---
_id: '1817'
abstract:
- lang: eng
text: 'Vertebrates have a unique 3D body shape in which correct tissue and organ
shape and alignment are essential for function. For example, vision requires the
lens to be centred in the eye cup which must in turn be correctly positioned in
the head. Tissue morphogenesis depends on force generation, force transmission
through the tissue, and response of tissues and extracellular matrix to force.
Although a century ago D''Arcy Thompson postulated that terrestrial animal body
shapes are conditioned by gravity, there has been no animal model directly demonstrating
how the aforementioned mechano-morphogenetic processes are coordinated to generate
a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias
latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir
embryos display a markedly flattened body caused by mutation of YAP, a nuclear
executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated
tissue tension is reduced in hir embryos, leading to tissue flattening and tissue
misalignment, both of which contribute to body flattening. By analysing YAP function
in 3D spheroids of human cells, we identify the Rho GTPase activating protein
ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these
findings reveal a previously unrecognised function of YAP in regulating tissue
shape and alignment required for proper 3D body shape. Understanding this morphogenetic
function of YAP could facilitate the use of embryonic stem cells to generate complex
organs requiring correct alignment of multiple tissues. '
author:
- first_name: Sean
full_name: Porazinski, Sean
last_name: Porazinski
- first_name: Huijia
full_name: Wang, Huijia
last_name: Wang
- first_name: Yoichi
full_name: Asaoka, Yoichi
last_name: Asaoka
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Tatsuo
full_name: Miyamoto, Tatsuo
last_name: Miyamoto
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Shoji
full_name: Hata, Shoji
last_name: Hata
- first_name: Takashi
full_name: Sasaki, Takashi
last_name: Sasaki
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Yumi
full_name: Osada, Yumi
last_name: Osada
- first_name: Satoshi
full_name: Asaka, Satoshi
last_name: Asaka
- first_name: Akihiro
full_name: Momoi, Akihiro
last_name: Momoi
- first_name: Sarah
full_name: Linton, Sarah
last_name: Linton
- first_name: Joel
full_name: Miesfeld, Joel
last_name: Miesfeld
- first_name: Brian
full_name: Link, Brian
last_name: Link
- first_name: Takeshi
full_name: Senga, Takeshi
last_name: Senga
- first_name: Atahualpa
full_name: Castillo Morales, Atahualpa
last_name: Castillo Morales
- first_name: Araxi
full_name: Urrutia, Araxi
last_name: Urrutia
- first_name: Nobuyoshi
full_name: Shimizu, Nobuyoshi
last_name: Shimizu
- first_name: Hideaki
full_name: Nagase, Hideaki
last_name: Nagase
- first_name: Shinya
full_name: Matsuura, Shinya
last_name: Matsuura
- first_name: Stefan
full_name: Bagby, Stefan
last_name: Bagby
- first_name: Hisato
full_name: Kondoh, Hisato
last_name: Kondoh
- first_name: Hiroshi
full_name: Nishina, Hiroshi
last_name: Nishina
- 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: Makoto
full_name: Furutani Seiki, Makoto
last_name: Furutani Seiki
citation:
ama: Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension
to ensure vertebrate 3D body shape. Nature. 2015;521(7551):217-221. doi:10.1038/nature14215
apa: Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H.,
… Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate
3D body shape. Nature. Nature Publishing Group. https://doi.org/10.1038/nature14215
chicago: Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto,
Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure
Vertebrate 3D Body Shape.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature14215.
ieee: S. Porazinski et al., “YAP is essential for tissue tension to ensure
vertebrate 3D body shape,” Nature, vol. 521, no. 7551. Nature Publishing
Group, pp. 217–221, 2015.
ista: Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki
T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T,
Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh
H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue
tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221.
mla: Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate
3D Body Shape.” Nature, vol. 521, no. 7551, Nature Publishing Group, 2015,
pp. 217–21, doi:10.1038/nature14215.
short: S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S.
Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld,
B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S.
Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki,
Nature 521 (2015) 217–221.
date_created: 2018-12-11T11:54:10Z
date_published: 2015-03-16T00:00:00Z
date_updated: 2021-01-12T06:53:23Z
day: '16'
department:
- _id: CaHe
doi: 10.1038/nature14215
external_id:
pmid:
- '25778702'
intvolume: ' 521'
issue: '7551'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/
month: '03'
oa: 1
oa_version: Submitted Version
page: 217 - 221
pmid: 1
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5289'
quality_controlled: '1'
scopus_import: 1
status: public
title: YAP is essential for tissue tension to ensure vertebrate 3D body shape
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 521
year: '2015'
...
---
_id: '1820'
abstract:
- lang: eng
text: 'We consider partially observable Markov decision processes (POMDPs) with
a set of target states and every transition is associated with an integer cost.
The optimization objec- tive we study asks to minimize the expected total cost
till the target set is reached, while ensuring that the target set is reached
almost-surely (with probability 1). We show that for integer costs approximating
the optimal cost is undecidable. For positive costs, our results are as follows:
(i) we establish matching lower and upper bounds for the optimal cost and the
bound is double exponential; (ii) we show that the problem of approximating the
optimal cost is decidable and present ap- proximation algorithms developing on
the existing algorithms for POMDPs with finite-horizon objectives. While the worst-
case running time of our algorithm is double exponential, we present efficient
stopping criteria for the algorithm and show experimentally that it performs well
in many examples.'
acknowledgement: ' The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307:
Graph Games), and Microsoft faculty fellows award.'
alternative_title:
- Artifical Intelligence
author:
- 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: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
citation:
ama: 'Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability
in POMDPs. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial
Intelligence . Vol 5. AAAI Press; 2015:3496-3502.'
apa: 'Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Optimal
cost almost-sure reachability in POMDPs. In Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3496–3502). Austin,
TX, USA: AAAI Press.'
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
“Optimal Cost Almost-Sure Reachability in POMDPs.” In Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence , 5:3496–3502. AAAI Press, 2015.
ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure
reachability in POMDPs,” in Proceedings of the Twenty-Ninth AAAI Conference
on Artificial Intelligence , Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.
ista: 'Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure
reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial
Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical
Intelligence, vol. 5, 3496–3502.'
mla: Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.”
Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence
, vol. 5, AAAI Press, 2015, pp. 3496–502.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the
Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp.
3496–3502.
conference:
end_date: 2015-01-30
location: Austin, TX, USA
name: 'IAAI: Innovative Applications of Artificial Intelligence'
start_date: 2015-01-25
date_created: 2018-12-11T11:54:11Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-02-23T10:02:57Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
arxiv:
- '1411.3880'
intvolume: ' 5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1411.3880
month: '06'
oa: 1
oa_version: Preprint
page: 3496-3502
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: 'Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence '
publication_status: published
publisher: AAAI Press
publist_id: '5286'
quality_controlled: '1'
related_material:
record:
- id: '1529'
relation: later_version
status: public
scopus_import: 1
status: public
title: Optimal cost almost-sure reachability in POMDPs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2015'
...
---
_id: '1814'
abstract:
- lang: eng
text: 'We present an efficient wavefront tracking algorithm for animating bodies
of water that interact with their environment. Our contributions include: a novel
wavefront tracking technique that enables dispersion, refraction, reflection,
and diffraction in the same simulation; a unique multivalued function interpolation
method that enables our simulations to elegantly sidestep the Nyquist limit; a
dispersion approximation for efficiently amplifying the number of simulated waves
by several orders of magnitude; and additional extensions that allow for time-dependent
effects and interactive artistic editing of the resulting animation. Our contributions
combine to give us multitudes more wave details than similar algorithms, while
maintaining high frame rates and allowing close camera zooms.'
article_number: '27'
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation.
ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572
apa: Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter
interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572
chicago: Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront
Parameter Interpolation.” ACM Transactions on Graphics. ACM, 2015. https://doi.org/10.1145/2714572.
ieee: S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,”
ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015.
ista: Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation.
ACM Transactions on Graphics. 34(3), 27.
mla: Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter
Interpolation.” ACM Transactions on Graphics, vol. 34, no. 3, 27, ACM,
2015, doi:10.1145/2714572.
short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).
date_created: 2018-12-11T11:54:09Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-23T10:15:40Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2714572
ec_funded: 1
file:
- access_level: open_access
checksum: 67c9f4fa370def68cdf31299e48bc91f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:15Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4933'
file_name: IST-2016-575-v1+1_wavefront_preprint.pdf
file_size: 23712153
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '3'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
project:
- _id: 25357BD2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 24352-N23
name: 'Deep Pictures: Creating Visual and Haptic Vector Images'
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '5292'
pubrep_id: '575'
quality_controlled: '1'
scopus_import: 1
status: public
title: Water wave animation via wavefront parameter interpolation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1818'
abstract:
- lang: eng
text: 'Why do species not adapt to ever-wider ranges of conditions, gradually expanding
their ecological niche and geographic range? Gene flow across environments has
two conflicting effects: although it increases genetic variation, which is a prerequisite
for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane
proposed that, when the environment varies across space, "swamping"
by gene flow creates a positive feedback between low population size and maladaptation,
leading to a sharp range margin. However, current deterministic theory shows that,
when variance can evolve, there is no such limit. Using simple analytical tools
and simulations, we show that genetic drift can generate a sharp margin to a species''
range, by reducing genetic variance below the level needed for adaptation to spatially
variable conditions. Aided by separation of ecological and evolutionary timescales,
the identified effective dimensionless parameters reveal a simple threshold that
predicts when adaptation at the range margin fails. Two observable parameters
determine the threshold: (i) the effective environmental gradient, which can be
measured by the loss of fitness due to dispersal to a different environment; and
(ii) the efficacy of selection relative to genetic drift. The theory predicts
sharp range margins even in the absence of abrupt changes in the environment.
Furthermore, it implies that gradual worsening of conditions across a species''
habitat may lead to a sudden range fragmentation, when adaptation to a wide span
of conditions within a single species becomes impossible.'
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Polechova J, Barton NH. Limits to adaptation along environmental gradients.
PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112
apa: Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental
gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112
chicago: Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental
Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.
ieee: J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,”
PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.
ista: Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients.
PNAS. 112(20), 6401–6406.
mla: Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental
Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015,
pp. 6401–06, doi:10.1073/pnas.1421515112.
short: J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.
date_created: 2018-12-11T11:54:11Z
date_published: 2015-05-19T00:00:00Z
date_updated: 2021-01-12T06:53:24Z
day: '19'
department:
- _id: NiBa
doi: 10.1073/pnas.1421515112
ec_funded: 1
external_id:
pmid:
- '25941385'
intvolume: ' 112'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/
month: '05'
oa: 1
oa_version: Submitted Version
page: 6401 - 6406
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5288'
quality_controlled: '1'
scopus_import: 1
status: public
title: Limits to adaptation along environmental gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1819'
abstract:
- lang: eng
text: 'The sessile life style of plants creates the need to deal with an often adverse
environment, in which water availability can change on a daily basis, challenging
the cellular physiology and integrity. Changes in osmotic conditions disrupt the
equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic
environment decrease the cell volume. Here, we show that short-term extracellular
osmotic treatments are closely followed by a shift in the balance between endocytosis
and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and
nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis,
whereas hypoosmotic treatments have the opposite effects. In addition to clathrin
recruitment to the plasma membrane, components of early endocytic trafficking
are essential during hyperosmotic stress responses. Consequently, growth of seedlings
defective in elements of clathrin or early endocytic machinery is more sensitive
to hyperosmotic treatments. We also found that the endocytotic response to a change
of osmotic status in the environment is dominant over the presumably evolutionary
more recent regulatory effect of plant hormones, such as auxin. These results
imply that osmotic perturbation influences the balance between endocytosis and
exocytosis acting through clathrin-mediated endocytosis. We propose that tension
on the plasma membrane determines the addition or removal of membranes at the
cell surface, thus preserving cell integrity.'
acknowledgement: This work was supported by the European Research Council (project
ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the
Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009)
co-financed by the European Social Fund and the state budget of the Czech Republic
to M.Z. and T.N..
author:
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jiřĺ
full_name: Friml, Jiřĺ
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates
the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis
thaliana. Molecular Plant. 2015;8(8):1175-1187. doi:10.1016/j.molp.2015.03.007
apa: Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., & Friml, J. (2015).
Osmotic stress modulates the balance between exocytosis and clathrin mediated
endocytosis in Arabidopsis thaliana. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2015.03.007
chicago: Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and
Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin
Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant. Elsevier,
2015. https://doi.org/10.1016/j.molp.2015.03.007.
ieee: M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress
modulates the balance between exocytosis and clathrin mediated endocytosis in
Arabidopsis thaliana,” Molecular Plant, vol. 8, no. 8. Elsevier, pp. 1175–1187,
2015.
ista: Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress
modulates the balance between exocytosis and clathrin mediated endocytosis in
Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.
mla: Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis
and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant,
vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:10.1016/j.molp.2015.03.007.
short: M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant
8 (2015) 1175–1187.
date_created: 2018-12-11T11:54:11Z
date_published: 2015-08-03T00:00:00Z
date_updated: 2021-01-12T06:53:24Z
day: '03'
department:
- _id: JiFr
doi: 10.1016/j.molp.2015.03.007
ec_funded: 1
intvolume: ' 8'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1175 - 1187
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Molecular Plant
publication_status: published
publisher: Elsevier
publist_id: '5287'
quality_controlled: '1'
scopus_import: 1
status: public
title: Osmotic stress modulates the balance between exocytosis and clathrin mediated
endocytosis in Arabidopsis thaliana
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2015'
...
---
_id: '1823'
abstract:
- lang: eng
text: Abstract Drug combinations are increasingly important in disease treatments,
for combating drug resistance, and for elucidating fundamental relationships in
cell physiology. When drugs are combined, their individual effects on cells may
be amplified or weakened. Such drug interactions are crucial for treatment efficacy,
but their underlying mechanisms remain largely unknown. To uncover the causes
of drug interactions, we developed a systematic approach based on precise quantification
of the individual and joint effects of antibiotics on growth of genome-wide Escherichia
coli gene deletion strains. We found that drug interactions between antibiotics
representing the main modes of action are highly robust to genetic perturbation.
This robustness is encapsulated in a general principle of bacterial growth, which
enables the quantitative prediction of mutant growth rates under drug combinations.
Rare violations of this principle exposed recurring cellular functions controlling
drug interactions. In particular, we found that polysaccharide and ATP synthesis
control multiple drug interactions with previously unexplained mechanisms, and
small molecule adjuvants targeting these functions synthetically reshape drug
interactions in predictable ways. These results provide a new conceptual framework
for the design of multidrug combinations and suggest that there are universal
mechanisms at the heart of most drug interactions. Synopsis A general principle
of bacterial growth enables the prediction of mutant growth rates under drug combinations.
