---
_id: '2270'
abstract:
- lang: eng
text: "Representation languages for coalitional games are a key research area in
algorithmic game theory. There is an inher-\r\nent tradeoff between how general
a language is, allowing it to capture more elaborate games, and how hard
\ it is computationally to optimize and solve such games. One prominent such
\ language is the simple yet expressive\r\nWeighted Graph Games (WGGs) representation
(Deng and Papadimitriou 1994), which maintains knowledge about synergies between
agents in the form of an edge weighted graph. We consider the problem of finding
\ the optimal coalition structure in WGGs. The agents in such games are vertices
in a graph, and the value of a coalition is the sum of the weights of the edges
present between coalition members. The optimal coalition structure is a partition
of the agents to coalitions, that maximizes the sum of utilities obtained by the
coalitions. We show that finding the optimal coalition structure is not
only hard for general graphs, but is also intractable for restricted families
such as planar graphs which are amenable for many other combinatorial problems.
\ We then provide algorithms with constant factor approximations for planar, minorfree
and bounded degree graphs."
author:
- first_name: Yoram
full_name: Bachrach, Yoram
last_name: Bachrach
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Morteza
full_name: Zadimoghaddam, Morteza
last_name: Zadimoghaddam
citation:
ama: 'Bachrach Y, Kohli P, Kolmogorov V, Zadimoghaddam M. Optimal Coalition Structures
in Cooperative Graph Games. In: AAAI Press; 2013:81-87.'
apa: 'Bachrach, Y., Kohli, P., Kolmogorov, V., & Zadimoghaddam, M. (2013). Optimal
Coalition Structures in Cooperative Graph Games (pp. 81–87). Presented at the
AAAI: Conference on Artificial Intelligence, Bellevue, WA, United States: AAAI
Press.'
chicago: Bachrach, Yoram, Pushmeet Kohli, Vladimir Kolmogorov, and Morteza Zadimoghaddam.
“Optimal Coalition Structures in Cooperative Graph Games,” 81–87. AAAI Press,
2013.
ieee: 'Y. Bachrach, P. Kohli, V. Kolmogorov, and M. Zadimoghaddam, “Optimal Coalition
Structures in Cooperative Graph Games,” presented at the AAAI: Conference on Artificial
Intelligence, Bellevue, WA, United States, 2013, pp. 81–87.'
ista: 'Bachrach Y, Kohli P, Kolmogorov V, Zadimoghaddam M. 2013. Optimal Coalition
Structures in Cooperative Graph Games. AAAI: Conference on Artificial Intelligence,
81–87.'
mla: Bachrach, Yoram, et al. Optimal Coalition Structures in Cooperative Graph
Games. AAAI Press, 2013, pp. 81–87.
short: Y. Bachrach, P. Kohli, V. Kolmogorov, M. Zadimoghaddam, in:, AAAI Press,
2013, pp. 81–87.
conference:
end_date: 2013-07-18
location: Bellevue, WA, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2013-07-14
date_created: 2018-12-11T11:56:41Z
date_published: 2013-12-31T00:00:00Z
date_updated: 2021-01-12T06:56:25Z
day: '31'
department:
- _id: VlKo
external_id:
arxiv:
- '1108.5248'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1108.5248
month: '12'
oa: 1
oa_version: None
page: 81-87
publication_status: published
publisher: AAAI Press
publist_id: '4674'
quality_controlled: '1'
status: public
title: Optimal Coalition Structures in Cooperative Graph Games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2273'
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 Diusion (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. We present such a generalization
for the case of higher-order graphical models, and test it on several real-world
problems with promising results.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Kolmogorov V. Reweighted Message Passing Revisited. IST Austria; 2013.
apa: Kolmogorov, V. (2013). Reweighted message passing revisited. IST Austria.
chicago: Kolmogorov, Vladimir. Reweighted Message Passing Revisited. IST
Austria, 2013.
ieee: V. Kolmogorov, Reweighted message passing revisited. IST Austria, 2013.
ista: Kolmogorov V. 2013. Reweighted message passing revisited, IST Austria,p.
mla: Kolmogorov, Vladimir. Reweighted Message Passing Revisited. IST Austria,
2013.
short: V. Kolmogorov, Reweighted Message Passing Revisited, IST Austria, 2013.
date_created: 2018-12-11T11:56:42Z
date_published: 2013-09-22T00:00:00Z
date_updated: 2019-01-24T13:07:32Z
day: '22'
department:
- _id: VlKo
extern: 0
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1309.5655
month: '09'
oa: 1
publication_status: published
publisher: IST Austria
publist_id: '4671'
quality_controlled: 0
status: public
title: Reweighted message passing revisited
type: report
year: '2013'
...
---
_id: '2278'
abstract:
- lang: eng
text: It is firmly established that interactions between neurons and glia are fundamental
across species for the correct establishment of a functional brain. Here, we found
that the glia of the Drosophila larval brain display an essential non-autonomous
role during the development of the optic lobe. The optic lobe develops from neuroepithelial
cells that proliferate by dividing symmetrically until they switch to asymmetric/differentiative
divisions that generate neuroblasts. The proneural gene lethal of scute (l9sc)
is transiently activated by the epidermal growth factor receptor (EGFR)-Ras signal
transduction pathway at the leading edge of a proneural wave that sweeps from
medial to lateral neuroepithelium, promoting this switch. This process is tightly
regulated by the tissue-autonomous function within the neuroepithelium of multiple
signaling pathways, including EGFR-Ras and Notch. This study shows that the Notch
ligand Serrate (Ser) is expressed in the glia and it forms a complex in vivo with
Notch and Canoe, which colocalize at the adherens junctions of neuroepithelial
cells. This complex is crucial for interactions between glia and neuroepithelial
cells during optic lobe development. Ser is tissue-autonomously required in the
glia where it activates Notch to regulate its proliferation, and non-autonomously
in the neuroepithelium where Ser induces Notch signaling to avoid the premature
activation of the EGFR-Ras pathway and hence of L9sc. Interestingly, different
Notch activity reporters showed very different expression patterns in the glia
and in the neuroepithelium, suggesting the existence of tissue-specific factors
that promote the expression of particular Notch target genes or/and a reporter
response dependent on different thresholds of Notch signaling.
author:
- first_name: Raquel
full_name: Pérez Gómez, Raquel
last_name: Pérez Gómez
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Noemí
full_name: Rives Quinto, Noemí
last_name: Rives Quinto
- first_name: Alena
full_name: Krejčí, Alena
last_name: Krejčí
- first_name: Ana
full_name: Carmena, Ana
last_name: Carmena
citation:
ama: Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. A serrate-notch-canoe
complex mediates essential interactions between glia and neuroepithelial cells
during Drosophila optic lobe development. Journal of Cell Science. 2013;126(21):4873-4884.
doi:10.1242/jcs.125617
apa: Pérez Gómez, R., Slovakova, J., Rives Quinto, N., Krejčí, A., & Carmena,
A. (2013). A serrate-notch-canoe complex mediates essential interactions between
glia and neuroepithelial cells during Drosophila optic lobe development. Journal
of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.125617
chicago: Pérez Gómez, Raquel, Jana Slovakova, Noemí Rives Quinto, Alena Krejčí,
and Ana Carmena. “A Serrate-Notch-Canoe Complex Mediates Essential Interactions
between Glia and Neuroepithelial Cells during Drosophila Optic Lobe Development.”
Journal of Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.125617.
ieee: R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, and A. Carmena,
“A serrate-notch-canoe complex mediates essential interactions between glia and
neuroepithelial cells during Drosophila optic lobe development,” Journal of
Cell Science, vol. 126, no. 21. Company of Biologists, pp. 4873–4884, 2013.
ista: Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. 2013. A serrate-notch-canoe
complex mediates essential interactions between glia and neuroepithelial cells
during Drosophila optic lobe development. Journal of Cell Science. 126(21), 4873–4884.
mla: Pérez Gómez, Raquel, et al. “A Serrate-Notch-Canoe Complex Mediates Essential
Interactions between Glia and Neuroepithelial Cells during Drosophila Optic Lobe
Development.” Journal of Cell Science, vol. 126, no. 21, Company of Biologists,
2013, pp. 4873–84, doi:10.1242/jcs.125617.
short: R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, A. Carmena, Journal
of Cell Science 126 (2013) 4873–4884.
date_created: 2018-12-11T11:56:43Z
date_published: 2013-11-01T00:00:00Z
date_updated: 2021-01-12T06:56:29Z
day: '01'
department:
- _id: CaHe
doi: 10.1242/jcs.125617
intvolume: ' 126'
issue: '21'
language:
- iso: eng
month: '11'
oa_version: None
page: 4873 - 4884
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '4658'
quality_controlled: '1'
scopus_import: 1
status: public
title: A serrate-notch-canoe complex mediates essential interactions between glia
and neuroepithelial cells during Drosophila optic lobe development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 126
year: '2013'
...
---
_id: '2276'
abstract:
- lang: eng
text: The problem of minimizing the Potts energy function frequently occurs in computer
vision applications. One way to tackle this NP-hard problem was proposed by Kovtun
[19, 20]. It identifies a part of an optimal solution by running k maxflow computations,
where k is the number of labels. The number of “labeled” pixels can be significant
in some applications, e.g. 50-93% in our tests for stereo. We show how to reduce
the runtime to O (log k) maxflow computations (or one parametric maxflow computation).
Furthermore, the output of our algorithm allows to speed-up the subsequent alpha
expansion for the unlabeled part, or can be used as it is for time-critical applications.
To derive our technique, we generalize the algorithm of Felzenszwalb et al. [7]
for Tree Metrics . We also show a connection to k-submodular functions from combinatorial
optimization, and discuss k-submodular relaxations for general energy functions.
author:
- first_name: Igor
full_name: Gridchyn, Igor
id: 4B60654C-F248-11E8-B48F-1D18A9856A87
last_name: Gridchyn
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Gridchyn I, Kolmogorov V. Potts model, parametric maxflow and k-submodular
functions. In: IEEE; 2013:2320-2327. doi:10.1109/ICCV.2013.288'
apa: 'Gridchyn, I., & Kolmogorov, V. (2013). Potts model, parametric maxflow
and k-submodular functions (pp. 2320–2327). Presented at the ICCV: International
Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.288'
chicago: Gridchyn, Igor, and Vladimir Kolmogorov. “Potts Model, Parametric Maxflow
and k-Submodular Functions,” 2320–27. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.288.
ieee: 'I. Gridchyn and V. Kolmogorov, “Potts model, parametric maxflow and k-submodular
functions,” presented at the ICCV: International Conference on Computer Vision,
Sydney, Australia, 2013, pp. 2320–2327.'
ista: 'Gridchyn I, Kolmogorov V. 2013. Potts model, parametric maxflow and k-submodular
functions. ICCV: International Conference on Computer Vision, 2320–2327.'
mla: Gridchyn, Igor, and Vladimir Kolmogorov. Potts Model, Parametric Maxflow
and k-Submodular Functions. IEEE, 2013, pp. 2320–27, doi:10.1109/ICCV.2013.288.
short: I. Gridchyn, V. Kolmogorov, in:, IEEE, 2013, pp. 2320–2327.
conference:
end_date: 2013-12-08
location: Sydney, Australia
name: 'ICCV: International Conference on Computer Vision'
start_date: 2013-12-01
date_created: 2018-12-11T11:56:43Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T06:56:28Z
day: '01'
department:
- _id: JoCs
- _id: VlKo
doi: 10.1109/ICCV.2013.288
external_id:
arxiv:
- '1310.1771'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1310.1771
month: '12'
oa: 1
oa_version: Preprint
page: 2320 - 2327
publication_status: published
publisher: IEEE
publist_id: '4668'
quality_controlled: '1'
status: public
title: Potts model, parametric maxflow and k-submodular functions
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2280'
abstract:
- lang: eng
text: The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal
container so as to minimize a measure of overlap between ellipsoids is considered.
A bilevel optimization formulation is given, together with an algorithm for the
general case and a simpler algorithm for the special case in which all ellipsoids
are in fact spheres. Convergence results are proved and computational experience
is described and illustrated. The motivating application-chromosome organization
in the human cell nucleus-is discussed briefly, and some illustrative results
are presented.
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Stephen
full_name: Wright, Stephen
last_name: Wright
citation:
ama: Uhler C, Wright S. Packing ellipsoids with overlap. SIAM Review. 2013;55(4):671-706.
doi:10.1137/120872309
apa: Uhler, C., & Wright, S. (2013). Packing ellipsoids with overlap. SIAM
Review. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/120872309
chicago: Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.”
SIAM Review. Society for Industrial and Applied Mathematics , 2013. https://doi.org/10.1137/120872309.
ieee: C. Uhler and S. Wright, “Packing ellipsoids with overlap,” SIAM Review,
vol. 55, no. 4. Society for Industrial and Applied Mathematics , pp. 671–706,
2013.
ista: Uhler C, Wright S. 2013. Packing ellipsoids with overlap. SIAM Review. 55(4),
671–706.
mla: Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” SIAM
Review, vol. 55, no. 4, Society for Industrial and Applied Mathematics , 2013,
pp. 671–706, doi:10.1137/120872309.
short: C. Uhler, S. Wright, SIAM Review 55 (2013) 671–706.
date_created: 2018-12-11T11:56:44Z
date_published: 2013-11-07T00:00:00Z
date_updated: 2021-01-12T06:56:30Z
day: '07'
department:
- _id: CaUh
doi: 10.1137/120872309
external_id:
arxiv:
- '1204.0235'
intvolume: ' 55'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1204.0235
month: '11'
oa: 1
oa_version: Preprint
page: 671 - 706
publication: SIAM Review
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '4655'
quality_controlled: '1'
scopus_import: 1
status: public
title: Packing ellipsoids with overlap
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2013'
...
---
_id: '2287'
abstract:
- lang: eng
text: Negative frequency-dependent selection should result in equal sex ratios in
large populations of dioecious flowering plants, but deviations from equality
are commonly reported. A variety of ecological and genetic factors can explain
biased sex ratios, although the mechanisms involved are not well understood. Most
dioecious species are long-lived and/or clonal complicating efforts to identify
stages during the life cycle when biases develop. We investigated the demographic
correlates of sex-ratio variation in two chromosome races of Rumex hastatulus,
an annual, wind-pollinated colonizer of open habitats from the southern USA. We
examined sex ratios in 46 populations and evaluated the hypothesis that the proximity
of males in the local mating environment, through its influence on gametophytic
selection, is the primary cause of female-biased sex ratios. Female-biased sex
ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62),
with significant female bias in 89% of populations. Large, high-density populations
had the highest proportion of females, whereas smaller, low-density populations
had sex ratios closer to equality. Progeny sex ratios were more female biased
when males were in closer proximity to females, a result consistent with the gametophytic
selection hypothesis. Our results suggest that interactions between demographic
and genetic factors are probably the main cause of female-biased sex ratios in
R. hastatulus. The annual life cycle of this species may limit the scope for selection
against males and may account for the weaker degree of bias in comparison with
perennial Rumex species.
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Spencer
full_name: Barrett, Spencer
last_name: Barrett
citation:
ama: Pickup M, Barrett S. The influence of demography and local mating environment
on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution.
2013;3(3):629-639. doi:10.1002/ece3.465
apa: Pickup, M., & Barrett, S. (2013). The influence of demography and local
mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology
and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.465
chicago: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and
Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.”
Ecology and Evolution. Wiley-Blackwell, 2013. https://doi.org/10.1002/ece3.465.
ieee: M. Pickup and S. Barrett, “The influence of demography and local mating environment
on sex ratios in a wind-pollinated dioecious plant,” Ecology and Evolution,
vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013.
ista: Pickup M, Barrett S. 2013. The influence of demography and local mating environment
on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 3(3),
629–639.
mla: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local
Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology
and Evolution, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:10.1002/ece3.465.
short: M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639.
date_created: 2018-12-11T11:56:47Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T06:56:32Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1002/ece3.465
file:
- access_level: open_access
checksum: b5531bab4c0dec396bf5c8497fe178bf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:35Z
date_updated: 2020-07-14T12:45:37Z
file_id: '5290'
file_name: IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf
file_size: 626949
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 629 - 639
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4644'
pubrep_id: '416'
quality_controlled: '1'
scopus_import: 1
status: public
title: The influence of demography and local mating environment on sex ratios in a
wind-pollinated dioecious plant
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: 3
year: '2013'
...
