statistical Mechanics Theory and Experiment. 2013(3), P03011.
mla: Tkačik, Gašper, et al. “The Simplest Maximum Entropy Model for Collective Behavior
in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment,
vol. 2013, no. 3, P03011, IOP Publishing, 2013, doi:10.1088/1742-5468/2013/03/P03011.
short: G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of
Statistical Mechanics Theory and Experiment 2013 (2013).
date_created: 2018-12-11T11:59:55Z
date_published: 2013-03-12T00:00:00Z
date_updated: 2025-09-29T13:42:18Z
day: '12'
department:
- _id: GaTk
doi: 10.1088/1742-5468/2013/03/P03011
external_id:
arxiv:
- '1207.6319'
isi:
- '000316056900011'
intvolume: ' 2013'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.6319
month: '03'
oa: 1
oa_version: Preprint
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing
publist_id: '3942'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The simplest maximum entropy model for collective behavior in a neural network
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2013
year: '2013'
...
---
_id: '2851'
abstract:
- lang: eng
text: The number of possible activity patterns in a population of neurons grows
exponentially with the size of the population. Typical experiments explore only
a tiny fraction of the large space of possible activity patterns in the case of
populations with more than 10 or 20 neurons. It is thus impossible, in this undersampled
regime, to estimate the probabilities with which most of the activity patterns
occur. As a result, the corresponding entropy - which is a measure of the computational
power of the neural population - cannot be estimated directly. We propose a simple
scheme for estimating the entropy in the undersampled regime, which bounds its
value from both below and above. The lower bound is the usual 'naive' entropy
of the experimental frequencies. The upper bound results from a hybrid approximation
of the entropy which makes use of the naive estimate, a maximum entropy fit, and
a coverage adjustment. We apply our simple scheme to artificial data, in order
to check their accuracy; we also compare its performance to those of several previously
defined entropy estimators. We then apply it to actual measurements of neural
activity in populations with up to 100 cells. Finally, we discuss the similarities
and differences between the proposed simple estimation scheme and various earlier
methods. © 2013 IOP Publishing Ltd and SISSA Medialab srl.
article_number: P03015
article_processing_charge: No
author:
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Julien
full_name: Dubuis, Julien
last_name: Dubuis
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Ravá
full_name: Da Silveira, Ravá
last_name: Da Silveira
citation:
ama: Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. A simple method for estimating
the entropy of neural activity. Journal of Statistical Mechanics Theory and
Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03015
apa: Berry, M., Tkačik, G., Dubuis, J., Marre, O., & Da Silveira, R. (2013).
A simple method for estimating the entropy of neural activity. Journal of Statistical
Mechanics Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/2013/03/P03015
chicago: Berry, Michael, Gašper Tkačik, Julien Dubuis, Olivier Marre, and Ravá Da
Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal
of Statistical Mechanics Theory and Experiment. IOP Publishing, 2013. https://doi.org/10.1088/1742-5468/2013/03/P03015.
ieee: M. Berry, G. Tkačik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method
for estimating the entropy of neural activity,” Journal of Statistical Mechanics
Theory and Experiment, vol. 2013, no. 3. IOP Publishing, 2013.
ista: Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. 2013. A simple method
for estimating the entropy of neural activity. Journal of Statistical Mechanics
Theory and Experiment. 2013(3), P03015.
mla: Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural
Activity.” Journal of Statistical Mechanics Theory and Experiment, vol.
2013, no. 3, P03015, IOP Publishing, 2013, doi:10.1088/1742-5468/2013/03/P03015.
short: M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical
Mechanics Theory and Experiment 2013 (2013).
date_created: 2018-12-11T11:59:56Z
date_published: 2013-03-12T00:00:00Z
date_updated: 2025-09-29T13:41:46Z
day: '12'
department:
- _id: GaTk
doi: 10.1088/1742-5468/2013/03/P03015
external_id:
isi:
- '000316056900015'
intvolume: ' 2013'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing
publist_id: '3941'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A simple method for estimating the entropy of neural activity
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2013
year: '2013'
...
---
_id: '2853'
abstract:
- lang: eng
text: High relatedness among interacting individuals has generally been considered
a precondition for the evolution of altruism. However, kin-selection theory also
predicts the evolution of altruism when relatedness is low, as long as the cost
of the altruistic act is minor compared with its benefit. Here, we demonstrate
evidence for a low-cost altruistic act in bacteria. We investigated Escherichia
coli responding to the attack of an obligately lytic phage by committing suicide
in order to prevent parasite transmission to nearby relatives. We found that bacterial
suicide provides large benefits to survivors at marginal costs to committers.
The cost of suicide was low, because infected cells are moribund, rapidly dying
upon phage infection, such that no more opportunity for reproduction remains.
As a consequence of its marginal cost, host suicide was selectively favoured even
when relatedness between committers and survivors approached zero. Altogether,
our findings demonstrate that low-cost suicide can evolve with ease, represents
an effective host-defence strategy, and seems to be widespread among microbes.
Moreover, low-cost suicide might also occur in higher organisms as exemplified
by infected social insect workers leaving the colony to die in isolation.
article_processing_charge: No
article_type: original
author:
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
citation:
ama: 'Refardt D, Bergmiller T, Kümmerli R. Altruism can evolve when relatedness
is low: Evidence from bacteria committing suicide upon phage infection. Proceedings
of the Royal Society of London Series B Biological Sciences. 2013;280(1759).
doi:10.1098/rspb.2012.3035'
apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Altruism can evolve
when relatedness is low: Evidence from bacteria committing suicide upon phage
infection. Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society. https://doi.org/10.1098/rspb.2012.3035'
chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can
Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon
Phage Infection.” Proceedings of the Royal Society of London Series B Biological
Sciences. The Royal Society, 2013. https://doi.org/10.1098/rspb.2012.3035.'
ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Altruism can evolve when relatedness
is low: Evidence from bacteria committing suicide upon phage infection,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 280, no.