Rare violations of this principle expose cellular functions that control drug
interactions and can be targeted by small molecules to alter drug interactions
in predictable ways. Drug interactions between antibiotics are highly robust to
genetic perturbations. A general principle of bacterial growth enables the prediction
of mutant growth rates under drug combinations. Rare violations of this principle
expose cellular functions that control drug interactions. Diverse drug interactions
are controlled by recurring cellular functions, including LPS synthesis and ATP
synthesis. A general principle of bacterial growth enables the prediction of mutant
growth rates under drug combinations. Rare violations of this principle expose
cellular functions that control drug interactions and can be targeted by small
molecules to alter drug interactions in predictable ways.
article_number: '807'
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms.
Molecular Systems Biology. 2015;11(4). doi:10.15252/msb.20156098
apa: Chevereau, G., & Bollenbach, M. T. (2015). Systematic discovery of drug
interaction mechanisms. Molecular Systems Biology. Nature Publishing Group.
https://doi.org/10.15252/msb.20156098
chicago: Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery
of Drug Interaction Mechanisms.” Molecular Systems Biology. Nature Publishing
Group, 2015. https://doi.org/10.15252/msb.20156098.
ieee: G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction
mechanisms,” Molecular Systems Biology, vol. 11, no. 4. Nature Publishing
Group, 2015.
ista: Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction
mechanisms. Molecular Systems Biology. 11(4), 807.
mla: Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of
Drug Interaction Mechanisms.” Molecular Systems Biology, vol. 11, no. 4,
807, Nature Publishing Group, 2015, doi:10.15252/msb.20156098.
short: G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015).
date_created: 2018-12-11T11:54:12Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:26Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.15252/msb.20156098
ec_funded: 1
file:
- access_level: open_access
checksum: 4289b518fbe2166682fb1a1ef9b405f3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:34Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5087'
file_name: IST-2015-395-v1+1_807.full.pdf
file_size: 1273573
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5283'
pubrep_id: '395'
quality_controlled: '1'
scopus_import: 1
status: public
title: Systematic discovery of drug interaction mechanisms
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '1824'
abstract:
- lang: eng
text: Condensation phenomena arise through a collective behaviour of particles.
They are observed in both classical and quantum systems, ranging from the formation
of traffic jams in mass transport models to the macroscopic occupation of the
energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation).
Recently, it has been shown that a driven and dissipative system of bosons may
form multiple condensates. Which states become the condensates has, however, remained
elusive thus far. The dynamics of this condensation are described by coupled birth-death
processes, which also occur in evolutionary game theory. Here we apply concepts
from evolutionary game theory to explain the formation of multiple condensates
in such driven-dissipative bosonic systems. We show that the vanishing of relative
entropy production determines their selection. The condensation proceeds exponentially
fast, but the system never comes to rest. Instead, the occupation numbers of condensates
may oscillate, as we demonstrate for a rock-paper-scissors game of condensates.
article_number: '6977'
author:
- first_name: Johannes
full_name: Knebel, Johannes
last_name: Knebel
- first_name: Markus
full_name: Weber, Markus
last_name: Weber
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Erwin
full_name: Frey, Erwin
last_name: Frey
citation:
ama: Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in
coupled birth-death processes. Nature Communications. 2015;6. doi:10.1038/ncomms7977
apa: Knebel, J., Weber, M., Krüger, T. H., & Frey, E. (2015). Evolutionary games
of condensates in coupled birth-death processes. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms7977
chicago: Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary
Games of Condensates in Coupled Birth-Death Processes.” Nature Communications.
Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7977.
ieee: J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates
in coupled birth-death processes,” Nature Communications, vol. 6. Nature
Publishing Group, 2015.
ista: Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates
in coupled birth-death processes. Nature Communications. 6, 6977.
mla: Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death
Processes.” Nature Communications, vol. 6, 6977, Nature Publishing Group,
2015, doi:10.1038/ncomms7977.
short: J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015).
date_created: 2018-12-11T11:54:13Z
date_published: 2015-04-24T00:00:00Z
date_updated: 2021-01-12T06:53:26Z
day: '24'
ddc:
- '530'
department:
- _id: LaEr
doi: 10.1038/ncomms7977
file:
- access_level: open_access
checksum: c4cffb5c8b245e658a34eac71a03e7cc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:54Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5245'
file_name: IST-2016-451-v1+1_ncomms7977.pdf
file_size: 1151501
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5282'
pubrep_id: '451'
quality_controlled: '1'
scopus_import: 1
status: public
title: Evolutionary games of condensates in coupled birth-death processes
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1831'
abstract:
- lang: eng
text: This paper introduces a theme issue presenting the latest developments in
research on the impacts of sociality on health and fitness. The articles that
follow cover research on societies ranging from insects to humans. Variation in
measures of fitness (i.e. survival and reproduction) has been linked to various
aspects of sociality in humans and animals alike, and variability in individual
health and condition has been recognized as a key mediator of these relationships.
Viewed from a broad evolutionary perspective, the evolutionary transitions from
a solitary lifestyle to group living have resulted in several new health-related
costs and benefits of sociality. Social transmission of parasites within groups
represents a major cost of group living, but some behavioural mechanisms, such
as grooming, have evolved repeatedly to reduce this cost. Group living also has
created novel costs in terms of altered susceptibility to infectious and non-infectious
disease as a result of the unavoidable physiological consequences of social competition
and integration, which are partly alleviated by social buffering in some vertebrates.
Here, we define the relevant aspects of sociality, summarize their health-related
costs and benefits, and discuss possible fitness measures in different study systems.
Given the pervasive effects of social factors on health and fitness, we propose
a synthesis of existing conceptual approaches in disease ecology, ecological immunology
and behavioural neurosciences by adding sociality as a key factor, with the goal
to generate a broader framework for organismal integration of health-related research.
acknowledgement: We thank the German Research Foundation (DFG), the Ministry of Science
and Culture of Lower-Saxony (MWK Hannover) and the German Primate Centre (DPZ) for
their support of the 9. Göttinger Freilandtage in 2013, a conference at which most
contributions to this issue were first presented, the referees of the contributions
to this issue for their constructive comments, Meggan Craft for comments, and Helen
Eaton for her support in producing this theme issue.
article_number: '20140116'
author:
- first_name: Peter
full_name: Kappeler, Peter
last_name: Kappeler
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Charles
full_name: Nunn, Charles
last_name: Nunn
citation:
ama: 'Kappeler P, Cremer S, Nunn C. Sociality and health: Impacts of sociality on
disease susceptibility and transmission in animal and human societies. Philosophical
Transactions of the Royal Society of London Series B, Biological Sciences.
2015;370(1669). doi:10.1098/rstb.2014.0116'
apa: 'Kappeler, P., Cremer, S., & Nunn, C. (2015). Sociality and health: Impacts
of sociality on disease susceptibility and transmission in animal and human societies.
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society. https://doi.org/10.1098/rstb.2014.0116'
chicago: 'Kappeler, Peter, Sylvia Cremer, and Charles Nunn. “Sociality and Health:
Impacts of Sociality on Disease Susceptibility and Transmission in Animal and
Human Societies.” Philosophical Transactions of the Royal Society of London.