---
_id: '2282'
abstract:
- lang: eng
text: Epithelial spreading is a common and fundamental aspect of various developmental
and disease-related processes such as epithelial closure and wound healing. A
key challenge for epithelial tissues undergoing spreading is to increase their
surface area without disrupting epithelial integrity. Here we show that orienting
cell divisions by tension constitutes an efficient mechanism by which the enveloping
cell layer (EVL) releases anisotropic tension while undergoing spreading during
zebrafish epiboly. The control of EVL cell-division orientation by tension involves
cell elongation and requires myosin II activity to align the mitotic spindle with
the main tension axis. We also found that in the absence of tension-oriented cell
divisions and in the presence of increased tissue tension, EVL cells undergo ectopic
fusions, suggesting that the reduction of tension anisotropy by oriented cell
divisions is required to prevent EVL cells from fusing. We conclude that cell-division
orientation by tension constitutes a key mechanism for limiting tension anisotropy
and thus promoting tissue spreading during EVL epiboly.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
acknowledgement: 'This work was supported by the IST Austria and MPI-CBG '
author:
- first_name: Pedro
full_name: Campinho, Pedro
id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87
last_name: Campinho
orcid: 0000-0002-8526-5416
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Jonas
full_name: Ranft, Jonas
last_name: Ranft
- first_name: Thomas
full_name: Risler, Thomas
last_name: Risler
- first_name: Nicolas
full_name: Minc, Nicolas
last_name: Minc
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. Tension-oriented
cell divisions limit anisotropic tissue tension in epithelial spreading during
zebrafish epiboly. Nature Cell Biology. 2013;15:1405-1414. doi:10.1038/ncb2869
apa: Campinho, P., Behrndt, M., Ranft, J., Risler, T., Minc, N., & Heisenberg,
C.-P. J. (2013). Tension-oriented cell divisions limit anisotropic tissue tension
in epithelial spreading during zebrafish epiboly. Nature Cell Biology.
Nature Publishing Group. https://doi.org/10.1038/ncb2869
chicago: Campinho, Pedro, Martin Behrndt, Jonas Ranft, Thomas Risler, Nicolas Minc,
and Carl-Philipp J Heisenberg. “Tension-Oriented Cell Divisions Limit Anisotropic
Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell
Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/ncb2869.
ieee: P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, and C.-P. J. Heisenberg,
“Tension-oriented cell divisions limit anisotropic tissue tension in epithelial
spreading during zebrafish epiboly,” Nature Cell Biology, vol. 15. Nature
Publishing Group, pp. 1405–1414, 2013.
ista: Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. 2013. Tension-oriented
cell divisions limit anisotropic tissue tension in epithelial spreading during
zebrafish epiboly. Nature Cell Biology. 15, 1405–1414.
mla: Campinho, Pedro, et al. “Tension-Oriented Cell Divisions Limit Anisotropic
Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell
Biology, vol. 15, Nature Publishing Group, 2013, pp. 1405–14, doi:10.1038/ncb2869.
short: P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, C.-P.J. Heisenberg,
Nature Cell Biology 15 (2013) 1405–1414.
date_created: 2018-12-11T11:56:45Z
date_published: 2013-11-10T00:00:00Z
date_updated: 2023-02-21T17:02:44Z
day: '10'
department:
- _id: CaHe
doi: 10.1038/ncb2869
intvolume: ' 15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://hal.upmc.fr/hal-00983313/
month: '11'
oa: 1
oa_version: Submitted Version
page: 1405 - 1414
project:
- _id: 252ABD0A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 930-B20
name: Control of Epithelial Cell Layer Spreading in Zebrafish
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '4652'
quality_controlled: '1'
related_material:
record:
- id: '1403'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial
spreading during zebrafish epiboly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2013'
...
---
_id: '2283'
abstract:
- lang: eng
text: Pathogens exert a strong selection pressure on organisms to evolve effective
immune defences. In addition to individual immunity, social organisms can act
cooperatively to produce collective defences. In many ant species, queens have
the option to found a colony alone or in groups with other, often unrelated, conspecifics.
These associations are transient, usually lasting only as long as each queen benefits
from the presence of others. In fact, once the first workers emerge, queens fight
to the death for dominance. One potential advantage of co-founding may be that
queens benefit from collective disease defences, such as mutual grooming, that
act against common soil pathogens. We test this hypothesis by exposing single
and co-founding queens to a fungal parasite, in order to assess whether queens
in co-founding associations have improved survival. Surprisingly, co-foundresses
exposed to the entomopathogenic fungus Metarhizium did not engage in cooperative
disease defences, and consequently, we find no direct benefit of multiple queens
on survival. However, an indirect benefit was observed, with parasite-exposed
queens producing more brood when they co-founded, than when they were alone. We
suggest this is due to a trade-off between reproduction and immunity. Additionally,
we report an extraordinary ability of the queens to tolerate an infection for
long periods after parasite exposure. Our study suggests that there are no social
immunity benefits for co-founding ant queens, but that in parasite-rich environments,
the presence of additional queens may nevertheless improve the chances of colony
founding success.
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: William
full_name: Hughes, William
last_name: Hughes
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
citation:
ama: 'Pull C, Hughes W, Brown M. Tolerating an infection: an indirect benefit of
co-founding queen associations in the ant Lasius niger . Naturwissenschaften.
2013;100(12):1125-1136. doi:10.1007/s00114-013-1115-5'
apa: 'Pull, C., Hughes, W., & Brown, M. (2013). Tolerating an infection: an
indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften.
Springer. https://doi.org/10.1007/s00114-013-1115-5'
chicago: 'Pull, Christopher, William Hughes, and Markus Brown. “Tolerating an Infection:
An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger
.” Naturwissenschaften. Springer, 2013. https://doi.org/10.1007/s00114-013-1115-5.'
ieee: 'C. Pull, W. Hughes, and M. Brown, “Tolerating an infection: an indirect benefit
of co-founding queen associations in the ant Lasius niger ,” Naturwissenschaften,
vol. 100, no. 12. Springer, pp. 1125–1136, 2013.'
ista: 'Pull C, Hughes W, Brown M. 2013. Tolerating an infection: an indirect benefit
of co-founding queen associations in the ant Lasius niger . Naturwissenschaften.
100(12), 1125–1136.'
mla: 'Pull, Christopher, et al. “Tolerating an Infection: An Indirect Benefit of
Co-Founding Queen Associations in the Ant Lasius Niger .” Naturwissenschaften,
vol. 100, no. 12, Springer, 2013, pp. 1125–36, doi:10.1007/s00114-013-1115-5.'
short: C. Pull, W. Hughes, M. Brown, Naturwissenschaften 100 (2013) 1125–1136.
date_created: 2018-12-11T11:56:45Z
date_published: 2013-11-14T00:00:00Z
date_updated: 2021-01-12T06:56:31Z
day: '14'
department:
- _id: SyCr
doi: 10.1007/s00114-013-1115-5
intvolume: ' 100'
issue: '12'
language:
- iso: eng
month: '11'
oa_version: None
page: 1125 - 1136
publication: Naturwissenschaften
publication_status: published
publisher: Springer
publist_id: '4649'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Tolerating an infection: an indirect benefit of co-founding queen associations
in the ant Lasius niger '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2013'
...
---
_id: '2286'
abstract:
- lang: eng
text: The spatiotemporal control of cell divisions is a key factor in epithelial
morphogenesis and patterning. Mao et al (2013) now describe how differential rates
of proliferation within the Drosophila wing disc epithelium give rise to anisotropic
tissue tension in peripheral/proximal regions of the disc. Such global tissue
tension anisotropy in turn determines the orientation of cell divisions by controlling
epithelial cell elongation.
author:
- first_name: Pedro
full_name: Campinho, Pedro
id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87
last_name: Campinho
orcid: 0000-0002-8526-5416
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Campinho P, Heisenberg C-PJ. The force and effect of cell proliferation. EMBO
Journal. 2013;32(21):2783-2784. doi:10.1038/emboj.2013.225
apa: Campinho, P., & Heisenberg, C.-P. J. (2013). The force and effect of cell
proliferation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2013.225
chicago: Campinho, Pedro, and Carl-Philipp J Heisenberg. “The Force and Effect of
Cell Proliferation.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2013.225.
ieee: P. Campinho and C.-P. J. Heisenberg, “The force and effect of cell proliferation,”
EMBO Journal, vol. 32, no. 21. Wiley-Blackwell, pp. 2783–2784, 2013.
ista: Campinho P, Heisenberg C-PJ. 2013. The force and effect of cell proliferation.
EMBO Journal. 32(21), 2783–2784.
mla: Campinho, Pedro, and Carl-Philipp J. Heisenberg. “The Force and Effect of Cell
Proliferation.” EMBO Journal, vol. 32, no. 21, Wiley-Blackwell, 2013, pp.
2783–84, doi:10.1038/emboj.2013.225.
short: P. Campinho, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 2783–2784.
date_created: 2018-12-11T11:56:46Z
date_published: 2013-10-04T00:00:00Z
date_updated: 2021-01-12T06:56:32Z
day: '04'
department:
- _id: CaHe
doi: 10.1038/emboj.2013.225
external_id:
pmid:
- '24097062'
intvolume: ' 32'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817470/
month: '10'
oa: 1
oa_version: Submitted Version
page: 2783 - 2784
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4645'
quality_controlled: '1'
scopus_import: 1
status: public
title: The force and effect of cell proliferation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2289'
abstract:
- lang: eng
text: Formal verification aims to improve the quality of software by detecting errors
before they do harm. At the basis of formal verification is the logical notion
of correctness, which purports to capture whether or not a program behaves as
desired. We suggest that the boolean partition of software into correct and incorrect
programs falls short of the practical need to assess the behavior of software
in a more nuanced fashion against multiple criteria. We therefore propose to introduce
quantitative fitness measures for programs, specifically for measuring the function,
performance, and robustness of reactive programs such as concurrent processes.
This article describes the goals of the ERC Advanced Investigator Project QUAREM.
The project aims to build and evaluate a theory of quantitative fitness measures
for reactive models. Such a theory must strive to obtain quantitative generalizations
of the paradigms that have been success stories in qualitative reactive modeling,
such as compositionality, property-preserving abstraction and abstraction refinement,
model checking, and synthesis. The theory will be evaluated not only in the context
of software and hardware engineering, but also in the context of systems biology.
In particular, we will use the quantitative reactive models and fitness measures
developed in this project for testing hypotheses about the mechanisms behind data
from biological experiments.
author:
- 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: Henzinger TA. Quantitative reactive modeling and verification. Computer
Science Research and Development. 2013;28(4):331-344. doi:10.1007/s00450-013-0251-7
apa: Henzinger, T. A. (2013). Quantitative reactive modeling and verification. Computer
Science Research and Development. Springer. https://doi.org/10.1007/s00450-013-0251-7
chicago: Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.”
Computer Science Research and Development. Springer, 2013. https://doi.org/10.1007/s00450-013-0251-7.
ieee: T. A. Henzinger, “Quantitative reactive modeling and verification,” Computer
Science Research and Development, vol. 28, no. 4. Springer, pp. 331–344, 2013.
ista: Henzinger TA. 2013. Quantitative reactive modeling and verification. Computer
Science Research and Development. 28(4), 331–344.
mla: Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” Computer
Science Research and Development, vol. 28, no. 4, Springer, 2013, pp. 331–44,
doi:10.1007/s00450-013-0251-7.
short: T.A. Henzinger, Computer Science Research and Development 28 (2013) 331–344.
date_created: 2018-12-11T11:56:47Z
date_published: 2013-10-05T00:00:00Z
date_updated: 2021-01-12T06:56:33Z
day: '05'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s00450-013-0251-7
ec_funded: 1
file:
- access_level: open_access
checksum: f117a00f9f046165bfa95595681e08a0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:51Z
date_updated: 2020-07-14T12:45:37Z
file_id: '5308'
file_name: IST-2016-626-v1+1_s00450-013-0251-7.pdf
file_size: 570361
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 28'
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 331 - 344
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Computer Science Research and Development
publication_status: published
publisher: Springer
publist_id: '4642'
pubrep_id: '626'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative reactive modeling and verification
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: 28
year: '2013'
...
---
_id: '2290'
abstract:
- lang: eng
text: The plant hormone indole-acetic acid (auxin) is essential for many aspects
of plant development. Auxin-mediated growth regulation typically involves the
establishment of an auxin concentration gradient mediated by polarly localized
auxin transporters. The localization of auxin carriers and their amount at the
plasma membrane are controlled by membrane trafficking processes such as secretion,
endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory
pathway mediates the localization of auxin carriers is not well understood. In
this study we have used the differential cell elongation process during apical
hook development to elucidate the mechanisms underlying the post-Golgi trafficking
of auxin carriers in Arabidopsis. We show that differential cell elongation during
apical hook development is defective in Arabidopsis mutant echidna (ech). ECH
protein is required for the trans-Golgi network (TGN)-mediated trafficking of
the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation
only marginally perturbs the trafficking of the highly related auxin influx carrier
LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook
development. Electron tomography reveals that the trafficking defects in ech mutant
are associated with the perturbation of secretory vesicle genesis from the TGN.
Our results identify differential mechanisms for the post-Golgi trafficking of
de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal
how trafficking of auxin influx carriers mediates the control of differential
cell elongation in apical hook development.
author:
- first_name: Yohann
full_name: Boutté, Yohann
last_name: Boutté
- first_name: Kristoffer
full_name: Jonsson, Kristoffer
last_name: Jonsson
- first_name: Heather
full_name: Mcfarlane, Heather
last_name: Mcfarlane
- first_name: Errin
full_name: Johnson, Errin
last_name: Johnson
- first_name: Delphine
full_name: Gendre, Delphine
last_name: Gendre
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Lacey
full_name: Samuels, Lacey
last_name: Samuels
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Rishikesh
full_name: Bhalerao, Rishikesh
last_name: Bhalerao
citation:
ama: Boutté Y, Jonsson K, Mcfarlane H, et al. ECHIDNA mediated post Golgi trafficking
of auxin carriers for differential cell elongation. PNAS. 2013;110(40):16259-16264.
doi:10.1073/pnas.1309057110
apa: Boutté, Y., Jonsson, K., Mcfarlane, H., Johnson, E., Gendre, D., Swarup, R.,
… Bhalerao, R. (2013). ECHIDNA mediated post Golgi trafficking of auxin carriers
for differential cell elongation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1309057110
chicago: Boutté, Yohann, Kristoffer Jonsson, Heather Mcfarlane, Errin Johnson, Delphine
Gendre, Ranjan Swarup, Jiří Friml, Lacey Samuels, Stéphanie Robert, and Rishikesh
Bhalerao. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential
Cell Elongation.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1309057110.
ieee: Y. Boutté et al., “ECHIDNA mediated post Golgi trafficking of auxin
carriers for differential cell elongation,” PNAS, vol. 110, no. 40. National
Academy of Sciences, pp. 16259–16264, 2013.
ista: Boutté Y, Jonsson K, Mcfarlane H, Johnson E, Gendre D, Swarup R, Friml J,
Samuels L, Robert S, Bhalerao R. 2013. ECHIDNA mediated post Golgi trafficking
of auxin carriers for differential cell elongation. PNAS. 110(40), 16259–16264.
mla: Boutté, Yohann, et al. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers
for Differential Cell Elongation.” PNAS, vol. 110, no. 40, National Academy
of Sciences, 2013, pp. 16259–64, doi:10.1073/pnas.1309057110.
short: Y. Boutté, K. Jonsson, H. Mcfarlane, E. Johnson, D. Gendre, R. Swarup, J.