1759. The Royal Society, 2013.'
ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Altruism can evolve when relatedness
is low: Evidence from bacteria committing suicide upon phage infection. Proceedings
of the Royal Society of London Series B Biological Sciences. 280(1759).'
mla: 'Refardt, Dominik, et al. “Altruism Can Evolve When Relatedness Is Low: Evidence
from Bacteria Committing Suicide upon Phage Infection.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 280, no. 1759,
The Royal Society, 2013, doi:10.1098/rspb.2012.3035.'
short: D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society
of London Series B Biological Sciences 280 (2013).
corr_author: '1'
date_created: 2018-12-11T11:59:56Z
date_published: 2013-05-22T00:00:00Z
date_updated: 2025-09-29T13:41:12Z
day: '22'
department:
- _id: CaGu
doi: 10.1098/rspb.2012.3035
external_id:
isi:
- '000317482100005'
pmid:
- '23516238'
intvolume: ' 280'
isi: 1
issue: '1759'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619501/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
publication_status: published
publisher: The Royal Society
publist_id: '3939'
quality_controlled: '1'
related_material:
record:
- id: '9751'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Altruism can evolve when relatedness is low: Evidence from bacteria committing
suicide upon phage infection'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 280
year: '2013'
...
---
_id: '2854'
abstract:
- lang: eng
text: We consider concurrent games played on graphs. At every round of a game, each
player simultaneously and independently selects a move; the moves jointly determine
the transition to a successor state. Two basic objectives are the safety objective
to stay forever in a given set of states, and its dual, the reachability objective
to reach a given set of states. First, we present a simple proof of the fact that
in concurrent reachability games, for all ε>0, memoryless ε-optimal strategies
exist. A memoryless strategy is independent of the history of plays, and an ε-optimal
strategy achieves the objective with probability within ε of the value of the
game. In contrast to previous proofs of this fact, our proof is more elementary
and more combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration)
algorithm for concurrent games with reachability objectives. Finally, we present
a strategy-improvement algorithm for turn-based stochastic games (where each player
selects moves in turns) with safety objectives. Our algorithms yield sequences
of player-1 strategies which ensure probabilities of winning that converge monotonically
(from below) to the value of the game. © 2012 Elsevier Inc.
acknowledgement: This work was partially supported in part by the NSF grants CCR-0132780,
CNS-0720884, CCR-0225610, by the Swiss National Science Foundation, ERC Start Grant
Graph Games (Project No. 279307), FWF NFN Grant S11407-N23 (RiSE), and a Microsoft
faculty fellows
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, De Alfaro L, Henzinger TA. Strategy improvement for concurrent
reachability and turn based stochastic safety games. Journal of Computer and
System Sciences. 2013;79(5):640-657. doi:10.1016/j.jcss.2012.12.001
apa: Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2013). Strategy improvement
for concurrent reachability and turn based stochastic safety games. Journal
of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2012.12.001
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy
Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.”
Journal of Computer and System Sciences. Elsevier, 2013. https://doi.org/10.1016/j.jcss.2012.12.001.
ieee: K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for
concurrent reachability and turn based stochastic safety games,” Journal of
Computer and System Sciences, vol. 79, no. 5. Elsevier, pp. 640–657, 2013.
ista: Chatterjee K, De Alfaro L, Henzinger TA. 2013. Strategy improvement for concurrent
reachability and turn based stochastic safety games. Journal of Computer and System
Sciences. 79(5), 640–657.
mla: Chatterjee, Krishnendu, et al. “Strategy Improvement for Concurrent Reachability
and Turn Based Stochastic Safety Games.” Journal of Computer and System Sciences,
vol. 79, no. 5, Elsevier, 2013, pp. 640–57, doi:10.1016/j.jcss.2012.12.001.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, Journal of Computer and System
Sciences 79 (2013) 640–657.
corr_author: '1'
date_created: 2018-12-11T11:59:57Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2025-09-29T13:40:38Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.jcss.2012.12.001
ec_funded: 1
external_id:
isi:
- '000316837300011'
file:
- access_level: open_access
checksum: 6d3ee12cceb946a0abe69594b6a22409
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:48Z
date_updated: 2020-07-14T12:45:51Z
file_id: '5370'
file_name: IST-2015-388-v1+1_1-s2.0-S0022000012001778-main.pdf
file_size: 425488
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 79'
isi: 1
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 640 - 657
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '3938'
pubrep_id: '388'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strategy improvement for concurrent reachability and turn based stochastic
safety games
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 79
year: '2013'
...
---
_id: '2855'
abstract:
- lang: eng
text: Genomic imprinting leads to preferred expression of either the maternal or
paternal alleles of a subset of genes. Imprinting is essential for mammalian development,
and its deregulation causes many diseases. However, the functional relevance of
imprinting at the cellular level is poorly understood for most imprinted genes.
We used mosaic analysis with double markers (MADM) in mice to create uniparental
disomies (UPDs) and to visualize imprinting effects with single-cell resolution.
Although chromosome 12 UPD did not produce detectable phenotypes, chromosome 7
UPD caused highly significant paternal growth dominance in the liver and lung,
but not in the brain or heart. A single gene on chromosome 7, encoding the secreted
insulin-like growth factor 2 (IGF2), accounts for most of the paternal dominance
effect. Mosaic analyses implied additional imprinted loci on chromosome 7 acting
cell autonomously to transmit the IGF2 signal. Our study reveals chromosome- and
cell-type specificity of genomic imprinting effects.
article_processing_charge: No
author:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Randy
full_name: Johnson, Randy
last_name: Johnson
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: Hippenmeyer S, Johnson R, Luo L. Mosaic analysis with double markers reveals
cell type specific paternal growth dominance. Cell Reports. 2013;3(3):960-967.
doi:10.1016/j.celrep.2013.02.002
apa: Hippenmeyer, S., Johnson, R., & Luo, L. (2013). Mosaic analysis with double
markers reveals cell type specific paternal growth dominance. Cell Reports.
Cell Press. https://doi.org/10.1016/j.celrep.2013.02.002
chicago: Hippenmeyer, Simon, Randy Johnson, and Liqun Luo. “Mosaic Analysis with
Double Markers Reveals Cell Type Specific Paternal Growth Dominance.” Cell
Reports. Cell Press, 2013. https://doi.org/10.1016/j.celrep.2013.02.002.
ieee: S. Hippenmeyer, R. Johnson, and L. Luo, “Mosaic analysis with double markers
reveals cell type specific paternal growth dominance,” Cell Reports, vol.
