---
_id: '11837'
abstract:
- lang: eng
text: "Online social networks allow the collection of large amounts of data about
the influence between users connected by a friendship-like relationship. When
distributing items among agents forming a social network, this information allows
us to exploit network externalities that each agent receives from his neighbors
that get the same item. In this paper we consider Friends-of-Friends (2-hop) network
externalities, i.e., externalities that not only depend on the neighbors that
get the same item but also on neighbors of neighbors. For these externalities
we study a setting where multiple different items are assigned to unit-demand
agents. Specifically, we study the problem of welfare maximization under different
types of externality functions. Let n be the number of agents and m be the number
of items. Our contributions are the following: (1) We show that welfare maximization
is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop)
externalities it is NP-hard to approximate social welfare better than (1-1/e).
(2) On the positive side we present (i) an O(sqrt n)-approximation algorithm for
general concave externality functions,\r\n(ii) an O(\\log m)-approximation algorithm
for linear externality functions, and (iii) an (1-1/e)\\frac{1}{6}-approximation
algorithm for 2-hop step function externalities. We also improve the result from
[6] for 1-hop step function externalities by giving a (1-1/e)/2-approximation
algorithm."
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- first_name: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: ' Martin'
full_name: Starnberger, Martin
last_name: Starnberger
citation:
ama: 'Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. Welfare maximization
with friends-of-friends network externalities. In: 32nd International Symposium
on Theoretical Aspects of Computer Science. Vol 30. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2015:90-102. doi:10.4230/LIPICS.STACS.2015.90'
apa: 'Bhattacharya, S., Dvorák, W., Henzinger, M. H., & Starnberger, Martin.
(2015). Welfare maximization with friends-of-friends network externalities. In
32nd International Symposium on Theoretical Aspects of Computer Science
(Vol. 30, pp. 90–102). Garching, Germany: Schloss Dagstuhl - Leibniz-Zentrum für
Informatik. https://doi.org/10.4230/LIPICS.STACS.2015.90'
chicago: Bhattacharya, Sayan, Wolfgang Dvorák, Monika H Henzinger, and Martin Starnberger.
“Welfare Maximization with Friends-of-Friends Network Externalities.” In 32nd
International Symposium on Theoretical Aspects of Computer Science, 30:90–102.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPICS.STACS.2015.90.
ieee: S. Bhattacharya, W. Dvorák, M. H. Henzinger, and Martin Starnberger, “Welfare
maximization with friends-of-friends network externalities,” in 32nd International
Symposium on Theoretical Aspects of Computer Science, Garching, Germany, 2015,
vol. 30, pp. 90–102.
ista: 'Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. 2015. Welfare
maximization with friends-of-friends network externalities. 32nd International
Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical
Aspects of Computer Science, LIPIcs, vol. 30, 90–102.'
mla: Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network
Externalities.” 32nd International Symposium on Theoretical Aspects of Computer
Science, vol. 30, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015,
pp. 90–102, doi:10.4230/LIPICS.STACS.2015.90.
short: S. Bhattacharya, W. Dvorák, M.H. Henzinger, Martin Starnberger, in:, 32nd
International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2015, pp. 90–102.
conference:
end_date: 2015-03-07
location: Garching, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2015-03-04
date_created: 2022-08-12T11:39:40Z
date_published: 2015-02-26T00:00:00Z
date_updated: 2023-02-21T16:32:37Z
day: '26'
doi: 10.4230/LIPICS.STACS.2015.90
extern: '1'
intvolume: ' 30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPICS.STACS.2015.90
month: '02'
oa: 1
oa_version: Published Version
page: 90-102
publication: 32nd International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
isbn:
- 978-3-939897-78-1
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '11903'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Welfare maximization with friends-of-friends network externalities
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2015'
...
---
_id: '11901'
abstract:
- lang: eng
text: We consider auctions of indivisible items to unit-demand bidders with budgets.
This setting was suggested as an expressive model for single sponsored search
auctions. Prior work presented mechanisms that compute bidder-optimal outcomes
and are truthful for a restricted set of inputs, i.e., inputs in so-called general
position. This condition is easily violated. We provide the first mechanism that
is truthful in expectation for all inputs and achieves for each bidder no worse
utility than the bidder-optimal outcome. Additionally we give a complete characterization
for which inputs mechanisms that compute bidder-optimal outcomes are truthful.
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: Henzinger MH, Loitzenbauer V. Truthful unit-demand auctions with budgets revisited.