Series B, Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rstb.2014.0116.'
ieee: 'P. Kappeler, S. Cremer, and C. Nunn, “Sociality and health: Impacts of sociality
on disease susceptibility and transmission in animal and human societies,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 370, no. 1669. Royal Society, 2015.'
ista: 'Kappeler P, Cremer S, Nunn C. 2015. Sociality and health: Impacts of sociality
on disease susceptibility and transmission in animal and human societies. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669),
20140116.'
mla: 'Kappeler, Peter, et al. “Sociality and Health: Impacts of Sociality on Disease
Susceptibility and Transmission in Animal and Human Societies.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 370, no. 1669, 20140116, Royal Society, 2015, doi:10.1098/rstb.2014.0116.'
short: P. Kappeler, S. Cremer, C. Nunn, Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences 370 (2015).
date_created: 2018-12-11T11:54:15Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2021-01-12T06:53:29Z
day: '01'
department:
- _id: SyCr
doi: 10.1098/rstb.2014.0116
external_id:
pmid:
- '25870402'
intvolume: ' 370'
issue: '1669'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '5272'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Sociality and health: Impacts of sociality on disease susceptibility and transmission
in animal and human societies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 370
year: '2015'
...
---
_id: '1828'
abstract:
- lang: eng
text: We construct a non-linear Markov process connected with a biological model
of a bacterial genome recombination. The description of invariant measures of
this process gives us the solution of one problem in elementary probability theory.
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Pirogov, Sergey
last_name: Pirogov
- first_name: Aleksandr
full_name: Rybko, Aleksandr
last_name: Rybko
citation:
ama: Akopyan A, Pirogov S, Rybko A. Invariant measures of genetic recombination
process. Journal of Statistical Physics. 2015;160(1):163-167. doi:10.1007/s10955-015-1238-5
apa: Akopyan, A., Pirogov, S., & Rybko, A. (2015). Invariant measures of genetic
recombination process. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-015-1238-5
chicago: Akopyan, Arseniy, Sergey Pirogov, and Aleksandr Rybko. “Invariant Measures
of Genetic Recombination Process.” Journal of Statistical Physics. Springer,
2015. https://doi.org/10.1007/s10955-015-1238-5.
ieee: A. Akopyan, S. Pirogov, and A. Rybko, “Invariant measures of genetic recombination
process,” Journal of Statistical Physics, vol. 160, no. 1. Springer, pp.
163–167, 2015.
ista: Akopyan A, Pirogov S, Rybko A. 2015. Invariant measures of genetic recombination
process. Journal of Statistical Physics. 160(1), 163–167.
mla: Akopyan, Arseniy, et al. “Invariant Measures of Genetic Recombination Process.”
Journal of Statistical Physics, vol. 160, no. 1, Springer, 2015, pp. 163–67,
doi:10.1007/s10955-015-1238-5.
short: A. Akopyan, S. Pirogov, A. Rybko, Journal of Statistical Physics 160 (2015)
163–167.
date_created: 2018-12-11T11:54:14Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:28Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s10955-015-1238-5
ec_funded: 1
intvolume: ' 160'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: arxiv.org/abs/1406.5313
month: '07'
oa: 1
oa_version: Preprint
page: 163 - 167
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '5276'
quality_controlled: '1'
scopus_import: 1
status: public
title: Invariant measures of genetic recombination process
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 160
year: '2015'
...
---
_id: '1836'
abstract:
- lang: eng
text: In the standard framework for worst-case execution time (WCET) analysis of
programs, the main data structure is a single instance of integer linear programming
(ILP) that represents the whole program. The instance of this NP-hard problem
must be solved to find an estimate forWCET, and it must be refined if the estimate
is not tight.We propose a new framework for WCET analysis, based on abstract segment
trees (ASTs) as the main data structure. The ASTs have two advantages. First,
they allow computing WCET by solving a number of independent small ILP instances.
Second, ASTs store more expressive constraints, thus enabling a more efficient
and precise refinement procedure. In order to realize our framework algorithmically,
we develop an algorithm for WCET estimation on ASTs, and we develop an interpolation-based
counterexample-guided refinement scheme for ASTs. Furthermore, we extend our framework
to obtain parametric estimates of WCET. We experimentally evaluate our approach
on a set of examples from WCET benchmark suites and linear-algebra packages. We
show that our analysis, with comparable effort, provides WCET estimates that in
many cases significantly improve those computed by existing tools.
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Jakob
full_name: Zwirchmayr, Jakob
last_name: Zwirchmayr
citation:
ama: Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. Segment abstraction
for worst-case execution time analysis. 2015;9032:105-131. doi:10.1007/978-3-662-46669-8_5
apa: 'Cerny, P., Henzinger, T. A., Kovács, L., Radhakrishna, A., & Zwirchmayr,
J. (2015). Segment abstraction for worst-case execution time analysis. Presented
at the ESOP: European Symposium on Programming, London, United Kingdom: Springer.
https://doi.org/10.1007/978-3-662-46669-8_5'
chicago: Cerny, Pavol, Thomas A Henzinger, Laura Kovács, Arjun Radhakrishna, and
Jakob Zwirchmayr. “Segment Abstraction for Worst-Case Execution Time Analysis.”
Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46669-8_5.
ieee: P. Cerny, T. A. Henzinger, L. Kovács, A. Radhakrishna, and J. Zwirchmayr,
“Segment abstraction for worst-case execution time analysis,” vol. 9032. Springer,
pp. 105–131, 2015.
ista: Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. 2015. Segment
abstraction for worst-case execution time analysis. 9032, 105–131.
mla: Cerny, Pavol, et al. Segment Abstraction for Worst-Case Execution Time Analysis.
Vol. 9032, Springer, 2015, pp. 105–31, doi:10.1007/978-3-662-46669-8_5.
short: P. Cerny, T.A. Henzinger, L. Kovács, A. Radhakrishna, J. Zwirchmayr, 9032
(2015) 105–131.
conference:
end_date: 2015-04-18
location: London, United Kingdom
name: 'ESOP: European Symposium on Programming'
start_date: 2015-04-11
date_created: 2018-12-11T11:54:16Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2020-08-11T10:09:32Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-662-46669-8_5
ec_funded: 1
intvolume: ' 9032'
language:
- iso: eng
month: '04'
oa_version: None
page: 105 - 131
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: '5266'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Segment abstraction for worst-case execution time analysis
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9032
year: '2015'
...
---
_id: '1838'
abstract:
- lang: eng
text: Synthesis of program parts is particularly useful for concurrent systems.