3, no. 3. Cell Press, pp. 960–967, 2013.
ista: Hippenmeyer S, Johnson R, Luo L. 2013. Mosaic analysis with double markers
reveals cell type specific paternal growth dominance. Cell Reports. 3(3), 960–967.
mla: Hippenmeyer, Simon, et al. “Mosaic Analysis with Double Markers Reveals Cell
Type Specific Paternal Growth Dominance.” Cell Reports, vol. 3, no. 3,
Cell Press, 2013, pp. 960–67, doi:10.1016/j.celrep.2013.02.002.
short: S. Hippenmeyer, R. Johnson, L. Luo, Cell Reports 3 (2013) 960–967.
corr_author: '1'
date_created: 2018-12-11T11:59:57Z
date_published: 2013-03-28T00:00:00Z
date_updated: 2025-09-29T13:40:05Z
day: '28'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.celrep.2013.02.002
external_id:
isi:
- '000321896000036'
file:
- access_level: open_access
checksum: 6e977b918e81384cd571ec5a9d812289
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:20Z
date_updated: 2020-07-14T12:45:51Z
file_id: '5274'
file_name: IST-2016-405-v1+1_1-s2.0-S2211124713000612-main.pdf
file_size: 1907211
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 960 - 967
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '3937'
pubrep_id: '405'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mosaic analysis with double markers reveals cell type specific paternal growth
dominance
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 3
year: '2013'
...
---
_id: '2856'
abstract:
- lang: eng
text: 'G protein–coupled receptors (GPCRs), the largest family of membrane signaling
proteins, respond to neurotransmitters, hormones and small environmental molecules.
The neuronal function of many GPCRs has been difficult to resolve because of an
inability to gate them with subtype specificity, spatial precision, speed and
reversibility. To address this, we developed an approach for opto-chemical engineering
of native GPCRs. We applied this to the metabotropic glutamate receptors (mGluRs)
to generate light-agonized and light-antagonized mGluRs (LimGluRs). The light-agonized
LimGluR2, on which we focused, was fast, bistable and supported multiple rounds
of on/off switching. Light gated two of the primary neuronal functions of mGluR2:
suppression of excitability and inhibition of neurotransmitter release. We found
that the light-antagonized tool LimGluR2-block was able to manipulate negative
feedback of synaptically released glutamate on transmitter release. We generalized
the optical control to two additional family members: mGluR3 and mGluR6. This
system worked in rodent brain slices and in zebrafish in vivo, where we found
that mGluR2 modulated the threshold for escape behavior. These light-gated mGluRs
pave the way for determining the roles of mGluRs in synaptic plasticity, memory
and disease.'
acknowledgement: National Science Foundation grants CHE-0233882 and CHE-0840505 (to
the College of Chemistry at the University of California, Berkeley), a postdoctoral
fellowship of the European Molecular Biology Organization (H.J.)
article_processing_charge: No
author:
- first_name: Joshua
full_name: Levitz, Joshua
last_name: Levitz
- first_name: Carlos
full_name: Pantoja, Carlos
last_name: Pantoja
- first_name: Benjamin
full_name: Gaub, Benjamin
last_name: Gaub
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Andreas
full_name: Reiner, Andreas
last_name: Reiner
- first_name: Adam
full_name: Hoagland, Adam
last_name: Hoagland
- first_name: David
full_name: Schoppik, David
last_name: Schoppik
- first_name: Brian
full_name: Kane, Brian
last_name: Kane
- first_name: Philipp
full_name: Stawski, Philipp
last_name: Stawski
- first_name: Alexander
full_name: Schier, Alexander
last_name: Schier
- first_name: Dirk
full_name: Trauner, Dirk
last_name: Trauner
- first_name: Ehud
full_name: Isacoff, Ehud
last_name: Isacoff
citation:
ama: Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate
receptors. Nature Neuroscience. 2013;16:507-516. doi:10.1038/nn.3346
apa: Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A.,
… Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. Nature
Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3346
chicago: Levitz, Joshua, Carlos Pantoja, Benjamin Gaub, Harald L Janovjak, Andreas
Reiner, Adam Hoagland, David Schoppik, et al. “Optical Control of Metabotropic
Glutamate Receptors.” Nature Neuroscience. Nature Publishing Group, 2013.
https://doi.org/10.1038/nn.3346.
ieee: J. Levitz et al., “Optical control of metabotropic glutamate receptors,”
Nature Neuroscience, vol. 16. Nature Publishing Group, pp. 507–516, 2013.
ista: Levitz J, Pantoja C, Gaub B, Janovjak HL, Reiner A, Hoagland A, Schoppik D,
Kane B, Stawski P, Schier A, Trauner D, Isacoff E. 2013. Optical control of metabotropic
glutamate receptors. Nature Neuroscience. 16, 507–516.
mla: Levitz, Joshua, et al. “Optical Control of Metabotropic Glutamate Receptors.”
Nature Neuroscience, vol. 16, Nature Publishing Group, 2013, pp. 507–16,
doi:10.1038/nn.3346.
short: J. Levitz, C. Pantoja, B. Gaub, H.L. Janovjak, A. Reiner, A. Hoagland, D.
Schoppik, B. Kane, P. Stawski, A. Schier, D. Trauner, E. Isacoff, Nature Neuroscience
16 (2013) 507–516.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-03-03T00:00:00Z
date_updated: 2025-09-29T13:39:33Z
day: '03'
department:
- _id: HaJa
doi: 10.1038/nn.3346
external_id:
isi:
- '000316723700023'
pmid:
- '23455609'
intvolume: ' 16'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/
month: '03'
oa: 1
oa_version: Submitted Version
page: 507 - 516
pmid: 1
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '3936'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optical control of metabotropic glutamate receptors
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2013'
...