Friml, L. Samuels, S. Robert, R. Bhalerao, PNAS 110 (2013) 16259–16264.
date_created: 2018-12-11T11:56:48Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T06:56:33Z
day: '01'
department:
- _id: JiFr
doi: 10.1073/pnas.1309057110
external_id:
pmid:
- '24043780'
intvolume: ' 110'
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791722/
month: '10'
oa: 1
oa_version: Submitted Version
page: 16259 - 16264
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '4639'
quality_controlled: '1'
scopus_import: 1
status: public
title: ECHIDNA mediated post Golgi trafficking of auxin carriers for differential
cell elongation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2294'
abstract:
- lang: eng
text: "In this work we propose a system for automatic classification of Drosophila
embryos into developmental stages.\r\nWhile the system is designed to solve an
actual problem in biological research, we believe that the principle underly-\r\ning
it is interesting not only for biologists, but also for researchers in computer
vision. The main idea is to combine two orthogonal sources of information: one
is a classifier trained on strongly invariant features, which makes it applicable
to images of very different conditions, but also leads to rather noisy predictions.
The other is a label propagation step based on a more powerful similarity measure
that however is only consistent within specific subsets of the data at a time.\r\nIn
our biological setup, the information sources are the shape and the staining patterns
of embryo images. We show\r\nexperimentally that while neither of the methods
\ can be used by itself to achieve satisfactory results, their combina-\r\ntion
achieves prediction quality comparable to human performance."
author:
- first_name: Tomas
full_name: Kazmar, Tomas
last_name: Kazmar
- first_name: Evgeny
full_name: Kvon, Evgeny
last_name: Kvon
- first_name: Alexander
full_name: Stark, Alexander
last_name: Stark
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kazmar T, Kvon E, Stark A, Lampert C. Drosophila Embryo Stage Annotation using
Label Propagation. In: IEEE; 2013. doi:10.1109/ICCV.2013.139'
apa: 'Kazmar, T., Kvon, E., Stark, A., & Lampert, C. (2013). Drosophila Embryo
Stage Annotation using Label Propagation. Presented at the ICCV: International
Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.139'
chicago: Kazmar, Tomas, Evgeny Kvon, Alexander Stark, and Christoph Lampert. “Drosophila
Embryo Stage Annotation Using Label Propagation.” IEEE, 2013. https://doi.org/10.1109/ICCV.2013.139.
ieee: 'T. Kazmar, E. Kvon, A. Stark, and C. Lampert, “Drosophila Embryo Stage Annotation
using Label Propagation,” presented at the ICCV: International Conference on Computer
Vision, Sydney, Australia, 2013.'
ista: 'Kazmar T, Kvon E, Stark A, Lampert C. 2013. Drosophila Embryo Stage Annotation
using Label Propagation. ICCV: International Conference on Computer Vision.'
mla: Kazmar, Tomas, et al. Drosophila Embryo Stage Annotation Using Label Propagation.
IEEE, 2013, doi:10.1109/ICCV.2013.139.
short: T. Kazmar, E. Kvon, A. Stark, C. Lampert, in:, IEEE, 2013.
conference:
end_date: 2013-12-08
location: Sydney, Australia
name: 'ICCV: International Conference on Computer Vision'
start_date: 2013-12-01
date_created: 2018-12-11T11:56:49Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T06:56:35Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/ICCV.2013.139
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.cv-foundation.org/openaccess/ICCV2013.py
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: IEEE
publist_id: '4634'
quality_controlled: '1'
scopus_import: 1
status: public
title: Drosophila Embryo Stage Annotation using Label Propagation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2292'
abstract:
- lang: eng
text: This book constitutes the thoroughly refereed conference proceedings of the
38th International Symposium on Mathematical Foundations of Computer Science,
MFCS 2013, held in Klosterneuburg, Austria, in August 2013. The 67 revised full
papers presented together with six invited talks were carefully selected from
191 submissions. Topics covered include algorithmic game theory, algorithmic learning
theory, algorithms and data structures, automata, formal languages, bioinformatics,
complexity, computational geometry, computer-assisted reasoning, concurrency theory,
databases and knowledge-based systems, foundations of computing, logic in computer
science, models of computation, semantics and verification of programs, and theoretical
issues in artificial intelligence.
alternative_title:
- LNCS
citation:
ama: Chatterjee K, Sgall J, eds. Mathematical Foundations of Computer Science
2013. Vol 8087. Springer; 2013:VI-854. doi:10.1007/978-3-642-40313-2
apa: 'Chatterjee, K., & Sgall, J. (Eds.). (2013). Mathematical Foundations
of Computer Science 2013 (Vol. 8087, p. VI-854). Presented at the MFCS: Mathematical
Foundations of Computer Science, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40313-2'
chicago: Chatterjee, Krishnendu, and Jiri Sgall, eds. Mathematical Foundations
of Computer Science 2013. Vol. 8087. Lecture Notes in Computer Science. Springer,
2013. https://doi.org/10.1007/978-3-642-40313-2.
ieee: K. Chatterjee and J. Sgall, Eds., Mathematical Foundations of Computer
Science 2013, vol. 8087. Springer, 2013, p. VI-854.
ista: Chatterjee K, Sgall J eds. 2013. Mathematical Foundations of Computer Science
2013, Springer,p.
mla: Chatterjee, Krishnendu, and Jiri Sgall, editors. Mathematical Foundations
of Computer Science 2013. Vol. 8087, Springer, 2013, p. VI-854, doi:10.1007/978-3-642-40313-2.
short: K. Chatterjee, J. Sgall, eds., Mathematical Foundations of Computer Science
2013, Springer, 2013.
conference:
end_date: 2013-08-30
location: Klosterneuburg, Austria
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2013-08-26
date_created: 2018-12-11T11:56:48Z
date_published: 2013-08-08T00:00:00Z
date_updated: 2020-08-11T10:09:45Z
day: '08'
department:
- _id: KrCh
doi: 10.1007/978-3-642-40313-2
editor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jiri
full_name: Sgall, Jiri
last_name: Sgall
intvolume: ' 8087'
language:
- iso: eng
month: '08'
oa_version: None
page: VI - 854
publication_identifier:
isbn:
- 978-3-642-40312-5
publication_status: published
publisher: Springer
publist_id: '4636'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Mathematical Foundations of Computer Science 2013
type: conference_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8087
year: '2013'
...
---
_id: '2293'
abstract:
- lang: eng
text: Many computer vision problems have an asymmetric distribution of information
between training and test time. In this work, we study the case where we are given
additional information about the training data, which however will not be available
at test time. This situation is called learning using privileged information (LUPI).
We introduce two maximum-margin techniques that are able to make use of this additional
source of information, and we show that the framework is applicable to several
scenarios that have been studied in computer vision before. Experiments with attributes,
bounding boxes, image tags and rationales as additional information in object
classification show promising results.
author:
- first_name: Viktoriia
full_name: Sharmanska, Viktoriia
id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
last_name: Sharmanska
orcid: 0000-0003-0192-9308
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Sharmanska V, Quadrianto N, Lampert C. Learning to rank using privileged information.
In: IEEE; 2013:825-832. doi:10.1109/ICCV.2013.107'
apa: 'Sharmanska, V., Quadrianto, N., & Lampert, C. (2013). Learning to rank
using privileged information (pp. 825–832). Presented at the ICCV: International
Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.107'
chicago: Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Learning
to Rank Using Privileged Information,” 825–32. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.107.
ieee: 'V. Sharmanska, N. Quadrianto, and C. Lampert, “Learning to rank using privileged
information,” presented at the ICCV: International Conference on Computer Vision,
Sydney, Australia, 2013, pp. 825–832.'
ista: 'Sharmanska V, Quadrianto N, Lampert C. 2013. Learning to rank using privileged
information. ICCV: International Conference on Computer Vision, 825–832.'
mla: Sharmanska, Viktoriia, et al. Learning to Rank Using Privileged Information.
IEEE, 2013, pp. 825–32, doi:10.1109/ICCV.2013.107.
short: V. Sharmanska, N. Quadrianto, C. Lampert, in:, IEEE, 2013, pp. 825–832.
conference:
end_date: 2013-12-08
location: Sydney, Australia
name: 'ICCV: International Conference on Computer Vision'
start_date: 2013-12-01
date_created: 2018-12-11T11:56:49Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2023-02-23T10:36:41Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/ICCV.2013.107
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: www.cv-foundation.org/openaccess/content_iccv_2013/papers/Sharmanska_Learning_to_Rank_2013_ICCV_paper.pdf
month: '12'
oa: 1
oa_version: Submitted Version
page: 825 - 832
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: IEEE
publist_id: '4635'
quality_controlled: '1'
scopus_import: 1
status: public
title: Learning to rank using privileged information
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2291'
abstract:
- lang: eng
text: "Cryptographic access control promises to offer easily distributed trust and
broader applicability, while reducing reliance on low-level online monitors. Traditional
implementations of cryptographic access control rely on simple cryptographic primitives
whereas recent endeavors employ primitives with richer functionality and security
guarantees. Worryingly, few of the existing cryptographic access-control schemes
come with precise guarantees, the gap between the policy specification and the
implementation being analyzed only informally, if at all. In this paper we begin
addressing this shortcoming. Unlike prior work that targeted ad-hoc policy specification,
we look at the well-established Role-Based Access Control (RBAC) model, as used
in a typical file system. In short, we provide a precise syntax for a computational
version of RBAC, offer rigorous definitions for cryptographic policy enforcement
of a large class of RBAC security policies, and demonstrate that an implementation
based on attribute-based encryption meets our security notions. We view our main
contribution as being at the conceptual level. Although we work with RBAC for
concreteness, our general methodology could guide future research for uses of
cryptography in other access-control models. \r\n"
author:
- first_name: Anna
full_name: Ferrara, Anna
last_name: Ferrara
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Bogdan
full_name: Warinschi, Bogdan
last_name: Warinschi
citation:
ama: 'Ferrara A, Fuchsbauer G, Warinschi B. Cryptographically enforced RBAC. In:
IEEE; 2013:115-129. doi:10.1109/CSF.2013.15'
apa: 'Ferrara, A., Fuchsbauer, G., & Warinschi, B. (2013). Cryptographically
enforced RBAC (pp. 115–129). Presented at the CSF: Computer Security Foundations,
New Orleans, LA, United States: IEEE. https://doi.org/10.1109/CSF.2013.15'
chicago: Ferrara, Anna, Georg Fuchsbauer, and Bogdan Warinschi. “Cryptographically
Enforced RBAC,” 115–29. IEEE, 2013. https://doi.org/10.1109/CSF.2013.15.
ieee: 'A. Ferrara, G. Fuchsbauer, and B. Warinschi, “Cryptographically enforced
RBAC,” presented at the CSF: Computer Security Foundations, New Orleans, LA, United
States, 2013, pp. 115–129.'
ista: 'Ferrara A, Fuchsbauer G, Warinschi B. 2013. Cryptographically enforced RBAC.
CSF: Computer Security Foundations, 115–129.'
mla: Ferrara, Anna, et al. Cryptographically Enforced RBAC. IEEE, 2013, pp.
115–29, doi:10.1109/CSF.2013.15.
short: A. Ferrara, G. Fuchsbauer, B. Warinschi, in:, IEEE, 2013, pp. 115–129.
conference:
end_date: 2013-09-28
location: New Orleans, LA, United States
name: 'CSF: Computer Security Foundations'
start_date: 2013-09-26
date_created: 2018-12-11T11:56:48Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T06:56:34Z
day: '01'
department:
- _id: KrPi
doi: 10.1109/CSF.2013.15
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2013/492
month: '09'
oa: 1
oa_version: Submitted Version
page: 115 - 129
publication_status: published
publisher: IEEE
publist_id: '4637'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cryptographically enforced RBAC
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2288'
abstract:
- lang: eng
text: This book constitutes the proceedings of the 11th International Conference
on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg,
Austria, in September 2013. The 15 regular papers included in this volume were
carefully reviewed and selected from 27 submissions. They deal with computational
models for all levels, from molecular and cellular, to organs and entire organisms.
alternative_title:
- LNCS
citation:
ama: Gupta A, Henzinger TA, eds. Computational Methods in Systems Biology.
Vol 8130. Springer; 2013. doi:10.1007/978-3-642-40708-6
apa: 'Gupta, A., & Henzinger, T. A. (Eds.). (2013). Computational Methods
in Systems Biology (Vol. 8130). Presented at the CMSB: Computational Methods
in Systems Biology, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40708-6'
chicago: Gupta, Ashutosh, and Thomas A Henzinger, eds. Computational Methods
in Systems Biology. Vol. 8130. Springer, 2013. https://doi.org/10.1007/978-3-642-40708-6.
ieee: A. Gupta and T. A. Henzinger, Eds., Computational Methods in Systems Biology,
vol. 8130. Springer, 2013.
ista: Gupta A, Henzinger TA eds. 2013. Computational Methods in Systems Biology,
Springer,p.
mla: Gupta, Ashutosh, and Thomas A. Henzinger, editors. Computational Methods
in Systems Biology. Vol. 8130, Springer, 2013, doi:10.1007/978-3-642-40708-6.
short: A. Gupta, T.A. Henzinger, eds., Computational Methods in Systems Biology,
Springer, 2013.
conference:
end_date: 2013-09-24
location: Klosterneuburg, Austria
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2013-09-22
date_created: 2018-12-11T11:56:47Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2019-08-02T12:37:44Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-40708-6
editor:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
intvolume: ' 8130'
language:
- iso: eng
month: '07'
oa_version: None
publication_identifier:
isbn:
- 978-3-642-40707-9
publication_status: published
publisher: Springer
publist_id: '4643'
quality_controlled: '1'
status: public
title: Computational Methods in Systems Biology
type: conference_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8130
year: '2013'
...
---
_id: '2298'
abstract:
- lang: eng
text: "We present a shape analysis for programs that manipulate overlaid data structures
which share sets of objects. The abstract domain contains Separation Logic formulas
that (1) combine a per-object separating conjunction with a per-field separating
conjunction and (2) constrain a set of variables interpreted as sets of objects.
The definition of the abstract domain operators is based on a notion of homomorphism
between formulas, viewed as graphs, used recently to define optimal decision procedures
for fragments of the Separation Logic. Based on a Frame Rule that supports the
two versions of the separating conjunction, the analysis is able to reason in
a modular manner about non-overlaid data structures and then, compose information
only at a few program points, e.g., procedure returns. We have implemented this
analysis in a prototype tool and applied it on several interesting case studies
that manipulate overlaid and nested linked lists.\r\n"
alternative_title:
- LNCS
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- first_name: Constantin
full_name: Enea, Constantin
last_name: Enea
- first_name: Mihaela
full_name: Sighireanu, Mihaela
last_name: Sighireanu
citation:
ama: 'Dragoi C, Enea C, Sighireanu M. Local shape analysis for overlaid data structures.
In: Vol 7935. Springer; 2013:150-171. doi:10.1007/978-3-642-38856-9_10'
apa: 'Dragoi, C., Enea, C., & Sighireanu, M. (2013). Local shape analysis for
overlaid data structures (Vol. 7935, pp. 150–171). Presented at the SAS: Static
Analysis Symposium, Seattle, WA, United States: Springer. https://doi.org/10.1007/978-3-642-38856-9_10'
chicago: Dragoi, Cezara, Constantin Enea, and Mihaela Sighireanu. “Local Shape Analysis
for Overlaid Data Structures,” 7935:150–71. Springer, 2013. https://doi.org/10.1007/978-3-642-38856-9_10.
ieee: 'C. Dragoi, C. Enea, and M. Sighireanu, “Local shape analysis for overlaid
data structures,” presented at the SAS: Static Analysis Symposium, Seattle, WA,
United States, 2013, vol. 7935, pp. 150–171.'
ista: 'Dragoi C, Enea C, Sighireanu M. 2013. Local shape analysis for overlaid data
structures. SAS: Static Analysis Symposium, LNCS, vol. 7935, 150–171.'
mla: Dragoi, Cezara, et al. Local Shape Analysis for Overlaid Data Structures.