However, most approaches do not support common design tasks, like modifying a
single process without having to re-synthesize or verify the whole system. Assume-guarantee
synthesis (AGS) provides robustness against modifications of system parts, but
thus far has been limited to the perfect information setting. This means that
local variables cannot be hidden from other processes, which renders synthesis
results cumbersome or even impossible to realize.We resolve this shortcoming by
defining AGS under partial information. We analyze the complexity and decidability
in different settings, showing that the problem has a high worstcase complexity
and is undecidable in many interesting cases. Based on these observations, we
present a pragmatic algorithm based on bounded synthesis, and demonstrate its
practical applicability on several examples.
acknowledgement: 'This work was supported by the Austrian Science Fund (FWF) through
the research network RiSE (S11406-N23, S11407-N23) and grant nr. P23499-N23, by
the European Commission through an ERC Start grant (279307: Graph Games) and project
STANCE (317753), as well as by the German Research Foundation (DFG) through SFB/TR
14 AVACS and project ASDPS(JA 2357/2-1).'
alternative_title:
- LNCS
author:
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Swen
full_name: Jacobs, Swen
last_name: Jacobs
- first_name: Robert
full_name: Könighofer, Robert
last_name: Könighofer
citation:
ama: 'Bloem R, Chatterjee K, Jacobs S, Könighofer R. Assume-guarantee synthesis
for concurrent reactive programs with partial information. In: Vol 9035. Springer;
2015:517-532. doi:10.1007/978-3-662-46681-0_50'
apa: 'Bloem, R., Chatterjee, K., Jacobs, S., & Könighofer, R. (2015). Assume-guarantee
synthesis for concurrent reactive programs with partial information (Vol. 9035,
pp. 517–532). Presented at the TACAS: Tools and Algorithms for the Construction
and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_50'
chicago: Bloem, Roderick, Krishnendu Chatterjee, Swen Jacobs, and Robert Könighofer.
“Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information,”
9035:517–32. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_50.
ieee: 'R. Bloem, K. Chatterjee, S. Jacobs, and R. Könighofer, “Assume-guarantee
synthesis for concurrent reactive programs with partial information,” presented
at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
London, United Kingdom, 2015, vol. 9035, pp. 517–532.'
ista: 'Bloem R, Chatterjee K, Jacobs S, Könighofer R. 2015. Assume-guarantee synthesis
for concurrent reactive programs with partial information. TACAS: Tools and Algorithms
for the Construction and Analysis of Systems, LNCS, vol. 9035, 517–532.'
mla: Bloem, Roderick, et al. Assume-Guarantee Synthesis for Concurrent Reactive
Programs with Partial Information. Vol. 9035, Springer, 2015, pp. 517–32,
doi:10.1007/978-3-662-46681-0_50.
short: R. Bloem, K. Chatterjee, S. Jacobs, R. Könighofer, in:, Springer, 2015, pp.
517–532.
conference:
end_date: 2015-04-18
location: London, United Kingdom
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2015-04-11
date_created: 2018-12-11T11:54:17Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:32Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-46681-0_50
ec_funded: 1
intvolume: ' 9035'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1411.4604
month: '01'
oa: 1
oa_version: Preprint
page: 517 - 532
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Springer
publist_id: '5264'
scopus_import: 1
status: public
title: Assume-guarantee synthesis for concurrent reactive programs with partial information
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9035
year: '2015'
...
---
_id: '1839'
abstract:
- lang: eng
text: We present MultiGain, a tool to synthesize strategies for Markov decision
processes (MDPs) with multiple mean-payoff objectives. Our models are described
in PRISM, and our tool uses the existing interface and simulator of PRISM. Our
tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives,
and also provides features such as (i) generating strategies and exploring them
for simulation, and checking them with respect to other properties; and (ii) generating
an approximate Pareto curve for two mean-payoff objectives. In addition, we present
a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives
under memoryless strategies.
alternative_title:
- LNCS
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vojtěch
full_name: Forejt, Vojtěch
last_name: Forejt
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
citation:
ama: 'Brázdil T, Chatterjee K, Forejt V, Kučera A. Multigain: A controller synthesis
tool for MDPs with multiple mean-payoff objectives. 2015;9035:181-187. doi:10.1007/978-3-662-46681-0_12'
apa: 'Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2015). Multigain:
A controller synthesis tool for MDPs with multiple mean-payoff objectives. Presented
at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_12'
chicago: 'Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera.
“Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives.”
Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_12.'
ieee: 'T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Multigain: A controller
synthesis tool for MDPs with multiple mean-payoff objectives,” vol. 9035. Springer,
pp. 181–187, 2015.'
ista: 'Brázdil T, Chatterjee K, Forejt V, Kučera A. 2015. Multigain: A controller
synthesis tool for MDPs with multiple mean-payoff objectives. 9035, 181–187.'
mla: 'Brázdil, Tomáš, et al. Multigain: A Controller Synthesis Tool for MDPs
with Multiple Mean-Payoff Objectives. Vol. 9035, Springer, 2015, pp. 181–87,
doi:10.1007/978-3-662-46681-0_12.'
short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187.
conference:
end_date: 2015-04-18
location: London, United Kingdom
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2015-04-11
date_created: 2018-12-11T11:54:18Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2020-01-21T13:18:52Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-46681-0_12
ec_funded: 1
intvolume: ' 9035'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.03093
month: '01'
oa: 1
oa_version: Preprint
page: 181 - 187
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Springer
publist_id: '5263'
quality_controlled: '1'
series_title: Lecture Notes in Computer Science
status: public
title: 'Multigain: A controller synthesis tool for MDPs with multiple mean-payoff
objectives'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9035
year: '2015'
...
---
_id: '1837'
abstract:
- lang: eng
text: 'Transition to turbulence in straight pipes occurs in spite of the linear
stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations
and the Reynolds number Re exceed a minimum threshold (subcritical transition).
As the pipe curvature increases, centrifugal effects become important, modifying
the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling
diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability)
is encountered before turbulence can be excited (subcritical instability). We
trace the instability thresholds in the Re - d/D parameter space in the range
0.01 ≤ d/D\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point
where the subcritical and supercritical instabilities meet. Two different experimental
set-ups are used: a closed system where the pipe forms an axisymmetric torus and
an open system employing a helical pipe. Implications for the measurement of friction
factors in curved pipes are discussed.'
article_number: R3
article_processing_charge: No
article_type: original
author:
- first_name: Jakob
full_name: Kühnen, Jakob
id: 3A47AE32-F248-11E8-B48F-1D18A9856A87
last_name: Kühnen
orcid: 0000-0003-4312-0179
- first_name: P
full_name: Braunshier, P
last_name: Braunshier
- first_name: M
full_name: Schwegel, M
last_name: Schwegel
- first_name: Hendrik
full_name: Kuhlmann, Hendrik
last_name: Kuhlmann
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. Subcritical versus supercritical
transition to turbulence in curved pipes. Journal of Fluid Mechanics. 2015;770(5).
doi:10.1017/jfm.2015.184
apa: Kühnen, J., Braunshier, P., Schwegel, M., Kuhlmann, H., & Hof, B. (2015).
Subcritical versus supercritical transition to turbulence in curved pipes. Journal
of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2015.184
chicago: Kühnen, Jakob, P Braunshier, M Schwegel, Hendrik Kuhlmann, and Björn Hof.
“Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal
of Fluid Mechanics. Cambridge University Press, 2015. https://doi.org/10.1017/jfm.2015.184.
ieee: J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, and B. Hof, “Subcritical
versus supercritical transition to turbulence in curved pipes,” Journal of
Fluid Mechanics, vol. 770, no. 5. Cambridge University Press, 2015.
ista: Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. 2015. Subcritical versus
supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics.
770(5), R3.
mla: Kühnen, Jakob, et al. “Subcritical versus Supercritical Transition to Turbulence
in Curved Pipes.” Journal of Fluid Mechanics, vol. 770, no. 5, R3, Cambridge
University Press, 2015, doi:10.1017/jfm.2015.184.
short: J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, B. Hof, Journal of Fluid
Mechanics 770 (2015).
date_created: 2018-12-11T11:54:17Z
date_published: 2015-04-08T00:00:00Z
date_updated: 2021-01-12T06:53:31Z
day: '08'
department:
- _id: BjHo
doi: 10.1017/jfm.2015.184
ec_funded: 1
external_id:
arxiv:
- '1508.06559'
intvolume: ' 770'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.06559
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluid Mechanics
publication_status: published
publisher: Cambridge University Press
publist_id: '5265'
quality_controlled: '1'
scopus_import: 1
status: public
title: Subcritical versus supercritical transition to turbulence in curved pipes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 770
year: '2015'
...