---
_id: '2857'
abstract:
- lang: eng
text: In the vibrant field of optogenetics, optics and genetic targeting are combined
to commandeer cellular functions, such as the neuronal action potential, by optically
stimulating light-sensitive ion channels expressed in the cell membrane. One broadly
applicable manifestation of this approach are covalently attached photochromic
tethered ligands (PTLs) that allow activating ligand-gated ion channels with outstanding
spatial and temporal resolution. Here, we describe all steps towards the successful
development and application of PTL-gated ion channels in cell lines and primary
cells. The basis for these experiments forms a combination of molecular modeling,
genetic engineering, cell culture, and electrophysiology. The light-gated glutamate
receptor (LiGluR), which consists of the PTL-functionalized GluK2 receptor, serves
as a model.
alternative_title:
- MIMB
author:
- first_name: Stephanie
full_name: Szobota, Stephanie
last_name: Szobota
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Szobota S, Mckenzie C, Janovjak HL. Optical control of ligand-gated ion channels.
Methods in Molecular Biology. 2013;998:417-435. doi:10.1007/978-1-62703-351-0_32
apa: Szobota, S., Mckenzie, C., & Janovjak, H. L. (2013). Optical control of
ligand-gated ion channels. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-62703-351-0_32
chicago: Szobota, Stephanie, Catherine Mckenzie, and Harald L Janovjak. “Optical
Control of Ligand-Gated Ion Channels.” Methods in Molecular Biology. Springer,
2013. https://doi.org/10.1007/978-1-62703-351-0_32.
ieee: S. Szobota, C. Mckenzie, and H. L. Janovjak, “Optical control of ligand-gated
ion channels,” Methods in Molecular Biology, vol. 998. Springer, pp. 417–435,
2013.
ista: Szobota S, Mckenzie C, Janovjak HL. 2013. Optical control of ligand-gated
ion channels. Methods in Molecular Biology. 998, 417–435.
mla: Szobota, Stephanie, et al. “Optical Control of Ligand-Gated Ion Channels.”
Methods in Molecular Biology, vol. 998, Springer, 2013, pp. 417–35, doi:10.1007/978-1-62703-351-0_32.
short: S. Szobota, C. Mckenzie, H.L. Janovjak, Methods in Molecular Biology 998
(2013) 417–435.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-02-22T00:00:00Z
date_updated: 2025-04-15T06:43:12Z
day: '22'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.1007/978-1-62703-351-0_32
ec_funded: 1
file:
- access_level: open_access
checksum: 1701f0d989f27ddac471b19a894ec0d1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:34Z
date_updated: 2020-07-14T12:45:51Z
file_id: '4952'
file_name: IST-2017-834-v1+1_szobota.pdf
file_size: 336734
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 998'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
page: 417 - 435
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
publication: Methods in Molecular Biology
publication_status: published
publisher: Springer
publist_id: '3932'
pubrep_id: '834'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optical control of ligand-gated ion channels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 998
year: '2013'
...
---
_id: '2858'
abstract:
- lang: eng
text: Tumor growth is caused by the acquisition of driver mutations, which enhance
the net reproductive rate of cells. Driver mutations may increase cell division,
reduce cell death, or allow cells to overcome density-limiting effects. We study
the dynamics of tumor growth as one additional driver mutation is acquired. Our
models are based on two-type branching processes that terminate in either tumor
disappearance or tumor detection. In our first model, both cell types grow exponentially,
with a faster rate for cells carrying the additional driver. We find that the
additional driver mutation does not affect the survival probability of the lesion,
but can substantially reduce the time to reach the detectable size if the lesion
is slow growing. In our second model, cells lacking the additional driver cannot
exceed a fixed carrying capacity, due to density limitations. In this case, the
time to detection depends strongly on this carrying capacity. Our model provides
a quantitative framework for studying tumor dynamics during different stages of
progression. We observe that early, small lesions need additional drivers, while
late stage metastases are only marginally affected by them. These results help
to explain why additional driver mutations are typically not detected in fast-growing
metastases.
article_processing_charge: No
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Ivana
full_name: Božić, Ivana
last_name: Božić
- first_name: Benjamin
full_name: Allen, Benjamin
id: 135B5B70-E9D2-11E9-BD74-BB415DA2B523
last_name: Allen
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. The effect of one additional
driver mutation on tumor progression. Evolutionary Applications. 2013;6(1):34-45.
doi:10.1111/eva.12020
apa: Reiter, J., Božić, I., Allen, B., Chatterjee, K., & Nowak, M. (2013). The
effect of one additional driver mutation on tumor progression. Evolutionary
Applications. Wiley-Blackwell. https://doi.org/10.1111/eva.12020
chicago: Reiter, Johannes, Ivana Božić, Benjamin Allen, Krishnendu Chatterjee, and
Martin Nowak. “The Effect of One Additional Driver Mutation on Tumor Progression.”
Evolutionary Applications. Wiley-Blackwell, 2013. https://doi.org/10.1111/eva.12020.
ieee: J. Reiter, I. Božić, B. Allen, K. Chatterjee, and M. Nowak, “The effect of
one additional driver mutation on tumor progression,” Evolutionary Applications,
vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013.
ista: Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. 2013. The effect of one
additional driver mutation on tumor progression. Evolutionary Applications. 6(1),
34–45.
mla: Reiter, Johannes, et al. “The Effect of One Additional Driver Mutation on Tumor
Progression.” Evolutionary Applications, vol. 6, no. 1, Wiley-Blackwell,
2013, pp. 34–45, doi:10.1111/eva.12020.
short: J. Reiter, I. Božić, B. Allen, K. Chatterjee, M. Nowak, Evolutionary Applications
6 (2013) 34–45.
corr_author: '1'
date_created: 2018-12-11T11:59:58Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2025-09-29T13:38:52Z
day: '01'
ddc:
- '570'
department:
- _id: KrCh
doi: 10.1111/eva.12020
ec_funded: 1
external_id:
isi:
- '000313878800004'
file:
- access_level: open_access
checksum: e2955b3889f8a823c3d5a72cb16f8957
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:50Z
date_updated: 2020-07-14T12:45:51Z
file_id: '5173'
file_name: IST-2016-415-v1+1_Reiter_et_al-2013-Evolutionary_Applications.pdf
file_size: 1172037
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 34 - 45
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Evolutionary Applications
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3931'
pubrep_id: '415'
quality_controlled: '1'
related_material:
record:
- id: '1400'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The effect of one additional driver mutation on tumor progression
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2013'
...