Theoretical Computer Science. 2015;573:1-15. doi:10.1016/j.tcs.2015.01.033
apa: Henzinger, M. H., & Loitzenbauer, V. (2015). Truthful unit-demand auctions
with budgets revisited. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.033
chicago: Henzinger, Monika H, and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions
with Budgets Revisited.” Theoretical Computer Science. Elsevier, 2015.
https://doi.org/10.1016/j.tcs.2015.01.033.
ieee: M. H. Henzinger and V. Loitzenbauer, “Truthful unit-demand auctions with budgets
revisited,” Theoretical Computer Science, vol. 573. Elsevier, pp. 1–15,
2015.
ista: Henzinger MH, Loitzenbauer V. 2015. Truthful unit-demand auctions with budgets
revisited. Theoretical Computer Science. 573, 1–15.
mla: Henzinger, Monika H., and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions
with Budgets Revisited.” Theoretical Computer Science, vol. 573, Elsevier,
2015, pp. 1–15, doi:10.1016/j.tcs.2015.01.033.
short: M.H. Henzinger, V. Loitzenbauer, Theoretical Computer Science 573 (2015)
1–15.
date_created: 2022-08-17T09:06:53Z
date_published: 2015-03-30T00:00:00Z
date_updated: 2023-02-17T14:50:04Z
day: '30'
doi: 10.1016/j.tcs.2015.01.033
extern: '1'
intvolume: ' 573'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.tcs.2015.01.033
month: '03'
oa: 1
oa_version: None
page: 1-15
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Truthful unit-demand auctions with budgets revisited
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 573
year: '2015'
...
---
_id: '121'
abstract:
- lang: eng
text: We show that the simplest building blocks of origami-based materials - rigid,
degree-four vertices - are generically multistable. The existence of two distinct
branches of folding motion emerging from the flat state suggests at least bistability,
but we show how nonlinearities in the folding motions allow generic vertex geometries
to have as many as five stable states. In special geometries with collinear folds
and symmetry, more branches emerge leading to as many as six stable states. Tuning
the fold energy parameters, we show how monostability is also possible. Finally,
we show how to program the stability features of a single vertex into a periodic
fold tessellation. The resulting metasheets provide a previously unanticipated
functionality - tunable and switchable shape and size via multistability.
acknowledgement: B. G. C. acknowledges support from FOM, and S. W. and M. v. H. acknowledge
support from NWO.
article_number: '055503'
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Rémi
full_name: Menaut, Rémi
last_name: Menaut
- first_name: Bryan
full_name: Chen, Bryan
last_name: Chen
- first_name: Martin
full_name: Van Hecke, Martin
last_name: Van Hecke
citation:
ama: 'Waitukaitis SR, Menaut R, Chen B, Van Hecke M. Origami multistability: From
single vertices to metasheets. APS Physics, Physical Review Letters. 2015;114(5).
doi:10.1103/PhysRevLett.114.055503'
apa: 'Waitukaitis, S. R., Menaut, R., Chen, B., & Van Hecke, M. (2015). Origami
multistability: From single vertices to metasheets. APS Physics, Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.055503'
chicago: 'Waitukaitis, Scott R, Rémi Menaut, Bryan Chen, and Martin Van Hecke. “Origami
Multistability: From Single Vertices to Metasheets.” APS Physics, Physical
Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.055503.'
ieee: 'S. R. Waitukaitis, R. Menaut, B. Chen, and M. Van Hecke, “Origami multistability:
From single vertices to metasheets,” APS Physics, Physical Review Letters,
vol. 114, no. 5. American Physical Society, 2015.'
ista: 'Waitukaitis SR, Menaut R, Chen B, Van Hecke M. 2015. Origami multistability:
From single vertices to metasheets. APS Physics, Physical Review Letters. 114(5),
055503.'
mla: 'Waitukaitis, Scott R., et al. “Origami Multistability: From Single Vertices
to Metasheets.” APS Physics, Physical Review Letters, vol. 114, no. 5,
055503, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.055503.'
short: S.R. Waitukaitis, R. Menaut, B. Chen, M. Van Hecke, APS Physics, Physical
Review Letters 114 (2015).
date_created: 2018-12-11T11:44:44Z
date_published: 2015-02-04T00:00:00Z
date_updated: 2021-01-12T06:49:07Z
day: '04'
doi: 10.1103/PhysRevLett.114.055503
extern: '1'
external_id:
arxiv:
- '1408.1607'
intvolume: ' 114'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.1607
month: '02'
oa: 1
oa_version: Preprint
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7933'
quality_controlled: '1'
status: public
title: 'Origami multistability: From single vertices to metasheets'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2015'
...
---
_id: '1383'
abstract:
- lang: eng
text: In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi
network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has
impeded our understanding of how the pH homeostasis within the plant TGN/EE controls
exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3
(det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly
impairing secretion and recycling of the brassinosteroid receptor and the cellulose
synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized
V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency
defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility.