Vol. 7935, Springer, 2013, pp. 150–71, doi:10.1007/978-3-642-38856-9_10.
short: C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2013, pp. 150–171.
conference:
end_date: 2013-06-22
location: Seattle, WA, United States
name: 'SAS: Static Analysis Symposium'
start_date: 2013-06-20
date_created: 2018-12-11T11:56:50Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:36Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-38856-9_10
ec_funded: 1
file:
- access_level: open_access
checksum: 907edd33a5892e3af093365f1fd57ed7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:36Z
date_updated: 2020-07-14T12:45:37Z
file_id: '4824'
file_name: IST-2014-196-v1+1_sas13.pdf
file_size: 299004
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 7935'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 150 - 171
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '4630'
pubrep_id: '196'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local shape analysis for overlaid data structures
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7935
year: '2013'
...
---
_id: '2299'
abstract:
- lang: eng
text: 'The standard hardware design flow involves: (a) design of an integrated circuit
using a hardware description language, (b) extensive functional and formal verification,
and (c) logical synthesis. However, the above-mentioned processes consume significant
effort and time. An alternative approach is to use a formal specification language
as a high-level hardware description language and synthesize hardware from formal
specifications. Our work is a case study of the synthesis of the widely and industrially
used AMBA AHB protocol from formal specifications. Bloem et al. presented the
first formal specifications for the AMBA AHB Arbiter and synthesized the AHB Arbiter
circuit. However, in the first formal specification some important assumptions
were missing. Our contributions are as follows: (a) We present detailed formal
specifications for the AHB Arbiter incorporating the missing details, and obtain
significant improvements in the synthesis results (both with respect to the number
of gates in the synthesized circuit and with respect to the time taken to synthesize
the circuit), and (b) we present formal specifications to generate compact circuits
for the remaining two main components of AMBA AHB, namely, AHB Master and AHB
Slave. Thus with systematic description we are able to automatically and completely
synthesize an important and widely used industrial protocol.'
author:
- first_name: Yashdeep
full_name: Godhal, Yashdeep
id: 5B547124-EB61-11E9-8887-89D9C04DBDF5
last_name: Godhal
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: 'Godhal Y, Chatterjee K, Henzinger TA. Synthesis of AMBA AHB from formal specification:
A case study. International Journal on Software Tools for Technology Transfer.
2013;15(5-6):585-601. doi:10.1007/s10009-011-0207-9'
apa: 'Godhal, Y., Chatterjee, K., & Henzinger, T. A. (2013). Synthesis of AMBA
AHB from formal specification: A case study. International Journal on Software
Tools for Technology Transfer. Springer. https://doi.org/10.1007/s10009-011-0207-9'
chicago: 'Godhal, Yashdeep, Krishnendu Chatterjee, and Thomas A Henzinger. “Synthesis
of AMBA AHB from Formal Specification: A Case Study.” International Journal
on Software Tools for Technology Transfer. Springer, 2013. https://doi.org/10.1007/s10009-011-0207-9.'
ieee: 'Y. Godhal, K. Chatterjee, and T. A. Henzinger, “Synthesis of AMBA AHB from
formal specification: A case study,” International Journal on Software Tools
for Technology Transfer, vol. 15, no. 5–6. Springer, pp. 585–601, 2013.'
ista: 'Godhal Y, Chatterjee K, Henzinger TA. 2013. Synthesis of AMBA AHB from formal
specification: A case study. International Journal on Software Tools for Technology
Transfer. 15(5–6), 585–601.'
mla: 'Godhal, Yashdeep, et al. “Synthesis of AMBA AHB from Formal Specification:
A Case Study.” International Journal on Software Tools for Technology Transfer,
vol. 15, no. 5–6, Springer, 2013, pp. 585–601, doi:10.1007/s10009-011-0207-9.'
short: Y. Godhal, K. Chatterjee, T.A. Henzinger, International Journal on Software
Tools for Technology Transfer 15 (2013) 585–601.
date_created: 2018-12-11T11:56:51Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T06:56:37Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/s10009-011-0207-9
file:
- access_level: open_access
checksum: 57b06a732dd8d6349190dba6b5b0d33b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:53Z
date_updated: 2020-07-14T12:45:37Z
file_id: '4910'
file_name: IST-2012-87-v1+1_Synthesis_of_AMBA_AHB_from_formal_specifications-_A_case_study.pdf
file_size: 277372
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 15'
issue: 5-6
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 585 - 601
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: International Journal on Software Tools for Technology Transfer
publication_status: published
publisher: Springer
publist_id: '4629'
pubrep_id: '87'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Synthesis of AMBA AHB from formal specification: A case study'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2013'
...
---
_id: '2297'
abstract:
- lang: eng
text: We present an overview of mathematical results on the low temperature properties
of dilute quantum gases, which have been obtained in the past few years. The presentation
includes a discussion of Bose-Einstein condensation, the excitation spectrum for
trapped gases and its relation to superfluidity, as well as the appearance of
quantized vortices in rotating systems. All these properties are intensely being
studied in current experiments on cold atomic gases. We will give a description
of the mathematics involved in understanding these phenomena, starting from the
underlying many-body Schrödinger equation.
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Seiringer R. Hot topics in cold gases: A mathematical physics perspective.
Japanese Journal of Mathematics. 2013;8(2):185-232. doi:10.1007/s11537-013-1264-5'
apa: 'Seiringer, R. (2013). Hot topics in cold gases: A mathematical physics perspective.
Japanese Journal of Mathematics. Springer. https://doi.org/10.1007/s11537-013-1264-5'
chicago: 'Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.”
Japanese Journal of Mathematics. Springer, 2013. https://doi.org/10.1007/s11537-013-1264-5.'
ieee: 'R. Seiringer, “Hot topics in cold gases: A mathematical physics perspective,”
Japanese Journal of Mathematics, vol. 8, no. 2. Springer, pp. 185–232,
2013.'
ista: 'Seiringer R. 2013. Hot topics in cold gases: A mathematical physics perspective.
Japanese Journal of Mathematics. 8(2), 185–232.'
mla: 'Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.”
Japanese Journal of Mathematics, vol. 8, no. 2, Springer, 2013, pp. 185–232,
doi:10.1007/s11537-013-1264-5.'
short: R. Seiringer, Japanese Journal of Mathematics 8 (2013) 185–232.
date_created: 2018-12-11T11:56:50Z
date_published: 2013-09-24T00:00:00Z
date_updated: 2021-01-12T06:56:36Z
day: '24'
department:
- _id: RoSe
doi: 10.1007/s11537-013-1264-5
external_id:
arxiv:
- '0908.3686'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0908.3686
month: '09'
oa: 1
oa_version: Preprint
page: 185 - 232
publication: Japanese Journal of Mathematics
publication_status: published
publisher: Springer
publist_id: '4631'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Hot topics in cold gases: A mathematical physics perspective'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2013'
...
---
_id: '2306'
abstract:
- lang: ger
text: Das Buch ist sowohl eine Einführung in die Themen Linked Data, Open Data und
Open Linked Data als es auch den konkreten Bezug auf Bibliotheken behandelt. Hierzu
werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl
an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement,
die noch nicht mit dem Thema vertraut sind.
alternative_title:
- Bibliotheks- und Informationspraxis
article_processing_charge: No
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Adrian
full_name: Pohl, Adrian
last_name: Pohl
citation:
ama: Danowski P, Pohl A. (Open) Linked Data in Bibliotheken. Vol 50. De Gruyter;
2013. doi:10.1515/9783110278736
apa: Danowski, P., & Pohl, A. (2013). (Open) Linked Data in Bibliotheken
(Vol. 50). De Gruyter. https://doi.org/10.1515/9783110278736
chicago: Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken.
Vol. 50. De Gruyter, 2013. https://doi.org/10.1515/9783110278736.
ieee: P. Danowski and A. Pohl, (Open) Linked Data in Bibliotheken, vol. 50.
De Gruyter, 2013.
ista: Danowski P, Pohl A. 2013. (Open) Linked Data in Bibliotheken, De Gruyter,p.
mla: Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken.
Vol. 50, De Gruyter, 2013, doi:10.1515/9783110278736.
short: P. Danowski, A. Pohl, (Open) Linked Data in Bibliotheken, De Gruyter, 2013.
date_created: 2018-12-11T11:56:53Z
date_published: 2013-09-13T00:00:00Z
date_updated: 2021-12-21T12:17:19Z
day: '13'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.1515/9783110278736
file:
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has_accepted_license: '1'
intvolume: ' 50'
language:
- iso: ger
month: '09'
oa: 1
oa_version: Published Version
publication_identifier:
eisbn:
- 9-783-1102-7873-6
isbn:
- ' 978-3-11-027634-3'
issn:
- 2191-3587
publication_status: published
publisher: De Gruyter
publist_id: '4621'
pubrep_id: '725'
quality_controlled: '1'
status: public
title: (Open) Linked Data in Bibliotheken
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: book
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 50
year: '2013'
...
---
_id: '2301'
abstract:
- lang: eng
text: We describe the design and implementation of P, a domain-specific language
to write asynchronous event driven code. P allows the programmer to specify the
system as a collection of interacting state machines, which communicate with each
other using events. P unifies modeling and programming into one activity for the
programmer. Not only can a P program be compiled into executable code, but it
can also be tested using model checking techniques. P allows the programmer to
specify the environment, used to "close" the system during testing,
as nondeterministic ghost machines. Ghost machines are erased during compilation
to executable code; a type system ensures that the erasure is semantics preserving.
The P language is designed so that a P program can be checked for responsiveness-the
ability to handle every event in a timely manner. By default, a machine needs
to handle every event that arrives in every state. But handling every event in
every state is impractical. The language provides a notion of deferred events
where the programmer can annotate when she wants to delay processing an event.
The default safety checker looks for presence of unhan-dled events. The language
also provides default liveness checks that an event cannot be potentially deferred
forever. P was used to implement and verify the core of the USB device driver
stack that ships with Microsoft Windows 8. The resulting driver is more reliable
and performs better than its prior incarnation (which did not use P); we have
more confidence in the robustness of its design due to the language abstractions
and verification provided by P.
author:
- first_name: Ankush
full_name: Desai, Ankush
last_name: Desai
- first_name: Vivek
full_name: Gupta, Vivek
last_name: Gupta
- first_name: Ethan
full_name: Jackson, Ethan
last_name: Jackson
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
- first_name: Sriram
full_name: Rajamani, Sriram
last_name: Rajamani
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. P: Safe asynchronous
event-driven programming. In: Proceedings of the 34th ACM SIGPLAN Conference
on Programming Language Design and Implementation. ACM; 2013:321-331. doi:10.1145/2491956.2462184'
apa: 'Desai, A., Gupta, V., Jackson, E., Qadeer, S., Rajamani, S., & Zufferey,
D. (2013). P: Safe asynchronous event-driven programming. In Proceedings of
the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation
(pp. 321–331). Seattle, WA, United States: ACM. https://doi.org/10.1145/2491956.2462184'
chicago: 'Desai, Ankush, Vivek Gupta, Ethan Jackson, Shaz Qadeer, Sriram Rajamani,
and Damien Zufferey. “P: Safe Asynchronous Event-Driven Programming.” In Proceedings
of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation,
321–31. ACM, 2013. https://doi.org/10.1145/2491956.2462184.'
ieee: 'A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, and D. Zufferey,
“P: Safe asynchronous event-driven programming,” in Proceedings of the 34th
ACM SIGPLAN Conference on Programming Language Design and Implementation,
Seattle, WA, United States, 2013, pp. 321–331.'
ista: 'Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. 2013. P: Safe
asynchronous event-driven programming. Proceedings of the 34th ACM SIGPLAN Conference
on Programming Language Design and Implementation. PLDI: Programming Languages
Design and Implementation, 321–331.'
mla: 'Desai, Ankush, et al. “P: Safe Asynchronous Event-Driven Programming.” Proceedings
of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation,
ACM, 2013, pp. 321–31, doi:10.1145/2491956.2462184.'
short: A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, D. Zufferey, in:,
Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design
and Implementation, ACM, 2013, pp. 321–331.
conference:
end_date: 2013-06-19
location: Seattle, WA, United States
name: 'PLDI: Programming Languages Design and Implementation'
start_date: 2013-06-16
date_created: 2018-12-11T11:56:52Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T06:56:38Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2491956.2462184
ec_funded: 1
language:
- iso: eng
main_file_link:
- url: http://research.microsoft.com/pubs/191069/pldi212_desai.pdf
month: '06'
oa_version: None
page: 321 - 331
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Proceedings of the 34th ACM SIGPLAN Conference on Programming Language
Design and Implementation
publication_status: published
publisher: ACM
publist_id: '4626'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'P: Safe asynchronous event-driven programming'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2300'
abstract:
- lang: eng
text: We consider Ising models in two and three dimensions with nearest neighbor
ferromagnetic interactions and long-range, power law decaying, antiferromagnetic
interactions. If the strength of the ferromagnetic coupling J is larger than a
critical value Jc, then the ground state is homogeneous and ferromagnetic. As
the critical value is approached from smaller values of J, it is believed that
the ground state consists of a periodic array of stripes (d=2) or slabs (d=3),
all of the same size and alternating magnetization. Here we prove rigorously that
the ground state energy per site converges to that of the optimal periodic striped
or slabbed state, in the limit that J tends to the ferromagnetic transition point.
While this theorem does not prove rigorously that the ground state is precisely
striped or slabbed, it does prove that in any suitably large box the ground state
is striped or slabbed with high probability.
article_number: '064401'
author:
- first_name: Alessandro
full_name: Giuliani, Alessandro
last_name: Giuliani
- first_name: Élliott
full_name: Lieb, Élliott
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Giuliani A, Lieb É, Seiringer R. Realization of stripes and slabs in two and
three dimensions. Physical Review B. 2013;88(6). doi:10.1103/PhysRevB.88.064401
apa: Giuliani, A., Lieb, É., & Seiringer, R. (2013). Realization of stripes
and slabs in two and three dimensions. Physical Review B. American Physical
Society. https://doi.org/10.1103/PhysRevB.88.064401
chicago: Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Realization
of Stripes and Slabs in Two and Three Dimensions.” Physical Review B. American
Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.064401.
ieee: A. Giuliani, É. Lieb, and R. Seiringer, “Realization of stripes and slabs
in two and three dimensions,” Physical Review B, vol. 88, no. 6. American
Physical Society, 2013.
ista: Giuliani A, Lieb É, Seiringer R. 2013. Realization of stripes and slabs in
two and three dimensions. Physical Review B. 88(6), 064401.
mla: Giuliani, Alessandro, et al. “Realization of Stripes and Slabs in Two and Three
Dimensions.” Physical Review B, vol. 88, no. 6, 064401, American Physical
Society, 2013, doi:10.1103/PhysRevB.88.064401.
short: A. Giuliani, É. Lieb, R. Seiringer, Physical Review B 88 (2013).
date_created: 2018-12-11T11:56:51Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T06:56:38Z
day: '01'
department:
- _id: RoSe
doi: 10.1103/PhysRevB.88.064401
external_id:
arxiv:
- '1305.5323'
intvolume: ' 88'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1305.5323
month: '08'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '4627'
quality_controlled: '1'
scopus_import: 1
status: public
title: Realization of stripes and slabs in two and three dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2013'
...
---
_id: '2303'
abstract:
- lang: eng
text: MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach
in mice to visualize and concomitantly manipulate genetically defined cells at
clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent
interchromosomal mitotic recombination to reconstitute two split marker genes—green
GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in
one color and wild-type cells in the other color in an otherwise unlabeled background.