---
_id: '2859'
abstract:
- lang: eng
text: Given a continuous function f:X-R on a topological space, we consider the
preimages of intervals and their homology groups and show how to read the ranks
of these groups from the extended persistence diagram of f. In addition, we quantify
the robustness of the homology classes under perturbations of f using well groups,
and we show how to read the ranks of these groups from the same extended persistence
diagram. The special case X=R3 has ramifications in the fields of medical imaging
and scientific visualization.
article_processing_charge: No
arxiv: 1
author:
- first_name: Paul
full_name: Bendich, Paul
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level
and interlevel sets. Homology, Homotopy and Applications. 2013;15(1):51-72.
doi:10.4310/HHA.2013.v15.n1.a3
apa: Bendich, P., Edelsbrunner, H., Morozov, D., & Patel, A. (2013). Homology
and robustness of level and interlevel sets. Homology, Homotopy and Applications.
International Press. https://doi.org/10.4310/HHA.2013.v15.n1.a3
chicago: Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology
and Robustness of Level and Interlevel Sets.” Homology, Homotopy and Applications.
International Press, 2013. https://doi.org/10.4310/HHA.2013.v15.n1.a3.
ieee: P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness
of level and interlevel sets,” Homology, Homotopy and Applications, vol.
15, no. 1. International Press, pp. 51–72, 2013.
ista: Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness
of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72.
mla: Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.”
Homology, Homotopy and Applications, vol. 15, no. 1, International Press,
2013, pp. 51–72, doi:10.4310/HHA.2013.v15.n1.a3.
short: P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and
Applications 15 (2013) 51–72.
date_created: 2018-12-11T11:59:58Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2025-09-29T13:38:09Z
day: '01'
department:
- _id: HeEd
doi: 10.4310/HHA.2013.v15.n1.a3
external_id:
arxiv:
- '1102.3389'
isi:
- '000322423600003'
intvolume: ' 15'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1102.3389v1
month: '05'
oa: 1
oa_version: Preprint
page: 51 - 72
publication: Homology, Homotopy and Applications
publication_status: published
publisher: International Press
publist_id: '3930'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Homology and robustness of level and interlevel sets
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2013'
...
---
_id: '2860'
abstract:
- lang: eng
text: 'In the hippocampus, cell assemblies forming mnemonic representations of space
are thought to arise as a result of changes in functional connections of pyramidal
cells. We have found that CA1 interneuron circuits are also reconfigured during
goal-oriented spatial learning through modification of inputs from pyramidal cells.
As learning progressed, new pyramidal assemblies expressed in theta cycles alternated
with previously established ones, and eventually overtook them. The firing patterns
of interneurons developed a relationship to new, learning-related assemblies:
some interneurons associated their activity with new pyramidal assemblies while
some others dissociated from them. These firing associations were explained by
changes in the weight of monosynaptic inputs received by interneurons from new
pyramidal assemblies, as these predicted the associational changes. Spatial learning
thus engages circuit modifications in the hippocampus that incorporate a redistribution
of inhibitory activity that might assist in the segregation of competing pyramidal
cell assembly patterns in space and time.'
acknowledgement: D.D. and J.C. were supported by a MRC Intramural Programme Grant
U138197111
article_processing_charge: No
author:
- first_name: David
full_name: Dupret, David
last_name: Dupret
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Dupret D, O’Neill J, Csicsvari JL. Dynamic reconfiguration of hippocampal interneuron
circuits during spatial learning. Neuron. 2013;78(1):166-180. doi:10.1016/j.neuron.2013.01.033
apa: Dupret, D., O’Neill, J., & Csicsvari, J. L. (2013). Dynamic reconfiguration
of hippocampal interneuron circuits during spatial learning. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2013.01.033
chicago: Dupret, David, Joseph O’Neill, and Jozsef L Csicsvari. “Dynamic Reconfiguration
of Hippocampal Interneuron Circuits during Spatial Learning.” Neuron. Elsevier,
2013. https://doi.org/10.1016/j.neuron.2013.01.033.
ieee: D. Dupret, J. O’Neill, and J. L. Csicsvari, “Dynamic reconfiguration of hippocampal
interneuron circuits during spatial learning,” Neuron, vol. 78, no. 1.
Elsevier, pp. 166–180, 2013.
ista: Dupret D, O’Neill J, Csicsvari JL. 2013. Dynamic reconfiguration of hippocampal
interneuron circuits during spatial learning. Neuron. 78(1), 166–180.
mla: Dupret, David, et al. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits
during Spatial Learning.” Neuron, vol. 78, no. 1, Elsevier, 2013, pp. 166–80,
doi:10.1016/j.neuron.2013.01.033.
short: D. Dupret, J. O’Neill, J.L. Csicsvari, Neuron 78 (2013) 166–180.
corr_author: '1'
date_created: 2018-12-11T11:59:59Z
date_published: 2013-03-21T00:00:00Z
date_updated: 2025-09-29T13:37:37Z
day: '21'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2013.01.033
ec_funded: 1
external_id:
isi:
- '000317556000015'
file:
- access_level: open_access
checksum: 0e18cb8561153ddb50bb5af16e7c9e97
content_type: application/pdf
creator: dernst
date_created: 2019-01-23T08:08:07Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5877'
file_name: 2013_Neuron_Dupret.pdf
file_size: 2637837
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 166 - 180
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '3929'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic reconfiguration of hippocampal interneuron circuits during spatial
learning
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 78
year: '2013'
...