---
_id: '1848'
abstract:
- lang: eng
text: The ability to escape apoptosis is a hallmark of cancer-initiating cells and
a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a
ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate
its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal
tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating
factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied
by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation
and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis
sensitivity were examined in cancer cells and zebrafish embryos. Expression of
FAM96A in GISTs and histogenetically related cells including interstitial cells
of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was
investigated by Northern blotting, reverse transcription—polymerase chain reaction,
immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells
and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied
by xeno- and allografting into immunocompromised mice. FAM96A was found to bind
APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein
or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing
three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed
normal counterparts of GIST, were found to robustly express FAM96A protein and
mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression
of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity
and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic
tumor suppressor that is lost during GIST tumorigenesis.
article_processing_charge: No
article_type: original
author:
- first_name: Bettina
full_name: Schwamb, Bettina
last_name: Schwamb
- first_name: Robert
full_name: Pick, Robert
last_name: Pick
- first_name: Sara
full_name: Fernández, Sara
last_name: Fernández
- first_name: Kirsten
full_name: Völp, Kirsten
last_name: Völp
- first_name: Jan
full_name: Heering, Jan
last_name: Heering
- first_name: Volker
full_name: Dötsch, Volker
last_name: Dötsch
- first_name: Susanne
full_name: Bösser, Susanne
last_name: Bösser
- first_name: Jennifer
full_name: Jung, Jennifer
last_name: Jung
- first_name: Rasa
full_name: Beinoravičiute Kellner, Rasa
last_name: Beinoravičiute Kellner
- first_name: Josephine
full_name: Wesely, Josephine
last_name: Wesely
- first_name: Inka
full_name: Zörnig, Inka
last_name: Zörnig
- first_name: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
- first_name: Matthias
full_name: Nowak, Matthias
id: 30845DAA-F248-11E8-B48F-1D18A9856A87
last_name: Nowak
- first_name: Roland
full_name: Penzel, Roland
last_name: Penzel
- first_name: Kurt
full_name: Zatloukal, Kurt
last_name: Zatloukal
- first_name: Stefan
full_name: Joos, Stefan
last_name: Joos
- first_name: Ralf
full_name: Rieker, Ralf
last_name: Rieker
- first_name: Abbas
full_name: Agaimy, Abbas
last_name: Agaimy
- first_name: Stephan
full_name: Söder, Stephan
last_name: Söder
- first_name: Kmarie
full_name: Reid Lombardo, Kmarie
last_name: Reid Lombardo
- first_name: Michael
full_name: Kendrick, Michael
last_name: Kendrick
- first_name: Michael
full_name: Bardsley, Michael
last_name: Bardsley
- first_name: Yujiro
full_name: Hayashi, Yujiro
last_name: Hayashi
- first_name: David
full_name: Asuzu, David
last_name: Asuzu
- first_name: Sabriya
full_name: Syed, Sabriya
last_name: Syed
- first_name: Tamás
full_name: Ördög, Tamás
last_name: Ördög
- first_name: Martin
full_name: Zörnig, Martin
last_name: Zörnig
citation:
ama: Schwamb B, Pick R, Fernández S, et al. FAM96A is a novel pro-apoptotic tumor
suppressor in gastrointestinal stromal tumors. International Journal of Cancer.
2015;137(6):1318-1329. doi:10.1002/ijc.29498
apa: Schwamb, B., Pick, R., Fernández, S., Völp, K., Heering, J., Dötsch, V., …
Zörnig, M. (2015). FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal
stromal tumors. International Journal of Cancer. Wiley. https://doi.org/10.1002/ijc.29498
chicago: Schwamb, Bettina, Robert Pick, Sara Fernández, Kirsten Völp, Jan Heering,
Volker Dötsch, Susanne Bösser, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor
in Gastrointestinal Stromal Tumors.” International Journal of Cancer. Wiley,
2015. https://doi.org/10.1002/ijc.29498.
ieee: B. Schwamb et al., “FAM96A is a novel pro-apoptotic tumor suppressor
in gastrointestinal stromal tumors,” International Journal of Cancer, vol.
137, no. 6. Wiley, pp. 1318–1329, 2015.
ista: Schwamb B, Pick R, Fernández S, Völp K, Heering J, Dötsch V, Bösser S, Jung
J, Beinoravičiute Kellner R, Wesely J, Zörnig I, Hammerschmidt M, Nowak M, Penzel
R, Zatloukal K, Joos S, Rieker R, Agaimy A, Söder S, Reid Lombardo K, Kendrick
M, Bardsley M, Hayashi Y, Asuzu D, Syed S, Ördög T, Zörnig M. 2015. FAM96A is
a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International
Journal of Cancer. 137(6), 1318–1329.
mla: Schwamb, Bettina, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor
in Gastrointestinal Stromal Tumors.” International Journal of Cancer, vol.
137, no. 6, Wiley, 2015, pp. 1318–29, doi:10.1002/ijc.29498.
short: B. Schwamb, R. Pick, S. Fernández, K. Völp, J. Heering, V. Dötsch, S. Bösser,
J. Jung, R. Beinoravičiute Kellner, J. Wesely, I. Zörnig, M. Hammerschmidt, M.
Nowak, R. Penzel, K. Zatloukal, S. Joos, R. Rieker, A. Agaimy, S. Söder, K. Reid
Lombardo, M. Kendrick, M. Bardsley, Y. Hayashi, D. Asuzu, S. Syed, T. Ördög, M.
Zörnig, International Journal of Cancer 137 (2015) 1318–1329.
date_created: 2018-12-11T11:54:20Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:53:36Z
day: '01'
department:
- _id: LifeSc
doi: 10.1002/ijc.29498
external_id:
pmid:
- '25716227'
intvolume: ' 137'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497860/
month: '09'
oa: 1
oa_version: Submitted Version
page: 1318 - 1329
pmid: 1
publication: International Journal of Cancer
publication_status: published
publisher: Wiley
publist_id: '5253'
quality_controlled: '1'
scopus_import: 1
status: public
title: FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal
tumors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2015'
...
---
_id: '1846'
abstract:
- lang: eng
text: Modal transition systems (MTS) is a well-studied specification formalism of
reactive systems supporting a step-wise refinement methodology. Despite its many
advantages, the formalism as well as its currently known extensions are incapable
of expressing some practically needed aspects in the refinement process like exclusive,
conditional and persistent choices. We introduce a new model called parametric
modal transition systems (PMTS) together with a general modal refinement notion
that overcomes many of the limitations. We investigate the computational complexity
of modal and thorough refinement checking on PMTS and its subclasses and provide
a direct encoding of the modal refinement problem into quantified Boolean formulae,
allowing us to employ state-of-the-art QBF solvers for modal refinement checking.