Thus, our results provide strong evidence that acidification of the TGN/EE, but
not of the vacuole, is indispensable for functional secretion and recycling in
plants.
article_number: '15094'
article_processing_charge: No
article_type: original
author:
- first_name: Luo
full_name: Yu, Luo
last_name: Yu
- first_name: Stefan
full_name: Scholl, Stefan
last_name: Scholl
- first_name: Anett
full_name: Doering, Anett
last_name: Doering
- first_name: Zhang
full_name: Yi, Zhang
last_name: Yi
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Lutz
full_name: Neumetzler, Lutz
last_name: Neumetzler
- first_name: Praveen
full_name: Krishnamoorthy, Praveen
last_name: Krishnamoorthy
- first_name: Isabelle
full_name: Van Houtte, Isabelle
last_name: Van Houtte
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Volker
full_name: Bischoff, Volker
last_name: Bischoff
- first_name: Samantha
full_name: Vernhettes, Samantha
last_name: Vernhettes
- first_name: Johan
full_name: Winne, Johan
last_name: Winne
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: York
full_name: Stierhof, York
last_name: Stierhof
- first_name: Karin
full_name: Schumacher, Karin
last_name: Schumacher
- first_name: Staffan
full_name: Persson, Staffan
last_name: Persson
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required
for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7).
doi:10.1038/nplants.2015.94
apa: Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova,
E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling
in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94
chicago: Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone
Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required
for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing
Group, 2015. https://doi.org/10.1038/nplants.2015.94.
ieee: L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis
and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing
Group, 2015.
ista: Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy
P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof
Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE
is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7),
15094.
mla: Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis
and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature
Publishing Group, 2015, doi:10.1038/nplants.2015.94.
short: L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler,
P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne,
J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants
1 (2015).
date_created: 2018-12-11T11:51:42Z
date_published: 2015-07-06T00:00:00Z
date_updated: 2021-01-12T06:50:18Z
day: '06'
department:
- _id: JiFr
doi: 10.1038/nplants.2015.94
external_id:
pmid:
- '27250258'
intvolume: ' 1'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '5827'
quality_controlled: '1'
scopus_import: 1
status: public
title: V-ATPase activity in the TGN/EE is required for exocytosis and recycling in
Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2015'
...
---
_id: '1425'
abstract:
- lang: eng
text: 'In this work we aim at extending the theoretical foundations of lifelong
learning. Previous work analyzing this scenario is based on the assumption that
learning tasks are sampled i.i.d. from a task environment or limited to strongly
constrained data distributions. Instead, we study two scenarios when lifelong
learning is possible, even though the observed tasks do not form an i.i.d. sample:
first, when they are sampled from the same environment, but possibly with dependencies,
and second, when the task environment is allowed to change over time in a consistent
way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct
generalization of the analogous previous result for the i.i.d. case. For the second
scenario we propose to learn an inductive bias in form of a transfer procedure.
We present a generalization bound and show on a toy example how it can be used
to identify a beneficial transfer algorithm.'
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015.
Neural Information Processing Systems; 2015:1540-1548.'
apa: 'Pentina, A., & Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks
(Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing
Systems, Montreal, Canada: Neural Information Processing Systems.'
chicago: Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d.
Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015.
ieee: 'A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented
at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol.
2015, pp. 1540–1548.'
ista: 'Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS:
Neural Information Processing Systems, Advances in Neural Information Processing
Systems, vol. 2015, 1540–1548.'
mla: Pentina, Anastasia, and Christoph Lampert. Lifelong Learning with Non-i.i.d.
Tasks. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48.
short: A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015,
pp. 1540–1548.
conference:
end_date: 2015-12-12
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2015-12-07
date_created: 2018-12-11T11:51:57Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:39Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
intvolume: ' 2015'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks
month: '01'
oa: 1
oa_version: None
page: 1540 - 1548
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5781'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lifelong learning with non-i.i.d. tasks
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '1424'
abstract:
- lang: eng
text: We consider the problem of statistical computations with persistence diagrams,
a summary representation of topological features in data. These diagrams encode
persistent homology, a widely used invariant in topological data analysis. While
several avenues towards a statistical treatment of the diagrams have been explored
recently, we follow an alternative route that is motivated by the success of methods
based on the embedding of probability measures into reproducing kernel Hilbert
spaces. In fact, a positive definite kernel on persistence diagrams has recently
been proposed, connecting persistent homology to popular kernel-based learning
techniques such as support vector machines. However, important properties of that
kernel enabling a principled use in the context of probability measure embeddings
remain to be explored. Our contribution is to close this gap by proving universality
of a variant of the original kernel, and to demonstrate its effective use in twosample
hypothesis testing on synthetic as well as real-world data.
acknowledgement: This work was partially supported by the Austrian Science FUnd, project
no. KLI 00012.