---
_id: '2861'
abstract:
- lang: eng
text: We consider a two-parameter family of piecewise linear maps in which the moduli
of the two slopes take different values. We provide numerical evidence of the
existence of some parameter regions in which the Lyapunov exponent and the topological
entropy remain constant. Analytical proof of this phenomenon is also given for
certain cases. Surprisingly however, the systems with that property are not conjugate
as we prove by using kneading theory.
article_number: '125101'
article_processing_charge: No
author:
- first_name: Vicente
full_name: Botella Soler, Vicente
id: 421234E8-F248-11E8-B48F-1D18A9856A87
last_name: Botella Soler
orcid: 0000-0002-8790-1914
- first_name: José
full_name: Oteo, José
last_name: Oteo
- first_name: Javier
full_name: Ros, Javier
last_name: Ros
- first_name: Paul
full_name: Glendinning, Paul
last_name: Glendinning
citation:
ama: 'Botella Soler V, Oteo J, Ros J, Glendinning P. Lyapunov exponent and topological
entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical
and Theoretical. 2013;46(12). doi:10.1088/1751-8113/46/12/125101'
apa: 'Botella Soler, V., Oteo, J., Ros, J., & Glendinning, P. (2013). Lyapunov
exponent and topological entropy plateaus in piecewise linear maps. Journal
of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8113/46/12/125101'
chicago: 'Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov
Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal
of Physics A: Mathematical and Theoretical. IOP Publishing, 2013. https://doi.org/10.1088/1751-8113/46/12/125101.'
ieee: 'V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent
and topological entropy plateaus in piecewise linear maps,” Journal of Physics
A: Mathematical and Theoretical, vol. 46, no. 12. IOP Publishing, 2013.'
ista: 'Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and
topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical
and Theoretical. 46(12), 125101.'
mla: 'Botella Soler, Vicente, et al. “Lyapunov Exponent and Topological Entropy
Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and
Theoretical, vol. 46, no. 12, 125101, IOP Publishing, 2013, doi:10.1088/1751-8113/46/12/125101.'
short: 'V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A:
Mathematical and Theoretical 46 (2013).'
corr_author: '1'
date_created: 2018-12-11T11:59:59Z
date_published: 2013-03-29T00:00:00Z
date_updated: 2025-09-29T13:36:56Z
day: '29'
department:
- _id: GaTk
doi: 10.1088/1751-8113/46/12/125101
external_id:
isi:
- '000316058200010'
intvolume: ' 46'
isi: 1
issue: '12'
language:
- iso: eng
month: '03'
oa_version: None
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_status: published
publisher: IOP Publishing
publist_id: '3928'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lyapunov exponent and topological entropy plateaus in piecewise linear maps
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 46
year: '2013'
...
---
_id: '2862'
abstract:
- lang: eng
text: Motile cilia perform crucial functions during embryonic development and throughout
adult life. Development of organs containing motile cilia involves regulation
of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis)
in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis
is not yet fully understood, and it remains unclear whether these processes are
coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently
in ciliated organs. Lgl proteins are involved in establishing cell polarity and
have been implicated in vesicle trafficking. Here, we identified a role for Lgl2
in development of ciliated epithelia in Kupffer's vesicle, which directs left-right
asymmetry of the embryo; the otic vesicles, which give rise to the inner ear;
and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated
organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia
number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle
morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed
loss of the adherens junction component E-cadherin at lateral membranes. Genetic
interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin
and mediate lumen formation that is uncoupled from cilia formation. These results
uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis
and ciliogenesis and indicate that these processes are genetically separable in
zebrafish.
acknowledgement: Deposited in PMC for release after 12 months. We thank members of
the Amack lab for helpful discussions and Mahendra Sonawane for donating reagents.
article_processing_charge: No
author:
- first_name: Hwee
full_name: Tay, Hwee
last_name: Tay
- first_name: Sabrina
full_name: Schulze, Sabrina
last_name: Schulze
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- first_name: Fiona
full_name: Foley, Fiona
last_name: Foley
- 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: H Joseph
full_name: Yost, H Joseph
last_name: Yost
- first_name: Salim
full_name: Abdelilah Seyfried, Salim
last_name: Abdelilah Seyfried
- first_name: Jeffrey
full_name: Amack, Jeffrey
last_name: Amack
citation:
ama: Tay H, Schulze S, Compagnon J, et al. Lethal giant larvae 2 regulates development
of the ciliated organ Kupffer’s vesicle. Development. 2013;140(7):1550-1559.
doi:10.1242/dev.087130
apa: Tay, H., Schulze, S., Compagnon, J., Foley, F., Heisenberg, C.-P. J., Yost,
H. J., … Amack, J. (2013). Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle. Development. Company of Biologists. https://doi.org/10.1242/dev.087130
chicago: Tay, Hwee, Sabrina Schulze, Julien Compagnon, Fiona Foley, Carl-Philipp
J Heisenberg, H Joseph Yost, Salim Abdelilah Seyfried, and Jeffrey Amack. “Lethal
Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.”
Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.087130.
ieee: H. Tay et al., “Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle,” Development, vol. 140, no. 7. Company
of Biologists, pp. 1550–1559, 2013.
ista: Tay H, Schulze S, Compagnon J, Foley F, Heisenberg C-PJ, Yost HJ, Abdelilah
Seyfried S, Amack J. 2013. Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle. Development. 140(7), 1550–1559.
mla: Tay, Hwee, et al. “Lethal Giant Larvae 2 Regulates Development of the Ciliated
Organ Kupffer’s Vesicle.” Development, vol. 140, no. 7, Company of Biologists,
2013, pp. 1550–59, doi:10.1242/dev.087130.
short: H. Tay, S. Schulze, J. Compagnon, F. Foley, C.-P.J. Heisenberg, H.J. Yost,
S. Abdelilah Seyfried, J. Amack, Development 140 (2013) 1550–1559.
date_created: 2018-12-11T11:59:59Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2025-09-29T13:36:20Z
day: '01'
department:
- _id: CaHe
doi: 10.1242/dev.087130
external_id:
isi:
- '000316096400018'
pmid:
- '23482490'
intvolume: ' 140'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/
month: '04'
oa: 1
oa_version: Submitted Version
page: 1550 - 1559
pmid: 1
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3927'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s
vesicle
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 140
year: '2013'
...
---
_id: '2863'
abstract:
- lang: eng
text: Neural populations encode information about their stimulus in a collective
fashion, by joint activity patterns of spiking and silence. A full account of
this mapping from stimulus to neural activity is given by the conditional probability
distribution over neural codewords given the sensory input. For large populations,
direct sampling of these distributions is impossible, and so we must rely on constructing
appropriate models. We show here that in a population of 100 retinal ganglion
cells in the salamander retina responding to temporal white-noise stimuli, dependencies
between cells play an important encoding role. We introduce the stimulus-dependent
maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear
model of a single neuron, to a pairwise-coupled neural population. We find that
the SDME model gives a more accurate account of single cell responses and in particular
significantly outperforms uncoupled models in reproducing the distributions of
population codewords emitted in response to a stimulus. We show how the SDME model,
in conjunction with static maximum entropy models of population vocabulary, can
be used to estimate information-theoretic quantities like average surprise and
information transmission in a neural population.
article_number: e1002922
article_processing_charge: No
author:
- first_name: Einat
full_name: Granot Atedgi, Einat
last_name: Granot Atedgi
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Ronen
full_name: Segev, Ronen
last_name: Segev
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum
entropy models of neural population codes. PLoS Computational Biology.