At present, major MADM applications include lineage tracing, single cell labeling,
conditional knockouts in small populations of cells and induction of uniparental
chromosome disomy to assess effects of genomic imprinting. MADM can be applied
universally in the mouse with the sole limitation being the specificity of the
promoter controlling Cre recombinase expression. Here I review recent developments
and extensions of the MADM technique and give an overview of the major discoveries
and progresses enabled by the implementation of the novel genetic MADM tools.
acknowledgement: This work was supported by IST Austria institutional funds.
article_type: review
author:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Hippenmeyer S. Dissection of gene function at clonal level using mosaic analysis
with double markers. Frontiers in Biology. 2013;8(6):557-568. doi:10.1007/s11515-013-1279-6
apa: Hippenmeyer, S. (2013). Dissection of gene function at clonal level using mosaic
analysis with double markers. Frontiers in Biology. Springer. https://doi.org/10.1007/s11515-013-1279-6
chicago: Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using
Mosaic Analysis with Double Markers.” Frontiers in Biology. Springer, 2013.
https://doi.org/10.1007/s11515-013-1279-6.
ieee: S. Hippenmeyer, “Dissection of gene function at clonal level using mosaic
analysis with double markers,” Frontiers in Biology, vol. 8, no. 6. Springer,
pp. 557–568, 2013.
ista: Hippenmeyer S. 2013. Dissection of gene function at clonal level using mosaic
analysis with double markers. Frontiers in Biology. 8(6), 557–568.
mla: Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic
Analysis with Double Markers.” Frontiers in Biology, vol. 8, no. 6, Springer,
2013, pp. 557–68, doi:10.1007/s11515-013-1279-6.
short: S. Hippenmeyer, Frontiers in Biology 8 (2013) 557–568.
date_created: 2018-12-11T11:56:52Z
date_published: 2013-09-03T00:00:00Z
date_updated: 2021-01-12T06:56:39Z
day: '03'
department:
- _id: SiHi
doi: 10.1007/s11515-013-1279-6
intvolume: ' 8'
issue: '6'
language:
- iso: eng
month: '09'
oa_version: None
page: 557 - 568
publication: Frontiers in Biology
publication_status: published
publisher: Springer
publist_id: '4624'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dissection of gene function at clonal level using mosaic analysis with double
markers
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2013'
...
---
_id: '2304'
abstract:
- lang: eng
text: This extended abstract is concerned with the irregularities of distribution
of one-dimensional permuted van der Corput sequences that are generated from linear
permutations. We show how to obtain upper bounds for the discrepancy and diaphony
of these sequences, by relating them to Kronecker sequences and applying earlier
results of Faure and Niederreiter.
acknowledgement: This research is supported by the Graduate school of IST Austria
(Institute of Science and Technology Austria).
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Pausinger F. Van der Corput sequences and linear permutations. Electronic
Notes in Discrete Mathematics. 2013;43:43-50. doi:10.1016/j.endm.2013.07.008
apa: Pausinger, F. (2013). Van der Corput sequences and linear permutations. Electronic
Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2013.07.008
chicago: Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.”
Electronic Notes in Discrete Mathematics. Elsevier, 2013. https://doi.org/10.1016/j.endm.2013.07.008.
ieee: F. Pausinger, “Van der Corput sequences and linear permutations,” Electronic
Notes in Discrete Mathematics, vol. 43. Elsevier, pp. 43–50, 2013.
ista: Pausinger F. 2013. Van der Corput sequences and linear permutations. Electronic
Notes in Discrete Mathematics. 43, 43–50.
mla: Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” Electronic
Notes in Discrete Mathematics, vol. 43, Elsevier, 2013, pp. 43–50, doi:10.1016/j.endm.2013.07.008.
short: F. Pausinger, Electronic Notes in Discrete Mathematics 43 (2013) 43–50.
date_created: 2018-12-11T11:56:53Z
date_published: 2013-09-05T00:00:00Z
date_updated: 2021-01-12T06:56:39Z
day: '05'
department:
- _id: HeEd
doi: 10.1016/j.endm.2013.07.008
intvolume: ' 43'
language:
- iso: eng
month: '09'
oa_version: None
page: 43 - 50
publication: Electronic Notes in Discrete Mathematics
publication_status: published
publisher: Elsevier
publist_id: '4623'
quality_controlled: '1'
scopus_import: 1
status: public
title: Van der Corput sequences and linear permutations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2013'
...
---
_id: '2315'
abstract:
- lang: eng
text: ' We study the effects of random scatterers on the ground state of the
one-dimensional Lieb-Liniger model of interacting bosons on the unit interval
in the Gross-Pitaevskii regime. We prove that Bose Einstein condensation survives
even a strong random potential with a high density of scatterers. The character
of the wave function of the condensate, however, depends in an essential way on
the interplay between randomness and the strength of the two-body interaction.
For low density of scatterers or strong interactions the wave function extends
over the whole interval. High density of scatterers and weak interaction, on the
other hand, leads to localization of the wave function in a fragmented subset
of the interval. '
article_processing_charge: No
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
- first_name: Valentin
full_name: Zagrebnov, Valentin
last_name: Zagrebnov
citation:
ama: 'Seiringer R, Yngvason J, Zagrebnov V. Disordered Bose-Einstein condensates
with interaction. In: World Scientific Publishing; 2013:610-619. doi:10.1142/9789814449243_0063'
apa: 'Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Disordered Bose-Einstein
condensates with interaction (pp. 610–619). Presented at the ICMP: International
Congress on Mathematical Physics, World Scientific Publishing. https://doi.org/10.1142/9789814449243_0063'
chicago: Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Disordered
Bose-Einstein Condensates with Interaction,” 610–19. World Scientific Publishing,
2013. https://doi.org/10.1142/9789814449243_0063.
ieee: 'R. Seiringer, J. Yngvason, and V. Zagrebnov, “Disordered Bose-Einstein condensates
with interaction,” presented at the ICMP: International Congress on Mathematical
Physics, 2013, pp. 610–619.'
ista: 'Seiringer R, Yngvason J, Zagrebnov V. 2013. Disordered Bose-Einstein condensates
with interaction. ICMP: International Congress on Mathematical Physics, 610–619.'
mla: Seiringer, Robert, et al. Disordered Bose-Einstein Condensates with Interaction.
World Scientific Publishing, 2013, pp. 610–19, doi:10.1142/9789814449243_0063.
short: R. Seiringer, J. Yngvason, V. Zagrebnov, in:, World Scientific Publishing,
2013, pp. 610–619.
conference:
name: 'ICMP: International Congress on Mathematical Physics'
date_created: 2018-12-11T11:56:57Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:43Z
doi: 10.1142/9789814449243_0063
extern: '1'
external_id:
arxiv:
- '1209.4046'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1209.4046
oa: 1
oa_version: None
page: 610-619
publication_status: published
publisher: World Scientific Publishing
publist_id: '4612'
status: public
title: Disordered Bose-Einstein condensates with interaction
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2319'
abstract:
- lang: eng
text: In a recent paper [7] we give the first rigorous derivation of the celebrated
Ginzburg-Landau (GL)theory, starting from the microscopic Bardeen- Cooper-Schrieffer
(BCS)model. Here we present our results in the simplified case of a one-dimensional
system of particles interacting via a δ-potential.
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan
full_name: Solovej, Jan P
last_name: Solovej
citation:
ama: 'Frank R, Hainzl C, Seiringer R, Solovej J. Derivation of Ginzburg-Landau
theory for a one-dimensional system with contact interaction. In: Springer; 2013:57-88.
doi:10.1007/978-3-0348-0531-5_3'
apa: 'Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2013). Derivation
of Ginzburg-Landau theory for a one-dimensional system with contact interaction
(pp. 57–88). Presented at the OTAMP: Operator Theory, Analysis and Mathematical
Physics, Springer. https://doi.org/10.1007/978-3-0348-0531-5_3'
chicago: Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “ Derivation
of Ginzburg-Landau Theory for a One-Dimensional System with Contact Interaction,”
57–88. Springer, 2013. https://doi.org/10.1007/978-3-0348-0531-5_3.
ieee: 'R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “ Derivation of Ginzburg-Landau
theory for a one-dimensional system with contact interaction,” presented at the
OTAMP: Operator Theory, Analysis and Mathematical Physics, 2013, pp. 57–88.'
ista: 'Frank R, Hainzl C, Seiringer R, Solovej J. 2013. Derivation of Ginzburg-Landau
theory for a one-dimensional system with contact interaction. OTAMP: Operator
Theory, Analysis and Mathematical Physics, 57–88.'
mla: Frank, Rupert, et al. Derivation of Ginzburg-Landau Theory for a One-Dimensional
System with Contact Interaction. Springer, 2013, pp. 57–88, doi:10.1007/978-3-0348-0531-5_3.
short: R. Frank, C. Hainzl, R. Seiringer, J. Solovej, in:, Springer, 2013, pp. 57–88.
conference:
name: 'OTAMP: Operator Theory, Analysis and Mathematical Physics'
date_created: 2018-12-11T11:56:58Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:45Z
day: '01'
doi: 10.1007/978-3-0348-0531-5_3
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1103.1866
month: '01'
oa: 1
page: 57 - 88
publication_status: published
publisher: Springer
publist_id: '4608'
quality_controlled: 0
status: public
title: ' Derivation of Ginzburg-Landau theory for a one-dimensional system with contact
interaction'
type: conference
year: '2013'
...
---
_id: '2328'
abstract:
- lang: eng
text: "Linearizability of concurrent data structures is usually proved by monolithic
simulation arguments relying on identifying the so-called linearization points.
Regrettably, such proofs, whether manual or automatic, are often complicated and
scale poorly to advanced non-blocking concurrency patterns, such as helping and
optimistic updates.\r\nIn response, we propose a more modular way of checking
linearizability of concurrent queue algorithms that does not involve identifying
linearization points. We reduce the task of proving linearizability with respect
to the queue specification to establishing four basic properties, each of which
can be proved independently by simpler arguments. As a demonstration of our approach,
we verify the Herlihy and Wing queue, an algorithm that is challenging to verify
by a simulation proof."
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
- first_name: Viktor
full_name: Vafeiadis, Viktor
last_name: Vafeiadis
citation:
ama: Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs.
2013;8052:242-256. doi:10.1007/978-3-642-40184-8_18
apa: 'Henzinger, T. A., Sezgin, A., & Vafeiadis, V. (2013). Aspect-oriented
linearizability proofs. Presented at the CONCUR: Concurrency Theory, Buenos Aires,
Argentina: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-40184-8_18'
chicago: Henzinger, Thomas A, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented
Linearizability Proofs.” Lecture Notes in Computer Science. Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.1007/978-3-642-40184-8_18.
ieee: T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability
proofs,” vol. 8052. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 242–256,
2013.
ista: Henzinger TA, Sezgin A, Vafeiadis V. 2013. Aspect-oriented linearizability
proofs. 8052, 242–256.
mla: Henzinger, Thomas A., et al. Aspect-Oriented Linearizability Proofs.
Vol. 8052, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 242–56,
doi:10.1007/978-3-642-40184-8_18.
short: T.A. Henzinger, A. Sezgin, V. Vafeiadis, 8052 (2013) 242–256.
conference:
end_date: 2013-08-30
location: Buenos Aires, Argentina
name: 'CONCUR: Concurrency Theory'
start_date: 2013-08-27
date_created: 2018-12-11T11:57:01Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2023-02-23T10:16:27Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-40184-8_18
ec_funded: 1
file:
- access_level: open_access
checksum: bdbb520de91751fe0136309ad4ef67e4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:58Z
date_updated: 2020-07-14T12:45:39Z
file_id: '4721'
file_name: IST-2014-197-v1+1_main-queue-verification.pdf
file_size: 337059
relation: main_file
file_date_updated: 2020-07-14T12:45:39Z
has_accepted_license: '1'
intvolume: ' 8052'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 242 - 256
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '4598'
pubrep_id: '197'
quality_controlled: '1'
related_material:
record:
- id: '1832'
relation: later_version
status: public
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Aspect-oriented linearizability proofs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8052
year: '2013'
...
---
_id: '2404'
abstract:
- lang: eng
text: The Lieb-Thirring inequalities give a bound on the negative eigenvalues of
a Schrödinger operator in terms of an Lp-norm of the potential. These are dual
to bounds on the H1-norms of a system of orthonormal functions. Here we extend
these bounds to analogous inequalities for perturbations of the Fermi sea of noninteracting
particles (i.e., for perturbations of the continuous spectrum of the Laplacian
by local potentials).
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Frank R, Lewin M, Lieb É, Seiringer R. A positive density analogue of the Lieb-Thirring
inequality. Duke Mathematical Journal. 2013;162(3):435-495. doi:10.1215/00127094-2019477
apa: Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2013). A positive density
analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. Duke
University Press. https://doi.org/10.1215/00127094-2019477
chicago: Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “A Positive
Density Analogue of the Lieb-Thirring Inequality.” Duke Mathematical Journal.
Duke University Press, 2013. https://doi.org/10.1215/00127094-2019477.
ieee: R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “A positive density analogue
of the Lieb-Thirring inequality,” Duke Mathematical Journal, vol. 162,
no. 3. Duke University Press, pp. 435–495, 2013.
ista: Frank R, Lewin M, Lieb É, Seiringer R. 2013. A positive density analogue of
the Lieb-Thirring inequality. Duke Mathematical Journal. 162(3), 435–495.
mla: Frank, Rupert, et al. “A Positive Density Analogue of the Lieb-Thirring Inequality.”
Duke Mathematical Journal, vol. 162, no. 3, Duke University Press, 2013,
pp. 435–95, doi:10.1215/00127094-2019477.
short: R. Frank, M. Lewin, É. Lieb, R. Seiringer, Duke Mathematical Journal 162
(2013) 435–495.
date_created: 2018-12-11T11:57:28Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T06:57:17Z
day: '01'
doi: 10.1215/00127094-2019477
extern: 1
intvolume: ' 162'
issue: '3'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1108.4246
month: '02'
oa: 1
page: 435 - 495
publication: Duke Mathematical Journal
publication_status: published
publisher: Duke University Press
publist_id: '4521'
quality_controlled: 0
status: public
title: A positive density analogue of the Lieb-Thirring inequality
type: journal_article
volume: 162
year: '2013'
...
---
_id: '2406'
abstract:
- lang: eng
text: We study the effects of random scatterers on the ground state of the one-dimensional
Lieb-Liniger model of interacting bosons on the unit interval. We prove that,
in the Gross-Pitaevskii limit, Bose Einstein condensation takes place in the whole
parameter range considered. The character of the wave function of the condensate,
however, depends in an essential way on the interplay between randomness and the
strength of the two-body interaction. For low density of scatterers or strong
interactions the wave function extends over the whole interval. High density of
scatterers and weak interaction, on the other hand, leads to localization of the
wave function in a fragmented subset of the unit interval.
author:
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
- first_name: Valentin
full_name: Zagrebnov, Valentin A
last_name: Zagrebnov
citation:
ama: 'Seiringer R, Yngvason J, Zagrebnov V. Condensation of interacting bosons in
a random potential. European Physical Journal: Special Topics. 2013;217(1):103-107.
doi:10.1140/epjst/e2013-01759-5'
apa: 'Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Condensation of interacting
bosons in a random potential. European Physical Journal: Special Topics.
Springer. https://doi.org/10.1140/epjst/e2013-01759-5'
chicago: 'Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Condensation
of Interacting Bosons in a Random Potential.” European Physical Journal: Special
Topics. Springer, 2013. https://doi.org/10.1140/epjst/e2013-01759-5.'
ieee: 'R. Seiringer, J. Yngvason, and V. Zagrebnov, “Condensation of interacting
bosons in a random potential,” European Physical Journal: Special Topics,
vol. 217, no. 1. Springer, pp. 103–107, 2013.'
ista: 'Seiringer R, Yngvason J, Zagrebnov V. 2013. Condensation of interacting bosons
in a random potential. European Physical Journal: Special Topics. 217(1), 103–107.'
mla: 'Seiringer, Robert, et al. “Condensation of Interacting Bosons in a Random
Potential.” European Physical Journal: Special Topics, vol. 217, no. 1,
Springer, 2013, pp. 103–07, doi:10.1140/epjst/e2013-01759-5.'
short: 'R. Seiringer, J. Yngvason, V. Zagrebnov, European Physical Journal: Special
Topics 217 (2013) 103–107.'
date_created: 2018-12-11T11:57:29Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T06:57:17Z
day: '01'
doi: 10.1140/epjst/e2013-01759-5
extern: 1
intvolume: ' 217'
issue: '1'
month: '02'
page: 103 - 107
publication: 'European Physical Journal: Special Topics'
publication_status: published
publisher: Springer
publist_id: '4520'
quality_controlled: 0
status: public
title: Condensation of interacting bosons in a random potential
type: journal_article
volume: 217
year: '2013'
...