The experiments we report on show that the feasibility of refinement checking
is more influenced by the degree of nondeterminism rather than by the syntactic
restrictions on the types of formulae allowed in the description of the PMTS.
article_processing_charge: No
article_type: original
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Kim
full_name: Larsen, Kim
last_name: Larsen
- first_name: Mikael
full_name: Möller, Mikael
last_name: Möller
- first_name: Salomon
full_name: Sickert, Salomon
last_name: Sickert
- first_name: Jiří
full_name: Srba, Jiří
last_name: Srba
citation:
ama: Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. Refinement checking
on parametric modal transition systems. Acta Informatica. 2015;52(2-3):269-297.
doi:10.1007/s00236-015-0215-4
apa: Beneš, N., Kretinsky, J., Larsen, K., Möller, M., Sickert, S., & Srba,
J. (2015). Refinement checking on parametric modal transition systems. Acta
Informatica. Springer. https://doi.org/10.1007/s00236-015-0215-4
chicago: Beneš, Nikola, Jan Kretinsky, Kim Larsen, Mikael Möller, Salomon Sickert,
and Jiří Srba. “Refinement Checking on Parametric Modal Transition Systems.” Acta
Informatica. Springer, 2015. https://doi.org/10.1007/s00236-015-0215-4.
ieee: N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, and J. Srba, “Refinement
checking on parametric modal transition systems,” Acta Informatica, vol.
52, no. 2–3. Springer, pp. 269–297, 2015.
ista: Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. 2015. Refinement
checking on parametric modal transition systems. Acta Informatica. 52(2–3), 269–297.
mla: Beneš, Nikola, et al. “Refinement Checking on Parametric Modal Transition Systems.”
Acta Informatica, vol. 52, no. 2–3, Springer, 2015, pp. 269–97, doi:10.1007/s00236-015-0215-4.
short: N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, J. Srba, Acta Informatica
52 (2015) 269–297.
date_created: 2018-12-11T11:54:20Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:35Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/s00236-015-0215-4
ec_funded: 1
file:
- access_level: open_access
checksum: fb4037ddc4fc05f33080dd3547ede350
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T08:57:44Z
date_updated: 2020-07-14T12:45:19Z
file_id: '7854'
file_name: 2015_ActaInfo_Benes.pdf
file_size: 488482
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 52'
issue: 2-3
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 269 - 297
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: Acta Informatica
publication_status: published
publisher: Springer
publist_id: '5255'
quality_controlled: '1'
scopus_import: 1
status: public
title: Refinement checking on parametric modal transition systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2015'
...
---
_id: '1845'
abstract:
- lang: eng
text: Based on extrapolation from excitatory synapses, it is often assumed that
depletion of the releasable pool of synaptic vesicles is the main factor underlying
depression at inhibitory synapses. In this issue of Neuron, using subcellular
patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba
(2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes
in presynaptic action potential waveform substantially contribute to synaptic
depression. Based on extrapolation from excitatory synapses, it is often assumed
that depletion of the releasable pool of synaptic vesicles is the main factor
underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular
patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba
(2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes
in presynaptic action potential waveform substantially contribute to synaptic
depression.
article_processing_charge: No
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vandael DH, Espinoza Martinez C, Jonas PM. Excitement about inhibitory presynaptic
terminals. Neuron. 2015;85(6):1149-1151. doi:10.1016/j.neuron.2015.03.006
apa: Vandael, D. H., Espinoza Martinez, C., & Jonas, P. M. (2015). Excitement
about inhibitory presynaptic terminals. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.03.006
chicago: Vandael, David H, Claudia Espinoza Martinez, and Peter M Jonas. “Excitement
about Inhibitory Presynaptic Terminals.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.03.006.
ieee: D. H. Vandael, C. Espinoza Martinez, and P. M. Jonas, “Excitement about inhibitory
presynaptic terminals,” Neuron, vol. 85, no. 6. Elsevier, pp. 1149–1151,
2015.
ista: Vandael DH, Espinoza Martinez C, Jonas PM. 2015. Excitement about inhibitory
presynaptic terminals. Neuron. 85(6), 1149–1151.
mla: Vandael, David H., et al. “Excitement about Inhibitory Presynaptic Terminals.”
Neuron, vol. 85, no. 6, Elsevier, 2015, pp. 1149–51, doi:10.1016/j.neuron.2015.03.006.
short: D.H. Vandael, C. Espinoza Martinez, P.M. Jonas, Neuron 85 (2015) 1149–1151.
date_created: 2018-12-11T11:54:19Z
date_published: 2015-03-18T00:00:00Z
date_updated: 2021-10-08T09:07:34Z
day: '18'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2015.03.006
file:
- access_level: open_access
checksum: d1808550e376a0eca2a950fda017cfa6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:07Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5192'
file_name: IST-2017-822-v1+1_Perspective_Fig__Final.pdf
file_size: 411832
relation: main_file
- access_level: open_access
checksum: a279f4ae61e6c8f33d68f69a0d02097d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:07Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5193'
file_name: IST-2017-822-v1+2_Perspective_Final2.pdf
file_size: 100769
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 85'
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 1149 - 1151
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5256'
pubrep_id: '822'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Excitement about inhibitory presynaptic terminals
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 85
year: '2015'
...
---
_id: '1840'
abstract:
- lang: eng
text: In this paper, we present a method for reducing a regular, discrete-time Markov
chain (DTMC) to another DTMC with a given, typically much smaller number of states.
The cost of reduction is defined as the Kullback-Leibler divergence rate between
a projection of the original process through a partition function and a DTMC on
the correspondingly partitioned state space. Finding the reduced model with minimal
cost is computationally expensive, as it requires an exhaustive search among all
state space partitions, and an exact evaluation of the reduction cost for each
candidate partition. Our approach deals with the latter problem by minimizing
an upper bound on the reduction cost instead of minimizing the exact cost. The
proposed upper bound is easy to compute and it is tight if the original chain
is lumpable with respect to the partition. Then, we express the problem in the
form of information bottleneck optimization, and propose using the agglomerative
information bottleneck algorithm for searching a suboptimal partition greedily,
rather than exhaustively. The theory is illustrated with examples and one application
scenario in the context of modeling bio-molecular interactions.
acknowledgement: "This work was supported by the Austrian Research Association under
Project 06/12684, by the Swiss National Science Foundation (SNSF) under Grant PP00P2
128503/1, by the SystemsX.ch (the Swiss Inititative for Systems Biology), and by
a SNSF Early Postdoc.Mobility Fellowship grant P2EZP2_148797.\r\n"
author:
- first_name: Bernhard
full_name: Geiger, Bernhard
last_name: Geiger
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
- first_name: Gernot
full_name: Kubin, Gernot
last_name: Kubin
- first_name: Heinz
full_name: Koeppl, Heinz
last_name: Koeppl
citation:
ama: Geiger B, Petrov T, Kubin G, Koeppl H. Optimal Kullback-Leibler aggregation
via information bottleneck. IEEE Transactions on Automatic Control. 2015;60(4):1010-1022.
doi:10.1109/TAC.2014.2364971
apa: Geiger, B., Petrov, T., Kubin, G., & Koeppl, H. (2015). Optimal Kullback-Leibler
aggregation via information bottleneck. IEEE Transactions on Automatic Control.
IEEE. https://doi.org/10.1109/TAC.2014.2364971
chicago: Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal
Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions
on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2014.2364971.
ieee: B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation
via information bottleneck,” IEEE Transactions on Automatic Control, vol.