2013;9(3). doi:10.1371/journal.pcbi.1002922
apa: Granot Atedgi, E., Tkačik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent
maximum entropy models of neural population codes. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1002922
chicago: Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman.
“Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS
Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1002922.
ieee: E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent
maximum entropy models of neural population codes,” PLoS Computational Biology,
vol. 9, no. 3. Public Library of Science, 2013.
ista: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent
maximum entropy models of neural population codes. PLoS Computational Biology.
9(3), e1002922.
mla: Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of
Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922,
Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.
short: E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational
Biology 9 (2013).
corr_author: '1'
date_created: 2018-12-11T12:00:00Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2025-09-29T13:35:44Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1002922
external_id:
isi:
- '000316864200003'
file:
- access_level: open_access
checksum: 5a30876c193209fa05b26db71845dd16
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:45Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5099'
file_name: IST-2013-120-v1+1_journal.pcbi.1002922.pdf
file_size: 1548120
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3926'
pubrep_id: '120'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stimulus-dependent maximum entropy models of neural population codes
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9
year: '2013'
...
---
_id: '2877'
abstract:
- lang: eng
text: 'Premise of the study: To reach favorable conditions for photosynthesis, seedlings
grow upward when deprived of light upon underground germination. To direct their
growth, they use their negative gravitropic capacity. Negative gravitropism is
under tight control of multiple hormones. • Methods: By counting the number of
standing plants in a population or by real time monitoring of the reorientation
of gravistimulated seedlings of Arabidopsis thaliana, we evaluated the negative
gravitropism of ethylene or brassinosteroid (BR) treated plants. Meta-analysis
of transcriptomic data on AUX / IAA genes was gathered, and subsequent mutant
analysis was performed. • Key results: Ethylene and BR have opposite effects in
regulating shoot gravitropism. Lack of BR enhances gravitropic reorientation in
2-d-old seedlings, whereas ethylene does not. Lack of ethylene signaling results
in enhanced BR sensitivity. Ethylene and BRs regulate overlapping sets of AUX
/ IAA genes. BRs regulate a wider range of auxin signaling components than ethylene.
• Conclusions: Upward growth in seedlings depends strongly on the internal hormonal
balance. Endogenous ethylene stimulates, whereas BRs reduce negative gravitropism
in a manner that depends on the function of different, yet overlapping sets of
auxin signaling components.'
author:
- first_name: Filip
full_name: Vandenbussche, Filip
last_name: Vandenbussche
- first_name: Pieter
full_name: Callebert, Pieter
last_name: Callebert
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Eva
full_name: Eva Benková
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: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. Brassinosteroid
control of shoot gravitropism interacts with ethylene and depends on auxin signaling
components. American Journal of Botany. 2013;100(1):215-225. doi:10.3732/ajb.1200264
apa: Vandenbussche, F., Callebert, P., Žádníková, P., Benková, E., & Van Der
Straeten, D. (2013). Brassinosteroid control of shoot gravitropism interacts with
ethylene and depends on auxin signaling components. American Journal of Botany.
Botanical Society of America. https://doi.org/10.3732/ajb.1200264
chicago: Vandenbussche, Filip, Pieter Callebert, Petra Žádníková, Eva Benková, and
Dominique Van Der Straeten. “Brassinosteroid Control of Shoot Gravitropism Interacts
with Ethylene and Depends on Auxin Signaling Components.” American Journal
of Botany. Botanical Society of America, 2013. https://doi.org/10.3732/ajb.1200264.
ieee: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, and D. Van Der Straeten,
“Brassinosteroid control of shoot gravitropism interacts with ethylene and depends
on auxin signaling components,” American Journal of Botany, vol. 100, no.
1. Botanical Society of America, pp. 215–225, 2013.
ista: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D.
2013. Brassinosteroid control of shoot gravitropism interacts with ethylene and
depends on auxin signaling components. American Journal of Botany. 100(1), 215–225.
mla: Vandenbussche, Filip, et al. “Brassinosteroid Control of Shoot Gravitropism
Interacts with Ethylene and Depends on Auxin Signaling Components.” American
Journal of Botany, vol. 100, no. 1, Botanical Society of America, 2013, pp.
215–25, doi:10.3732/ajb.1200264.
short: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, D. Van Der Straeten,
American Journal of Botany 100 (2013) 215–225.
date_created: 2018-12-11T12:00:06Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:25Z
day: '01'
doi: 10.3732/ajb.1200264
extern: 1
intvolume: ' 100'
issue: '1'
month: '01'
page: 215 - 225
publication: American Journal of Botany
publication_status: published
publisher: Botanical Society of America
publist_id: '3883'
quality_controlled: 0
status: public
title: Brassinosteroid control of shoot gravitropism interacts with ethylene and depends
on auxin signaling components
type: journal_article
volume: 100
year: '2013'
...