---
_id: '2405'
abstract:
- lang: eng
text: We consider the bipolaron in the Pekar-Tomasevich approximation and address
the question whether the ground state is spherically symmetric or not. Numerical
analysis has, so far, not completely settled the question. Our contribution is
to prove rigorously that the ground state remains spherical for small values of
the electron-electron Coulomb repulsion.
author:
- first_name: Rupert
full_name: Frank, Rupert L
last_name: Frank
- first_name: Élliott
full_name: Lieb, Élliott H
last_name: Lieb
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Frank R, Lieb É, Seiringer R. Symmetry of bipolaron bound states for small
Coulomb repulsion. Communications in Mathematical Physics. 2013;319(2):557-573.
doi:10.1007/s00220-012-1604-y
apa: Frank, R., Lieb, É., & Seiringer, R. (2013). Symmetry of bipolaron bound
states for small Coulomb repulsion. Communications in Mathematical Physics.
Springer. https://doi.org/10.1007/s00220-012-1604-y
chicago: Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Symmetry of Bipolaron
Bound States for Small Coulomb Repulsion.” Communications in Mathematical Physics.
Springer, 2013. https://doi.org/10.1007/s00220-012-1604-y.
ieee: R. Frank, É. Lieb, and R. Seiringer, “Symmetry of bipolaron bound states for
small Coulomb repulsion,” Communications in Mathematical Physics, vol.
319, no. 2. Springer, pp. 557–573, 2013.
ista: Frank R, Lieb É, Seiringer R. 2013. Symmetry of bipolaron bound states for
small Coulomb repulsion. Communications in Mathematical Physics. 319(2), 557–573.
mla: Frank, Rupert, et al. “Symmetry of Bipolaron Bound States for Small Coulomb
Repulsion.” Communications in Mathematical Physics, vol. 319, no. 2, Springer,
2013, pp. 557–73, doi:10.1007/s00220-012-1604-y.
short: R. Frank, É. Lieb, R. Seiringer, Communications in Mathematical Physics 319
(2013) 557–573.
date_created: 2018-12-11T11:57:28Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2021-01-12T06:57:17Z
day: '01'
doi: 10.1007/s00220-012-1604-y
extern: 1
intvolume: ' 319'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1201.3954
month: '04'
oa: 1
page: 557 - 573
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4522'
quality_controlled: 0
status: public
title: Symmetry of bipolaron bound states for small Coulomb repulsion
type: journal_article
volume: 319
year: '2013'
...
---
_id: '2408'
abstract:
- lang: eng
text: We investigate the low-energy excitation spectrum of a Bose gas confined in
a trap, with weak long-range repulsive interactions. In particular, we prove that
the spectrum can be described in terms of the eigenvalues of an effective one-particle
operator, as predicted by the Bogoliubov approximation.
author:
- first_name: Philip
full_name: Grech, Philip
last_name: Grech
- first_name: Robert
full_name: Robert Seiringer
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Grech P, Seiringer R. The excitation spectrum for weakly interacting Bosons
in a trap. Communications in Mathematical Physics. 2013;322(2):559-591.
doi:10.1007/s00220-013-1736-8
apa: Grech, P., & Seiringer, R. (2013). The excitation spectrum for weakly interacting
Bosons in a trap. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-013-1736-8
chicago: Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly
Interacting Bosons in a Trap.” Communications in Mathematical Physics.
Springer, 2013. https://doi.org/10.1007/s00220-013-1736-8.
ieee: P. Grech and R. Seiringer, “The excitation spectrum for weakly interacting
Bosons in a trap,” Communications in Mathematical Physics, vol. 322, no.
2. Springer, pp. 559–591, 2013.
ista: Grech P, Seiringer R. 2013. The excitation spectrum for weakly interacting
Bosons in a trap. Communications in Mathematical Physics. 322(2), 559–591.
mla: Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting
Bosons in a Trap.” Communications in Mathematical Physics, vol. 322, no.
2, Springer, 2013, pp. 559–91, doi:10.1007/s00220-013-1736-8.
short: P. Grech, R. Seiringer, Communications in Mathematical Physics 322 (2013)
559–591.
date_created: 2018-12-11T11:57:29Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T06:57:18Z
day: '01'
doi: 10.1007/s00220-013-1736-8
extern: 1
intvolume: ' 322'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1205.5259
month: '09'
oa: 1
page: 559 - 591
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4518'
quality_controlled: 0
status: public
title: The excitation spectrum for weakly interacting Bosons in a trap
type: journal_article
volume: 322
year: '2013'
...
---
_id: '2412'
abstract:
- lang: eng
text: 'Background: The CRISPR/Cas system is known to act as an adaptive and heritable
immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer
sequences. Each spacer can provide specific immunity to invasive elements that
carry the same or a similar sequence. Even in closely related strains, spacer
content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot
be applied to quantify its rate of change since processes other than single nucleotide
changes determine its evolution.Methods We present probabilistic models that are
specific for spacer content evolution. They account for the different processes
of insertion and deletion. Insertions can be constrained to occur on one end only
or are allowed to occur throughout the array. One deletion event can affect one
spacer or a whole fragment of adjacent spacers. Parameters of the underlying models
are estimated for a pair of arrays by maximum likelihood using explicit ancestor
enumeration.Results Simulations show that parameters are well estimated on average
under the models presented here. There is a bias in the rate estimation when including
fragment deletions. The models also estimate times between pairs of strains. But
with increasing time, spacer overlap goes to zero, and thus there is an upper
bound on the distance that can be estimated. Spacer content similarities are displayed
in a distance based phylogeny using the estimated times.We use the presented models
to analyze different Yersinia pestis data sets and find that the results among
them are largely congruent. The models also capture the variation in diversity
of spacers among the data sets. A comparison of spacer-based phylogenies and Cas
gene phylogenies shows that they resolve very different time scales for this data
set.Conclusions The simulations and data analyses show that the presented models
are useful for quantifying spacer content evolution and for displaying spacer
content similarities of closely related strains in a phylogeny. This allows for
comparisons of different CRISPR arrays or for comparisons between CRISPR arrays
and nucleotide substitution rates.'
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution
. BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54
apa: Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR
spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54
chicago: Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR
Spacer Content Evolution .” BMC Evolutionary Biology. BioMed Central, 2013.
https://doi.org/10.1186/1471-2148-13-54.
ieee: A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content
evolution ,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central,
pp. 54–54, 2013.
ista: Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content
evolution . BMC Evolutionary Biology. 13(1), 54–54.
mla: Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer
Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central,
2013, pp. 54–54, doi:10.1186/1471-2148-13-54.
short: A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.
date_created: 2018-12-11T11:57:31Z
date_published: 2013-02-26T00:00:00Z
date_updated: 2021-01-12T06:57:20Z
day: '26'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1471-2148-13-54
file:
- access_level: open_access
checksum: 029c7e0b198c19312b66ecce3cabb22f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:15Z
date_updated: 2020-07-14T12:45:40Z
file_id: '5268'
file_name: IST-2015-397-v1+1_1471-2148-13-54.pdf
file_size: 518729
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 54 - 54
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '4514'
pubrep_id: '397'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Probabilistic models for CRISPR spacer content evolution '
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: 13
year: '2013'
...
---
_id: '2413'
abstract:
- lang: eng
text: 'Progress in understanding the global brain dynamics has remained slow to
date in large part because of the highly multiscale nature of brain activity.
Indeed, normal brain dynamics is characterized by complex interactions between
multiple levels: from the microscopic scale of single neurons to the mesoscopic
level of local groups of neurons, and finally to the macroscopic level of the
whole brain. Among the most difficult tasks are those of identifying which scales
are significant for a given particular function and describing how the scales
affect each other. It is important to realize that the scales of time and space
are linked together, or even intertwined, and that causal inference is far more
ambiguous between than within levels. We approach this problem from the perspective
of our recent work on simultaneous recording from micro- and macroelectrodes in
the human brain. We propose a physiological description of these multilevel interactions,
based on phase–amplitude coupling of neuronal oscillations that operate at multiple
frequencies and on different spatial scales. Specifically, the amplitude of the
oscillations on a particular spatial scale is modulated by phasic variations in
neuronal excitability induced by lower frequency oscillations that emerge on a
larger spatial scale. Following this general principle, it is possible to scale
up or scale down the multiscale brain dynamics. It is expected that large-scale
network oscillations in the low-frequency range, mediating downward effects, may
play an important role in attention and consciousness.'
alternative_title:
- Reviews of Nonlinear Dynamics and Complexity
author:
- first_name: Mario
full_name: Valderrama, Mario
last_name: Valderrama
- 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: Michel
full_name: Le Van Quyen, Michel
last_name: Le Van Quyen
citation:
ama: 'Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale
up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. Multiscale
Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH; 2013.
doi:10.1002/9783527671632.ch08'
apa: 'Valderrama, M., Botella Soler, V., & Le Van Quyen, M. (2013). Neuronal
oscillations scale up and scale down the brain dynamics . In M. Meyer & Z.
Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to
the Brain. Wiley-VCH. https://doi.org/10.1002/9783527671632.ch08'
chicago: 'Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal
Oscillations Scale up and Scale down the Brain Dynamics .” In Multiscale Analysis
and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and
Z. Pesenson. Wiley-VCH, 2013. https://doi.org/10.1002/9783527671632.ch08.'
ieee: 'M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations
scale up and scale down the brain dynamics ,” in Multiscale Analysis and Nonlinear
Dynamics: From Genes to the Brain, M. Meyer and Z. Pesenson, Eds. Wiley-VCH,
2013.'
ista: 'Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations
scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear
Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity,
.'
mla: 'Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the
Brain Dynamics .” Multiscale Analysis and Nonlinear Dynamics: From Genes to
the Brain, edited by Misha Meyer and Z. Pesenson, Wiley-VCH, 2013, doi:10.1002/9783527671632.ch08.'
short: 'M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson
(Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH,
2013.'
date_created: 2018-12-11T11:57:31Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T06:57:20Z
day: '01'
department:
- _id: GaTk
doi: 10.1002/9783527671632.ch08
editor:
- first_name: Misha
full_name: Meyer, Misha
last_name: Meyer
- first_name: Z.
full_name: Pesenson, Z.
last_name: Pesenson
language:
- iso: eng
month: '08'
oa_version: None
publication: 'Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain'
publication_identifier:
eisbn:
- '9783527671632'
isbn:
- '9783527411986 '
publication_status: published
publisher: Wiley-VCH
publist_id: '4513'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Neuronal oscillations scale up and scale down the brain dynamics '
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2410'
abstract:
- lang: eng
text: 'Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis,
isolated from soil in Austria. It is the first phage to be discovered that infects
this species. Here, we present the complete genome sequence of this podovirus. '
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Gertraud
full_name: Stift, Gertraud
id: 2DB195CA-F248-11E8-B48F-1D18A9856A87
last_name: Stift
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence
of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements.
2013;1(3). doi:10.1128/genomeA.00216-13
apa: Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013).
Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis.
Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13
chicago: Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan
P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus
Weihenstephanensis.” Genome Announcements. American Society for Microbiology,
2013. https://doi.org/10.1128/genomeA.00216-13.
ieee: R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete
genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,”
Genome Announcements, vol. 1, no. 3. American Society for Microbiology,
2013.
ista: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome
sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome
Announcements. 1(3).
mla: Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel
Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements,
vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13.
short: R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements
1 (2013).
date_created: 2018-12-11T11:57:30Z
date_published: 2013-06-13T00:00:00Z
date_updated: 2021-01-12T06:57:19Z
day: '13'
ddc:
- '576'
department:
- _id: JoBo
- _id: LifeSc
doi: 10.1128/genomeA.00216-13
file:
- access_level: open_access
checksum: 0751ec74b695567e0cdf02aaf9c26829
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:36Z
date_updated: 2020-07-14T12:45:40Z
file_id: '5291'
file_name: IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf
file_size: 130026
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Genome Announcements
publication_status: published
publisher: American Society for Microbiology
publist_id: '4516'
pubrep_id: '398'
quality_controlled: '1'
scopus_import: 1
status: public
title: Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2013'
...
---
_id: '2447'
abstract:
- lang: eng
text: "Separation logic (SL) has gained widespread popularity because of its ability
to succinctly express complex invariants of a program’s heap configurations. Several
specialized provers have been developed for decidable SL fragments. However, these
provers cannot be easily extended or combined with solvers for other theories
that are important in program verification, e.g., linear arithmetic. In this paper,
we present a reduction of decidable SL fragments to a decidable first-order theory
that fits well into the satisfiability modulo theories (SMT) framework. We show
how to use this reduction to automate satisfiability, entailment, frame inference,
and abduction problems for separation logic using SMT solvers. Our approach provides
a simple method of integrating separation logic into existing verification tools
that provide SMT backends, and an elegant way of combining SL fragments with other
decidable first-order theories. We implemented this approach in a verification
tool and applied it to heap-manipulating programs whose verification involves
reasoning in theory combinations.\r\n"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ruzica
full_name: Piskac, Ruzica
last_name: Piskac
- 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: Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789.
doi:10.1007/978-3-642-39799-8_54
apa: 'Piskac, R., Wies, T., & Zufferey, D. (2013). Automating separation logic
using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg,
Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_54'
chicago: Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation
Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_54.
ieee: R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,”
vol. 8044. Springer, pp. 773–789, 2013.
ista: Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT.
8044, 773–789.
mla: Piskac, Ruzica, et al. Automating Separation Logic Using SMT. Vol. 8044,
Springer, 2013, pp. 773–89, doi:10.1007/978-3-642-39799-8_54.
short: R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:43Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-39799-8_54
file:
- access_level: open_access
checksum: 2e866932ab688f47ecd504acb4d5c7d4
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T11:13:01Z
date_updated: 2020-07-14T12:45:41Z
file_id: '7859'
file_name: 2013_CAV_Piskac.pdf
file_size: 309182
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8044'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 773 - 789
publication_status: published
publisher: Springer
publist_id: '4456'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Automating separation logic using SMT
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2443'
abstract:
- lang: eng
text: The mode of action of auxin is based on its non-uniform distribution within
tissues and organs. Despite the wide use of several auxin analogues in research
and agriculture, little is known about the specificity of different auxin-related
transport and signalling processes towards these compounds. Using seedlings of
Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2),
the physiological activity of several auxin analogues was investigated, together
with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis
and to be transported across the plasma membrane. This study shows that the specificity
criteria for different auxin-related processes vary widely. Notably, the special
behaviour of some synthetic auxin analogues suggests that they might be useful
tools in investigations of the molecular mechanism of auxin action. Thus, due
to their differential stimulatory effects on DR5 expression, indole-3-propionic
(IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of
TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin
signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate
between transcriptional and non-transcriptional pathways of auxin signalling.
The results demonstrate that the major determinants for the auxin-like physiological
potential of a particular compound are very complex and involve its chemical and
metabolic stability, its ability to distribute in tissues in a polar manner and
its activity towards auxin signalling machinery.
acknowledgement: The authors thank Dr Christian Luschnig (University of Natural Resources
and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor
Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds
and, last but not least, to Dr David Morris for critical reading of the manuscript.
We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance.
This work was supported by the Grant Agency of the Czech Republic (P305/11/0797
to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project
CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European
Research Council starting independent research grant ERC-2011-StG-20101109-PSDP
(to J.F.).
article_processing_charge: No
article_type: original
author:
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Martin
full_name: Kubeš, Martin
last_name: Kubeš
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: 'Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along
the auxin response chain: A study using auxin analogues. New Phytologist.
2013;200(4):1034-1048. doi:10.1111/nph.12437'
apa: 'Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová,
E. (2013). Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. Wiley. https://doi.org/10.1111/nph.12437'
chicago: 'Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev,
Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes
along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist.