60, no. 4. IEEE, pp. 1010–1022, 2015.
ista: Geiger B, Petrov T, Kubin G, Koeppl H. 2015. Optimal Kullback-Leibler aggregation
via information bottleneck. IEEE Transactions on Automatic Control. 60(4), 1010–1022.
mla: Geiger, Bernhard, et al. “Optimal Kullback-Leibler Aggregation via Information
Bottleneck.” IEEE Transactions on Automatic Control, vol. 60, no. 4, IEEE,
2015, pp. 1010–22, doi:10.1109/TAC.2014.2364971.
short: B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic
Control 60 (2015) 1010–1022.
date_created: 2018-12-11T11:54:18Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:33Z
day: '01'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1109/TAC.2014.2364971
intvolume: ' 60'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.6603
month: '04'
oa: 1
oa_version: Preprint
page: 1010 - 1022
publication: IEEE Transactions on Automatic Control
publication_identifier:
issn:
- 0018-9286
publication_status: published
publisher: IEEE
publist_id: '5262'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimal Kullback-Leibler aggregation via information bottleneck
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2015'
...
---
_id: '1841'
abstract:
- lang: eng
text: We propose a new family of message passing techniques for MAP estimation in
graphical models which we call Sequential Reweighted Message Passing (SRMP). Special
cases include well-known techniques such as Min-Sum Diffusion (MSD) and a faster
Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation
is simpler than the original derivation of TRW-S, and does not involve a decomposition
into trees. This allows easy generalizations. The new family of algorithms can
be viewed as a generalization of TRW-S from pairwise to higher-order graphical
models. We test SRMP on several real-world problems with promising results.
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Kolmogorov V. A new look at reweighted message passing. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 2015;37(5):919-930. doi:10.1109/TPAMI.2014.2363465
apa: Kolmogorov, V. (2015). A new look at reweighted message passing. IEEE Transactions
on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2014.2363465
chicago: Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE
Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2015. https://doi.org/10.1109/TPAMI.2014.2363465.
ieee: V. Kolmogorov, “A new look at reweighted message passing,” IEEE Transactions
on Pattern Analysis and Machine Intelligence, vol. 37, no. 5. IEEE, pp. 919–930,
2015.
ista: Kolmogorov V. 2015. A new look at reweighted message passing. IEEE Transactions
on Pattern Analysis and Machine Intelligence. 37(5), 919–930.
mla: Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions
on Pattern Analysis and Machine Intelligence, vol. 37, no. 5, IEEE, 2015,
pp. 919–30, doi:10.1109/TPAMI.2014.2363465.
short: V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence
37 (2015) 919–930.
date_created: 2018-12-11T11:54:18Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2021-01-12T06:53:33Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/TPAMI.2014.2363465
ec_funded: 1
intvolume: ' 37'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1309.5655
month: '05'
oa: 1
oa_version: Preprint
page: 919 - 930
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '5261'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new look at reweighted message passing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2015'
...
---
_id: '1849'
abstract:
- lang: eng
text: 'Cell polarity is a fundamental property of pro- and eukaryotic cells. It
is necessary for coordination of cell division, cell morphogenesis and signaling
processes. How polarity is generated and maintained is a complex issue governed
by interconnected feed-back regulations between small GTPase signaling and membrane
tension-based signaling that controls membrane trafficking, and cytoskeleton organization
and dynamics. Here, we will review the potential role for calcium as a crucial
signal that connects and coordinates the respective processes during polarization
processes in plants. This article is part of a Special Issue entitled: 13th European
Symposium on Calcium.'
acknowledgement: The contributing authors were supported by the Ghent University Special
Research Fund (to E.H.), the Interuniversity Attraction Poles Programme (IAP VI/33
and IUAP P7/29 ‘MARS’), the European Research Council (project ERC-2011-StG-20101109-PSDP,
to J.F.), and the Research Foundation Flanders (to S.V.).
author:
- first_name: Ellie
full_name: Himschoot, Ellie
last_name: Himschoot
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Jiřĺ
full_name: Friml, Jiřĺ
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
citation:
ama: Himschoot E, Beeckman T, Friml J, Vanneste S. Calcium is an organizer of cell
polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research.
2015;1853(9):2168-2172. doi:10.1016/j.bbamcr.2015.02.017
apa: Himschoot, E., Beeckman, T., Friml, J., & Vanneste, S. (2015). Calcium
is an organizer of cell polarity in plants. Biochimica et Biophysica Acta -
Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2015.02.017
chicago: Himschoot, Ellie, Tom Beeckman, Jiří Friml, and Steffen Vanneste. “Calcium
Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta
- Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2015.02.017.
ieee: E. Himschoot, T. Beeckman, J. Friml, and S. Vanneste, “Calcium is an organizer
of cell polarity in plants,” Biochimica et Biophysica Acta - Molecular Cell
Research, vol. 1853, no. 9. Elsevier, pp. 2168–2172, 2015.
ista: Himschoot E, Beeckman T, Friml J, Vanneste S. 2015. Calcium is an organizer
of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research.
1853(9), 2168–2172.
mla: Himschoot, Ellie, et al. “Calcium Is an Organizer of Cell Polarity in Plants.”
Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no.
9, Elsevier, 2015, pp. 2168–72, doi:10.1016/j.bbamcr.2015.02.017.
short: E. Himschoot, T. Beeckman, J. Friml, S. Vanneste, Biochimica et Biophysica
Acta - Molecular Cell Research 1853 (2015) 2168–2172.
date_created: 2018-12-11T11:54:21Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:53:36Z
day: '01'
department:
- _id: JiFr
doi: 10.1016/j.bbamcr.2015.02.017
intvolume: ' 1853'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 2168 - 2172
publication: Biochimica et Biophysica Acta - Molecular Cell Research
publication_status: published
publisher: Elsevier
publist_id: '5252'
quality_controlled: '1'
scopus_import: 1
status: public
title: Calcium is an organizer of cell polarity in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1853
year: '2015'
...
---
_id: '1847'
acknowledgement: This work was supported by the European Research Council (project
ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043), and
the Czech Science Foundation GAČR (GA13-40637S).
author:
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Jiřĺ
full_name: Friml, Jiřĺ
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Grones P, Friml J. ABP1: Finally docking. Molecular Plant. 2015;8(3):356-358.
doi:10.1016/j.molp.2014.12.013'
apa: 'Grones, P., & Friml, J. (2015). ABP1: Finally docking. Molecular Plant.
Elsevier. https://doi.org/10.1016/j.molp.2014.12.013'
chicago: 'Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant.
Elsevier, 2015. https://doi.org/10.1016/j.molp.2014.12.013.'
ieee: 'P. Grones and J. Friml, “ABP1: Finally docking,” Molecular Plant,
vol. 8, no. 3. Elsevier, pp. 356–358, 2015.'
ista: 'Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358.'
mla: 'Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant,
vol. 8, no. 3, Elsevier, 2015, pp. 356–58, doi:10.1016/j.molp.2014.12.013.'
short: P. Grones, J. Friml, Molecular Plant 8 (2015) 356–358.
date_created: 2018-12-11T11:54:20Z
date_published: 2015-03-02T00:00:00Z
date_updated: 2021-01-12T06:53:35Z
day: '02'
department:
- _id: JiFr
doi: 10.1016/j.molp.2014.12.013
intvolume: ' 8'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 356 - 358
publication: Molecular Plant
publication_status: published
publisher: Elsevier
publist_id: '5254'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'ABP1: Finally docking'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2015'
...