---
_id: '2880'
abstract:
- lang: eng
text: Lateral root (LR) formation is initiated when pericycle cells accumulate auxin,
thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions,
giving rise to a new primordium. How this auxin maximum in pericycle cells builds
up and remains focused is not understood. We report that the endodermis plays
an active role in the regulation of auxin accumulation and is instructive for
FCs to progress during the LR initiation (LRI) phase. We describe the functional
importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux
pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux
pathway causes dramatic defects in the progress of FCs towards the next initiation
phase. Our data identify an unexpected regulatory function for the endodermis
in LRI as part of the fine-tuning mechanism that appears to act as a check point
in LR organogenesis after FCs are specified.
article_processing_charge: No
author:
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Ding
full_name: Zhaojun, Ding
last_name: Zhaojun
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Vanstraelen M, De Rybel B, et al. Auxin reflux between the endodermis
and pericycle promotes lateral root initiation. EMBO Journal. 2013;32(1):149-158.
doi:10.1038/emboj.2012.303
apa: Marhavý, P., Vanstraelen, M., De Rybel, B., Zhaojun, D., Bennett, M., Beeckman,
T., & Benková, E. (2013). Auxin reflux between the endodermis and pericycle
promotes lateral root initiation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.303
chicago: Marhavý, Peter, Marleen Vanstraelen, Bert De Rybel, Ding Zhaojun, Malcolm
Bennett, Tom Beeckman, and Eva Benková. “Auxin Reflux between the Endodermis and
Pericycle Promotes Lateral Root Initiation.” EMBO Journal. Wiley-Blackwell,
2013. https://doi.org/10.1038/emboj.2012.303.
ieee: P. Marhavý et al., “Auxin reflux between the endodermis and pericycle
promotes lateral root initiation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell,
pp. 149–158, 2013.
ista: Marhavý P, Vanstraelen M, De Rybel B, Zhaojun D, Bennett M, Beeckman T, Benková
E. 2013. Auxin reflux between the endodermis and pericycle promotes lateral root
initiation. EMBO Journal. 32(1), 149–158.
mla: Marhavý, Peter, et al. “Auxin Reflux between the Endodermis and Pericycle Promotes
Lateral Root Initiation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell,
2013, pp. 149–58, doi:10.1038/emboj.2012.303.
short: P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman,
E. Benková, EMBO Journal 32 (2013) 149–158.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2025-09-29T13:35:12Z
day: '09'
department:
- _id: EvBe
doi: 10.1038/emboj.2012.303
ec_funded: 1
external_id:
isi:
- '000314141900014'
pmid:
- '23178590'
intvolume: ' 32'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/
month: '01'
oa: 1
oa_version: Submitted Version
page: 149 - 158
pmid: 1
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3882'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin reflux between the endodermis and pericycle promotes lateral root initiation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2881'
abstract:
- lang: eng
text: The puzzle piece-shaped Arabidopsis leaf pavement cells (PCs) with interdigitated
lobes and indents is a good model system to investigate the mechanisms that coordinate
cell polarity and shape formation within a tissue. Auxin has been shown to coordinate
the interdigitation by activating ROP GTPase-dependent signaling pathways. To
identify additional components or mechanisms, we screened for mutants with abnormal
PC morphogenesis and found that cytokinin signaling regulates the PC interdigitation
pattern. Reduction in cytokinin accumulation and defects in cytokinin signaling
(such as in ARR7-over-expressing lines, the ahk3cre1 cytokinin receptor mutant,
and the ahp12345 cytokinin signaling mutant) enhanced PC interdigitation, whereas
over-production of cytokinin and over-activation of cytokinin signaling in an
ARR20 over-expression line delayed or abolished PC interdigitation throughout
the cotyledon. Genetic and biochemical analyses suggest that cytokinin signaling
acts upstream of ROPs to suppress the formation of interdigitated pattern. Our
results provide novel mechanistic understanding of the pathways controlling PC
shape and uncover a new role for cytokinin signaling in cell morphogenesis.
acknowledgement: is work was supported by grants from the US National Institute of
General Medical Sciences (GM081451 and GM081451-03S2) to ZY. We thank National Science
Foundation grant (IOS-1147250) to GVR and MX. HL and DL were partially supported
by the Chinese Scholarship Council.
author:
- first_name: Hongjiang
full_name: Hongjiang Li
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Mingzhang
full_name: Wen, Mingzhang
last_name: Wen
- first_name: Mingtang
full_name: Xie, Mingtang
last_name: Xie
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Jungmook
full_name: Kim, Jungmook
last_name: Kim
- first_name: G Venugopala
full_name: Reddy, G Venugopala
last_name: Reddy
- first_name: Jianru
full_name: Zuo, Jianru
last_name: Zuo
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hongwei
full_name: Guo, Hongwei
last_name: Guo
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Li H, Xu T, Lin D, et al. Cytokinin signaling regulates pavement cell morphogenesis
in Arabidopsis. Cell Research. 2013;23(2):290-299. doi:10.1038/cr.2012.146
apa: Li, H., Xu, T., Lin, D., Wen, M., Xie, M., Duclercq, J., … Yang, Z. (2013).
Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell
Research. Nature Publishing Group. https://doi.org/10.1038/cr.2012.146
chicago: Li, Hongjiang, Tongda Xu, Deshu Lin, Mingzhang Wen, Mingtang Xie, Jérôme
Duclercq, Agnieszka Bielach, et al. “Cytokinin Signaling Regulates Pavement Cell
Morphogenesis in Arabidopsis.” Cell Research. Nature Publishing Group,
2013. https://doi.org/10.1038/cr.2012.146.
ieee: H. Li et al., “Cytokinin signaling regulates pavement cell morphogenesis
in Arabidopsis,” Cell Research, vol. 23, no. 2. Nature Publishing Group,
pp. 290–299, 2013.
ista: Li H, Xu T, Lin D, Wen M, Xie M, Duclercq J, Bielach A, Kim J, Reddy GV, Zuo
J, Benková E, Friml J, Guo H, Yang Z. 2013. Cytokinin signaling regulates pavement
cell morphogenesis in Arabidopsis. Cell Research. 23(2), 290–299.
mla: Li, Hongjiang, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis
in Arabidopsis.” Cell Research, vol. 23, no. 2, Nature Publishing Group,
2013, pp. 290–99, doi:10.1038/cr.2012.146.
short: H. Li, T. Xu, D. Lin, M. Wen, M. Xie, J. Duclercq, A. Bielach, J. Kim, G.V.
Reddy, J. Zuo, E. Benková, J. Friml, H. Guo, Z. Yang, Cell Research 23 (2013)
290–299.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T07:00:27Z
day: '01'
doi: 10.1038/cr.2012.146
extern: 1
intvolume: ' 23'
issue: '2'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567823/
month: '02'
oa: 1
page: 290 - 299
publication: Cell Research
publication_status: published
publisher: Nature Publishing Group
publist_id: '3881'
quality_controlled: 0
status: public
title: Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis
type: journal_article
volume: 23
year: '2013'
...