Wiley, 2013. https://doi.org/10.1111/nph.12437.'
ieee: 'S. Simon et al., “Defining the selectivity of processes along the
auxin response chain: A study using auxin analogues,” New Phytologist,
vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.'
ista: 'Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová
E. 2013. Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. 200(4), 1034–1048.'
mla: 'Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin
Response Chain: A Study Using Auxin Analogues.” New Phytologist, vol. 200,
no. 4, Wiley, 2013, pp. 1034–48, doi:10.1111/nph.12437.'
short: S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek,
E. Zažímalová, New Phytologist 200 (2013) 1034–1048.
date_created: 2018-12-11T11:57:41Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2022-06-07T08:57:52Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/nph.12437
ec_funded: 1
intvolume: ' 200'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nph.12437
month: '12'
oa: 1
oa_version: Published Version
page: 1034 - 1048
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: New Phytologist
publication_status: published
publisher: Wiley
publist_id: '4460'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Defining the selectivity of processes along the auxin response chain: A study
using auxin analogues'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 200
year: '2013'
...
---
_id: '2446'
abstract:
- lang: eng
text: The model-checking problem for probabilistic systems crucially relies on the
translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless
translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata
as compared to the traditional approach. In this work, instead of DRW we consider
deterministic automata with acceptance condition given as disjunction of generalized
Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results
in smaller automata as compared to DRW. We present algorithms for probabilistic
model-checking as well as game solving for DGRW conditions. Our new algorithms
lead to improvement both in terms of theoretical bounds as well as practical evaluation.
We compare PRISM with and without our new translation, and show that the new translation
leads to significant improvements.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Gaiser, Andreas
last_name: Gaiser
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs
for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:10.1007/978-3-642-39799-8_37
apa: 'Chatterjee, K., Gaiser, A., & Kretinsky, J. (2013). Automata with generalized
Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the
CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_37'
chicago: Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with
Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture
Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_37.
ieee: K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin
pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer,
pp. 559–575, 2013.
ista: Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin
pairs for probabilistic model checking and LTL synthesis. 8044, 559–575.
mla: Chatterjee, Krishnendu, et al. Automata with Generalized Rabin Pairs for
Probabilistic Model Checking and LTL Synthesis. Vol. 8044, Springer, 2013,
pp. 559–75, doi:10.1007/978-3-642-39799-8_37.
short: K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:42Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-39799-8_37
ec_funded: 1
external_id:
arxiv:
- '1304.5281'
intvolume: ' 8044'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.5281
month: '07'
oa: 1
oa_version: Preprint
page: 559 - 575
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4457'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Automata with generalized Rabin pairs for probabilistic model checking and
LTL synthesis
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2444'
abstract:
- lang: eng
text: 'We consider two core algorithmic problems for probabilistic verification:
the maximal end-component decomposition and the almost-sure reachability set computation
for Markov decision processes (MDPs). For MDPs with treewidth k, we present two
improved static algorithms for both the problems that run in time O(n·k 2.38·2k
) and O(m·logn· k), respectively, where n is the number of states and m is the
number of edges, significantly improving the previous known O(n·k·√n· k) bound
for low treewidth. We also present decremental algorithms for both problems for
MDPs with constant treewidth that run in amortized logarithmic time, which is
a huge improvement over the previously known algorithms that require amortized
linear time.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jakub
full_name: Ła̧Cki, Jakub
last_name: Ła̧Cki
citation:
ama: Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with
low treewidth. 2013;8044:543-558. doi:10.1007/978-3-642-39799-8_36
apa: 'Chatterjee, K., & Ła̧Cki, J. (2013). Faster algorithms for Markov decision
processes with low treewidth. Presented at the CAV: Computer Aided Verification,
St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_36'
chicago: Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov
Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer,
2013. https://doi.org/10.1007/978-3-642-39799-8_36.
ieee: K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes
with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.
ista: Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes
with low treewidth. 8044, 543–558.
mla: Chatterjee, Krishnendu, and Jakub Ła̧Cki. Faster Algorithms for Markov Decision
Processes with Low Treewidth. Vol. 8044, Springer, 2013, pp. 543–58, doi:10.1007/978-3-642-39799-8_36.
short: K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:42Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-39799-8_36
ec_funded: 1
external_id:
arxiv:
- '1304.0084'
intvolume: ' 8044'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.0084
month: '07'
oa: 1
oa_version: Preprint
page: 543 - 558
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4459'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Faster algorithms for Markov decision processes with low treewidth
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2449'
abstract:
- lang: eng
text: 'Intracellular protein routing is mediated by vesicular transport which is
tightly regulated in eukaryotes. The protein and lipid homeostasis depends on
coordinated delivery of de novo synthesized or recycled cargoes to the plasma
membrane by exocytosis and their subsequent removal by rerouting them for recycling
or degradation. Here, we report the characterization of protein affected trafficking
3 (pat3) mutant that we identified by an epifluorescence-based forward genetic
screen for mutants defective in subcellular distribution of Arabidopsis auxin
transporter PIN1–GFP. While pat3 displays largely normal plant morphology and
development in nutrient-rich conditions, it shows strong ectopic intracellular
accumulations of different plasma membrane cargoes in structures that resemble
prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed
that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit
of the retromer complex that mediates retrograde trafficking between the PVC and
trans-Golgi network. Similarly, a mutant defective in another retromer subunit,
vps29, shows comparable subcellular defects in PVC morphology and protein accumulation.
Thus, our data provide evidence that the retromer components VPS35A and VPS29
are essential for normal PVC morphology and normal trafficking of plasma membrane
proteins in plants. In addition, we show that, out of the three VPS35 retromer
subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing
role in trafficking to the lytic vacuole, presenting another level of complexity
in the retromer-dependent vacuolar sorting. '
author:
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Murguel
full_name: Feraru, Murguel
last_name: Feraru
- first_name: Sibylle
full_name: Hirsch, Sibylle
last_name: Hirsch
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Claudiu
full_name: Nicuales, Claudiu
last_name: Nicuales
- first_name: Jelle
full_name: Van Leene, Jelle
last_name: Van Leene
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29
mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant.
2013;6(6):1849-1862. doi:10.1093/mp/sst044
apa: Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene,
J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar
compartment (PVC) function in Arabidopsis. Molecular Plant. Cell Press.
https://doi.org/10.1093/mp/sst044
chicago: Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu
Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml.
“Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function
in Arabidopsis.” Molecular Plant. Cell Press, 2013. https://doi.org/10.1093/mp/sst044.
ieee: T. Nodzyński et al., “Retromer subunits VPS35A and VPS29 mediate prevacuolar
compartment (PVC) function in Arabidopsis,” Molecular Plant, vol. 6, no.
6. Cell Press, pp. 1849–1862, 2013.
ista: Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger
G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar
compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862.
mla: Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar
Compartment (PVC) Function in Arabidopsis.” Molecular Plant, vol. 6, no.
6, Cell Press, 2013, pp. 1849–62, doi:10.1093/mp/sst044.
short: T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene,
G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862.
date_created: 2018-12-11T11:57:44Z
date_published: 2013-11-01T00:00:00Z
date_updated: 2021-01-12T06:57:33Z
day: '01'
department:
- _id: JiFr
doi: 10.1093/mp/sst044
intvolume: ' 6'
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 1849 - 1862
publication: Molecular Plant
publication_status: published
publisher: Cell Press
publist_id: '4454'
quality_controlled: '1'
scopus_import: 1
status: public
title: Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function
in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2013'
...
---
_id: '2452'
abstract:
- lang: eng
text: 'Background: Abundance and distribution of the plant hormone auxin play important
roles in plant development. Besides other metabolic processes, various auxin carriers
control the cellular level of active auxin and, hence, are major regulators of
cellular auxin homeostasis. Despite the developmental importance of auxin transporters,
a simple medium-to-high throughput approach to assess carrier activities is still
missing. Here we show that carrier driven depletion of cellular auxin correlates
with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results:
We developed an easy to use transient single-cell-based system to detect carrier
activity. We use the relative changes in signaling output of the auxin responsive
promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility
of the transient approach was demonstrated by pharmacological and genetic interference
with auxin signaling and transport. As a proof of concept, we provide visual evidence
that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate
cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER),
respectively. Our data suggest that PIN2 and PIN5 have different sensitivities
to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative
PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our
system, indicating that NPA blocks intercellular, but not intracellular auxin
transport.Conclusions: This single-cell-based system is a useful tool by which
the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1
(WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover,
our single cell system might be useful to investigate also other hormonal signaling
pathways, such as cytokinin.'
author:
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Martina
full_name: Laňková, Martina
last_name: Laňková
- first_name: Markéta
full_name: Pařezová, Markéta
last_name: Pařezová
- first_name: Alexis
full_name: Maizel, Alexis
last_name: Maizel
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
citation:
ama: Barbez E, Laňková M, Pařezová M, et al. Single-cell-based system to monitor
carrier driven cellular auxin homeostasis. BMC Plant Biology. 2013;13(1).
doi:10.1186/1471-2229-13-20
apa: Barbez, E., Laňková, M., Pařezová, M., Maizel, A., Zažímalová, E., Petrášek,
J., … Kleine Vehn, J. (2013). Single-cell-based system to monitor carrier driven
cellular auxin homeostasis. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-13-20
chicago: Barbez, Elke, Martina Laňková, Markéta Pařezová, Alexis Maizel, Eva Zažímalová,
Jan Petrášek, Jiří Friml, and Jürgen Kleine Vehn. “Single-Cell-Based System to
Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology.
BioMed Central, 2013. https://doi.org/10.1186/1471-2229-13-20.
ieee: E. Barbez et al., “Single-cell-based system to monitor carrier driven
cellular auxin homeostasis,” BMC Plant Biology, vol. 13, no. 1. BioMed
Central, 2013.
ista: Barbez E, Laňková M, Pařezová M, Maizel A, Zažímalová E, Petrášek J, Friml
J, Kleine Vehn J. 2013. Single-cell-based system to monitor carrier driven cellular
auxin homeostasis. BMC Plant Biology. 13(1).
mla: Barbez, Elke, et al. “Single-Cell-Based System to Monitor Carrier Driven Cellular
Auxin Homeostasis.” BMC Plant Biology, vol. 13, no. 1, BioMed Central,
2013, doi:10.1186/1471-2229-13-20.
short: E. Barbez, M. Laňková, M. Pařezová, A. Maizel, E. Zažímalová, J. Petrášek,
J. Friml, J. Kleine Vehn, BMC Plant Biology 13 (2013).
date_created: 2018-12-11T11:57:45Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T06:57:34Z
day: '01'
doi: 10.1186/1471-2229-13-20
extern: 1
intvolume: ' 13'
issue: '1'
month: '02'
publication: BMC Plant Biology
publication_status: published
publisher: BioMed Central
publist_id: '4451'
quality_controlled: 0
status: public
title: Single-cell-based system to monitor carrier driven cellular auxin homeostasis
type: journal_article
volume: 13
year: '2013'
...
---
_id: '2450'
abstract:
- lang: eng
text: 'Understanding how hormones and genes interact to coordinate plant growth
is a major challenge in developmental biology. The activities of auxin, ethylene,
and cytokinin depend on cellular context and exhibit either synergistic or antagonistic
interactions. Here we use experimentation and network construction to elucidate
the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux
carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and
cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants
such as polaris (pls), we show experimentally that expression of both PIN1 and
PIN2 significantly increases. This relationship is analyzed in the context of
the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin,
ethylene and cytokinin concentration decreases, approximately remains unchanged
and increases, respectively. Experimental data are integrated into a hormonal
crosstalk network through combination with information in literature. Network
construction reveals that the regulation of both PIN1 and PIN2 is predominantly
via ethylene signaling. In addition, it is deduced that the relationship between
cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition
to its regulation to auxin, ethylene, and PLS levels. We discuss how the network
of hormones and genes coordinates plant growth by simultaneously regulating the
activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk,
root development, auxin flux, PIN proteins, PLS protein, signaling network'
author:
- first_name: Junli
full_name: Liu, Junli
last_name: Liu
- first_name: Saher
full_name: Menhi, Saher
last_name: Menhi
- first_name: Jennifer
full_name: Topping, Jennifer
last_name: Topping
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Keith
full_name: Lindsey, Keith
last_name: Lindsey
citation:
ama: Liu J, Menhi S, Topping J, Friml J, Lindsey K. Interaction of PLS and PIN and
hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science.
2013;4(75). doi:10.3389/fpls.2013.00075
apa: Liu, J., Menhi, S., Topping, J., Friml, J., & Lindsey, K. (2013). Interaction
of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers
in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00075
chicago: Liu, Junli, Saher Menhi, Jennifer Topping, Jiří Friml, and Keith Lindsey.
“Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.”
Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00075.
ieee: J. Liu, S. Menhi, J. Topping, J. Friml, and K. Lindsey, “Interaction of PLS
and PIN and hormonal crosstalk in Arabidopsis root development,” Frontiers
in Plant Science, vol. 4, no. 75. Frontiers Research Foundation, 2013.
ista: Liu J, Menhi S, Topping J, Friml J, Lindsey K. 2013. Interaction of PLS and
PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant
Science. 4(75).
mla: Liu, Junli, et al. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis
Root Development.” Frontiers in Plant Science, vol. 4, no. 75, Frontiers
Research Foundation, 2013, doi:10.3389/fpls.2013.00075.
short: J. Liu, S. Menhi, J. Topping, J. Friml, K. Lindsey, Frontiers in Plant Science
4 (2013).
date_created: 2018-12-11T11:57:44Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2021-01-12T06:57:34Z
day: '01'
doi: 10.3389/fpls.2013.00075
extern: 1
intvolume: ' 4'
issue: '75'
month: '04'
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '4453'
quality_controlled: 0
status: public
title: Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development
type: journal_article
volume: 4
year: '2013'
...
---
_id: '245'
abstract:
- lang: eng
text: For given non-zero integers a, b, q we investigate the density of solutions
(x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to
establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined
over ℚ.
author:
- first_name: Stephan
full_name: Baier, Stephan
last_name: Baier
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on
del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2013;(680):69-151.
doi:10.1515/crelle.2012.039
apa: Baier, S., & Browning, T. D. (2013). Inhomogeneous cubic congruences and
rational points on del Pezzo surfaces. Journal Fur Die Reine Und Angewandte
Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle.2012.039
chicago: Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences
and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte
Mathematik. Walter de Gruyter, 2013. https://doi.org/10.1515/crelle.2012.039.
ieee: S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational
points on del Pezzo surfaces,” Journal fur die Reine und Angewandte Mathematik,
no. 680. Walter de Gruyter, pp. 69–151, 2013.
ista: Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points
on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680),
69–151.
mla: Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and
Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte
Mathematik, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:10.1515/crelle.2012.039.
short: S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik
(2013) 69–151.
date_created: 2018-12-11T11:45:24Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T06:57:33Z
day: '01'
doi: 10.1515/crelle.2012.039
extern: 1
issue: '680'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1011.3434
month: '07'
oa: 1
page: 69 - 151
publication: Journal fur die Reine und Angewandte Mathematik
publication_status: published
publisher: Walter de Gruyter
publist_id: '7659'
quality_controlled: 0
status: public
title: Inhomogeneous cubic congruences and rational points on del Pezzo surfaces
type: journal_article
year: '2013'
...
---
_id: '2457'
author:
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Charles
full_name: Delwiche, Charles
last_name: Delwiche
- first_name: Stefan
full_name: Rensing, Stefan
last_name: Rensing
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin
transporters in the green lineage. Trends in Plant Science. 2013;18(1):5-10.
doi:10.1016/j.tplants.2012.08.009
apa: Viaene, T., Delwiche, C., Rensing, S., & Friml, J. (2013). Origin and evolution
of PIN auxin transporters in the green lineage. Trends in Plant Science.
Cell Press. https://doi.org/10.1016/j.tplants.2012.08.009
chicago: Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin
and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant
Science. Cell Press, 2013. https://doi.org/10.1016/j.tplants.2012.08.009.
ieee: T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of
PIN auxin transporters in the green lineage,” Trends in Plant Science,
vol. 18, no. 1. Cell Press, pp. 5–10, 2013.
ista: Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN
auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10.
mla: Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the
Green Lineage.” Trends in Plant Science, vol. 18, no. 1, Cell Press, 2013,
pp. 5–10, doi:10.1016/j.tplants.2012.08.009.
short: T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18
(2013) 5–10.
date_created: 2018-12-11T11:57:46Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:36Z
day: '01'
doi: 10.1016/j.tplants.2012.08.009
extern: '1'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 5 - 10
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '4446'
quality_controlled: '1'
status: public
title: Origin and evolution of PIN auxin transporters in the green lineage
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2013'
...
---
_id: '246'
abstract:
- lang: eng
text: Given an intersection of two quadrics X Pm1, with m > 9, the quantitative
arithmetic of the set X(Q) is investigated under the assumption that the singular
locus of X consists of a pair of conjugate singular points defined over Q(i).
acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council"
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Ritabrata
full_name: Munshi, Ritabrata
last_name: Munshi
citation:
ama: Browning TD, Munshi R. Rational points on singular intersections of quadrics.
Compositio Mathematica. 2013;149(9):1457-1494. doi:10.1112/S0010437X13007185
apa: Browning, T. D., & Munshi, R. (2013). Rational points on singular intersections
of quadrics. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X13007185
chicago: Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular
Intersections of Quadrics.” Compositio Mathematica. Cambridge University
Press, 2013. https://doi.org/10.1112/S0010437X13007185.
ieee: T. D. Browning and R. Munshi, “Rational points on singular intersections of
quadrics,” Compositio Mathematica, vol. 149, no. 9. Cambridge University
Press, pp. 1457–1494, 2013.
ista: Browning TD, Munshi R. 2013. Rational points on singular intersections of
quadrics. Compositio Mathematica. 149(9), 1457–1494.
mla: Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections
of Quadrics.” Compositio Mathematica, vol. 149, no. 9, Cambridge University
Press, 2013, pp. 1457–94, doi:10.1112/S0010437X13007185.
short: T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494.
date_created: 2018-12-11T11:45:25Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T06:57:37Z
day: '01'
doi: 10.1112/S0010437X13007185
extern: 1
intvolume: ' 149'
issue: '9'
month: '09'
page: 1457 - 1494
publication: Compositio Mathematica
publication_status: published
publisher: Cambridge University Press
publist_id: '7658'
quality_controlled: 0
status: public
title: Rational points on singular intersections of quadrics
type: journal_article
volume: 149
year: '2013'
...
---
_id: '2471'
abstract:
- lang: eng
text: The impact of disulfide bonds on protein stability goes beyond simple equilibrium
thermodynamics effects associated with the conformational entropy of the unfolded
state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional
association and strongly affect the rates of irreversible enzyme inactivation,
highly relevant in biotechnological applications. While these kinetic-stability
effects remain poorly understood, by analogy with proposed mechanisms for processes
of protein aggregation and fibrillogenesis, we propose that they may be determined
by the properties of sparsely-populated, partially-unfolded intermediates. Here
we report the successful design, on the basis of high temperature molecular-dynamics
simulations, of six thermodynamically and kinetically stabilized variants of phytase
from Citrobacter braakii (a biotechnologically important enzyme) with one, two
or three engineered disulfides. Activity measurements and 3D crystal structure
determination demonstrate that the engineered crosslinks do not cause dramatic
alterations in the native structure. The inactivation kinetics for all the variants
displays a strongly non-Arrhenius temperature dependence, with the time-scale
for the irreversible denaturation process reaching a minimum at a given temperature
within the range of the denaturation transition. We show this striking feature
to be a signature of a key role played by a partially unfolded, intermediate state/ensemble.
Energetic and mutational analyses confirm that the intermediate is highly unfolded
(akin to a proposed critical intermediate in the misfolding of the prion protein),
a result that explains the observed kinetic stabilization. Our results provide
a rationale for the kinetic-stability consequences of disulfide-crosslink engineering
and an experimental methodology to arrive at energetic/structural descriptions
of the sparsely populated and elusive intermediates that play key roles in irreversible
protein denaturation.
article_number: e70013
author:
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Antonio
full_name: Ariza, Antonio
last_name: Ariza
- first_name: Keith
full_name: Wilson, Keith
last_name: Wilson
- first_name: Michael
full_name: Skjøt, Michael
last_name: Skjøt
- first_name: Jesper
full_name: Vind, Jesper
last_name: Vind
- first_name: Leonardo
full_name: De Maria, Leonardo
last_name: De Maria
- first_name: Lars
full_name: Skov, Lars
last_name: Skov
- first_name: Jose
full_name: Sánchez Ruiz, Jose
last_name: Sánchez Ruiz
citation:
ama: Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization
by engineered disulfide crosslinks. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070013
apa: Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L.,
… Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered
disulfide crosslinks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070013
chicago: Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt,
Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of
Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070013.
ieee: I. Sanchez-Romero et al., “Mechanism of protein kinetic stabilization
by engineered disulfide crosslinks,” PLoS One, vol. 8, no. 7. Public Library
of Science, 2013.
ista: Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L,
Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered
disulfide crosslinks. PLoS One. 8(7), e70013.
mla: Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization
by Engineered Disulfide Crosslinks.” PLoS One, vol. 8, no. 7, e70013, Public
Library of Science, 2013, doi:10.1371/journal.pone.0070013.
short: I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L.
Skov, J. Sánchez Ruiz, PLoS One 8 (2013).
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-30T00:00:00Z
date_updated: 2021-01-12T06:57:41Z
day: '30'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.1371/journal.pone.0070013
file:
- access_level: open_access
checksum: c0c96cc76ed7ef0d036a31a7e33c9a37
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:07Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5124'
file_name: IST-2016-414-v1+1_journal.pone.0070013.pdf
file_size: 1323666
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4430'
pubrep_id: '414'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mechanism of protein kinetic stabilization by engineered disulfide crosslinks
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: 8
year: '2013'
...
---
_id: '2472'
abstract:
- lang: eng
text: Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone
auxin are required for tissue-specific directional auxin transport and cellular
auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important
roles in developmental processes such as embryogenesis, organogenesis, vascular
tissue differentiation, root meristem patterning and tropic growth. Here we analyzed
roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible
and is expressed during multiple auxin-regulated developmental processes. Loss
of pin6 function interfered with primary root growth and lateral root development.
Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis
in other growth processes such as shoot apical dominance, lateral root primordia
development, adventitious root formation, root hair outgrowth and root waving.
These changes in auxin-regulated growth correlated with a reduction in total auxin
transport as well as with an altered activity of DR5-GUS auxin response reporter.
Overall, the data indicate that PIN6 regulates auxin homeostasis during plant
development.
article_number: e70069
author:
- first_name: Christopher
full_name: Cazzonelli, Christopher
last_name: Cazzonelli
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Kuide
full_name: Yin, Kuide
last_name: Yin
- first_name: Ashley
full_name: Carron Arthur, Ashley
last_name: Carron Arthur
- first_name: Nazia
full_name: Nisar, Nazia
last_name: Nisar
- first_name: Gauri
full_name: Tarle, Gauri
last_name: Tarle
- first_name: Abby
full_name: Cuttriss, Abby
last_name: Cuttriss
- first_name: Iain
full_name: Searle, Iain
last_name: Searle
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ulrike
full_name: Mathesius, Ulrike
last_name: Mathesius
- first_name: Josette
full_name: Masle, Josette
last_name: Masle
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Barry
full_name: Pogson, Barry
last_name: Pogson
citation:
ama: Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin
transporter in auxin homeostasis and auxin-mediated development. PLoS One.
2013;8(7). doi:10.1371/journal.pone.0070069
apa: Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar,
N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin
homeostasis and auxin-mediated development. PLoS One. Public Library of
Science. https://doi.org/10.1371/journal.pone.0070069
chicago: Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley
Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6
Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS
One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070069.
ieee: C. Cazzonelli et al., “Role of the Arabidopsis PIN6 auxin transporter
in auxin homeostasis and auxin-mediated development,” PLoS One, vol. 8,
no. 7. Public Library of Science, 2013.
ista: Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle
G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013.
Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated
development. PLoS One. 8(7), e70069.
mla: Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter
in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One, vol. 8,
no. 7, e70069, Public Library of Science, 2013, doi:10.1371/journal.pone.0070069.
short: C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar,
G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml,
B. Pogson, PLoS One 8 (2013).
date_created: 2018-12-11T11:57:52Z
date_published: 2013-07-29T00:00:00Z
date_updated: 2021-01-12T06:57:41Z
day: '29'
ddc:
- '580'
- '570'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1371/journal.pone.0070069
ec_funded: 1
file:
- access_level: open_access
checksum: 3be71828b6c2ba9c90eb7056e3f7f57a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:34Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5222'
file_name: IST-2015-393-v1+1_journal.pone.0070069.pdf
file_size: 9003465
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4431'
pubrep_id: '393'
quality_controlled: '1'
scopus_import: 1
status: public
title: Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated
development
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: 8
year: '2013'
...
---
_id: '2470'
abstract:
- lang: eng
text: Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and
its function is indispensable for plant growth and development. ABP1 has been
shown to be involved in auxin-dependent regulation of cell division and expansion,
in plasma-membrane-related processes such as changes in transmembrane potential,
and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated
downstream pathway remains elusive.Methodology/Principal Findings:Using auxin
transport assays and quantitative analysis of cellular morphology we show that
ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can
counterbalance increased auxin efflux and auxin starvation phenotypes caused by
the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the
ABP1-controlled vesicle trafficking processes, including positive regulation of
endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery
after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The
findings indicate the involvement of ABP1 in control of rate of auxin transport
across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity
at the plasma membrane, and highlighting the relevance of ABP1 for the formation
of developmentally important, PIN-dependent auxin gradients.
article_number: e70050
author:
- first_name: Milada
full_name: Čovanová, Milada
last_name: Čovanová
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jan
full_name: Rychtář, Jan
last_name: Rychtář
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression
of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco
cells. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070050
apa: Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., & Zažímalová,
E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent
auxin transport in tobacco cells. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0070050
chicago: Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek,
and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent
Auxin Transport in Tobacco Cells.” PLoS One. Public Library of Science,
2013. https://doi.org/10.1371/journal.pone.0070050.
ieee: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová,
“Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport
in tobacco cells,” PLoS One, vol. 8, no. 7. Public Library of Science,
2013.
ista: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression
of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco
cells. PLoS One. 8(7), e70050.
mla: Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates
PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One, vol. 8, no.
7, e70050, Public Library of Science, 2013, doi:10.1371/journal.pone.0070050.
short: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová,
PLoS One 8 (2013).
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-23T00:00:00Z
date_updated: 2021-01-12T06:57:40Z
day: '23'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1371/journal.pone.0070050
file:
- access_level: open_access
checksum: 2d47ef47616ef4de1d517d146548184e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:21Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4681'
file_name: IST-2016-413-v1+1_journal.pone.0070050.pdf
file_size: 2294955
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4432'
pubrep_id: '413'
quality_controlled: '1'
scopus_import: 1
status: public
title: Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin
transport in tobacco cells
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: 8
year: '2013'
...
---
_id: '2466'
abstract:
- lang: eng
text: 'We introduce a new method for efficiently simulating liquid with extreme
amounts of spatial adaptivity. Our method combines several key components to drastically
speed up the simulation of large-scale fluid phenomena: We leverage an alternative
Eulerian tetrahedral mesh discretization to significantly reduce the complexity
of the pressure solve while increasing the robustness with respect to element
quality and removing the possibility of locking. Next, we enable subtle free-surface
phenomena by deriving novel second-order boundary conditions consistent with our
discretization. We couple this discretization with a spatially adaptive Fluid-Implicit
Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations
that can undergo sharp changes in spatial resolution while minimizing artifacts.
Along the way, we provide a new method for generating a smooth and detailed surface
from a set of particles with variable sizes. Finally, we explore several new sizing
functions for determining spatially adaptive simulation resolutions, and we show
how to couple them to our simulator. We combine each of these elements to produce
a simulation algorithm that is capable of creating animations at high maximum
resolutions while avoiding common pitfalls like inaccurate boundary conditions
and inefficient computation.'
article_number: '103'
author:
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- 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: Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral
meshes. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461982
apa: Ando, R., Thuerey, N., & Wojtan, C. (2013). Highly adaptive liquid simulations
on tetrahedral meshes. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461982
chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid
Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics. ACM,
2013. https://doi.org/10.1145/2461912.2461982.
ieee: R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on
tetrahedral meshes,” ACM Transactions on Graphics, vol. 32, no. 4. ACM,
2013.
ista: Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral
meshes. ACM Transactions on Graphics. 32(4), 103.
mla: Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.”
ACM Transactions on Graphics, vol. 32, no. 4, 103, ACM, 2013, doi:10.1145/2461912.2461982.
short: R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013).
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-02-23T10:44:14Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2461982
file:
- access_level: open_access
checksum: aeea6b0ff2b27c695aeb8408c7d2fc50
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:25Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5279'
file_name: IST-2016-605-v1+1_tetflip_fixed.pdf
file_size: 8601561
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4436'
pubrep_id: '605'
quality_controlled: '1'
scopus_import: 1
status: public
title: Highly adaptive liquid simulations on tetrahedral meshes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2467'
abstract:
- lang: eng
text: This paper presents a method for computing topology changes for triangle meshes
in an interactive geometric modeling environment. Most triangle meshes in practice
do not exhibit desirable geometric properties, so we develop a solution that is
independent of standard assumptions and robust to geometric errors. Specifically,
we provide the first method for topology change applicable to arbitrary non-solid,
non-manifold, non-closed, self-intersecting surfaces. We prove that this new method
for topology change produces the expected conventional results when applied to
solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a
backwards-compatibility property relative to prior work. Beyond solid surfaces,
we present empirical evidence that our method remains tolerant to a variety of
surface aberrations through the incorporation of a novel error correction scheme.
Finally, we demonstrate how topology change applied to non-solid objects enables
wholly new and useful behaviors.
article_number: '34'
author:
- first_name: Gilbert
full_name: Bernstein, Gilbert
last_name: Bernstein
- 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: 'Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for
arbitrary surfaces. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2462027'
apa: 'Bernstein, G., & Wojtan, C. (2013). Putting holes in holey geometry: Topology
change for arbitrary surfaces. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2462027'
chicago: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry:
Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics.
ACM, 2013. https://doi.org/10.1145/2461912.2462027.'
ieee: 'G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change
for arbitrary surfaces,” ACM Transactions on Graphics, vol. 32, no. 4.
ACM, 2013.'
ista: 'Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change
for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.'
mla: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology
Change for Arbitrary Surfaces.” ACM Transactions on Graphics, vol. 32,
no. 4, 34, ACM, 2013, doi:10.1145/2461912.2462027.'
short: G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013).
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-02-23T10:44:16Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2462027
file:
- access_level: open_access
checksum: 9c8425d62246996ca632c5a01870515b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:43Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4768'
file_name: IST-2016-604-v1+1_toptop2013.pdf
file_size: 3514674
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4435'
pubrep_id: '604'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Putting holes in holey geometry: Topology change for arbitrary surfaces'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2013'
...
---
_id: '2468'
abstract:
- lang: eng
text: Our work concerns the combination of an Eulerian liquid simulation with a
high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle
mesh). The naive application of a high-resolution surface tracker to a low-resolution
velocity field can produce many visually disturbing physical and topological artifacts
that limit their use in practice. We address these problems by defining an error
function which compares the current state of the surface tracker to the set of
physically valid surface states. By reducing this error with a gradient descent
technique, we introduce a novel physics-based surface fairing method. Similarly,
by treating this error function as a potential energy, we derive a new surface
correction force that mimics the vortex sheet equations. We demonstrate our results
with both level set and mesh-based surface trackers.
article_number: '68'
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
- 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: Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation.
ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461991
apa: Bojsen-Hansen, M., & Wojtan, C. (2013). Liquid surface tracking with error
compensation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461991
chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with
Error Compensation.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461991.
ieee: M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,”
ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.
ista: Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation.
ACM Transactions on Graphics. 32(4), 68.
mla: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error
Compensation.” ACM Transactions on Graphics, vol. 32, no. 4, 68, ACM, 2013,
doi:10.1145/2461912.2461991.
short: M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-02-23T10:44:18Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
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title: Liquid surface tracking with error compensation
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...