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Marc
full_name: Niethammer, Marc
last_name: Niethammer
- first_name: Weili
full_name: Lin, Weili
last_name: Lin
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
citation:
ama: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data
analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems;
2015:3070-3078.'
apa: 'Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical
topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented
at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information
Processing Systems.'
chicago: Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer.
“Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural
Information Processing Systems, 2015.
ieee: 'R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological
data analysis-A kernel perspective,” presented at the NIPS: Neural Information
Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.'
ista: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological
data analysis-A kernel perspective. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 28, 3070–3078.'
mla: Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective.
Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78.
short: R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information
Processing Systems, 2015, pp. 3070–3078.
conference:
end_date: 2015-12-12
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2015-12-07
date_created: 2018-12-11T11:51:56Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:50:38Z
day: '01'
department:
- _id: HeEd
intvolume: ' 28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective
month: '12'
oa: 1
oa_version: Submitted Version
page: 3070 - 3078
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5782'
quality_controlled: '1'
status: public
title: Statistical topological data analysis-A kernel perspective
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2015'
...
---
_id: '1430'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse their runtime on many illustrative
problems. Here we apply this theory to a simple model of natural evolution. In
the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between
occurrence of new mutations is much longer than the time it takes for a new beneficial
mutation to take over the population. In this situation, the population only contains
copies of one genotype and evolution can be modelled as a (1+1)-type process where
the probability of accepting a new genotype (improvements or worsenings) depends
on the change in fitness. We present an initial runtime analysis of SSWM, quantifying
its performance for various parameters and investigating differences to the (1+1)
EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing
fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking
advantage of information on the fitness gradient.
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: 'Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime
comparison of natural and artificial evolution. In: Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462.
doi:10.1145/2739480.2754758'
apa: 'Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps
towards a runtime comparison of natural and artificial evolution. In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp.
1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758'
chicago: Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First
Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62.
ACM, 2015. https://doi.org/10.1145/2739480.2754758.
ieee: T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards
a runtime comparison of natural and artificial evolution,” in Proceedings of
the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid,
Spain, 2015, pp. 1455–1462.
ista: 'Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a
runtime comparison of natural and artificial evolution. Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and
evolutionary computation conference, 1455–1462.'
mla: Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural
and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic
and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.
short: T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the
2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp.
1455–1462.
conference:
end_date: 2015-07-15
location: Madrid, Spain
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2015-07-11
date_created: 2018-12-11T11:51:58Z
date_published: 2015-07-11T00:00:00Z
date_updated: 2021-01-12T06:50:41Z
day: '11'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2739480.2754758
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.06260
month: '07'
oa: 1
oa_version: Preprint
page: 1455 - 1462
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary
Computation
publication_status: published
publisher: ACM
publist_id: '5768'
quality_controlled: '1'
scopus_import: 1
status: public
title: First steps towards a runtime comparison of natural and artificial evolution
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1474'
abstract:
- lang: eng
text: Cryptographic access control offers selective access to encrypted data via
a combination of key management and functionality-rich cryptographic schemes,
such as attribute-based encryption. Using this approach, publicly available meta-data
may inadvertently leak information on the access policy that is enforced by cryptography,
which renders cryptographic access control unusable in settings where this information
is highly sensitive. We begin to address this problem by presenting rigorous definitions
for policy privacy in cryptographic access control. For concreteness we set our
results in the model of Role-Based Access Control (RBAC), where we identify and
formalize several different flavors of privacy, however, our framework should
serve as inspiration for other models of access control. Based on our insights
we propose a new system which significantly improves on the privacy properties
of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving
attribute-based encryption, which we introduce and show how to instantiate. We
present our results in the context of a cryptographic RBAC system by Ferrara et
al. (CSF'13), which uses cryptography to control read access to files, while write
access is still delegated to trusted monitors. We give an extension of the construction
that permits cryptographic control over write access. Our construction assumes
that key management uses out-of-band channels between the policy enforcer and
the users but eliminates completely the need for monitoring read/write access
to the data.
article_processing_charge: No
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: Bin
full_name: Liu, Bin
last_name: Liu
- first_name: Bogdan
full_name: Warinschi, Bogdan
last_name: Warinschi
citation:
ama: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic
access control. In: IEEE; 2015:46-60. doi:10.1109/CSF.2015.11'
apa: 'Ferrara, A., Fuchsbauer, G., Liu, B., & Warinschi, B. (2015). Policy privacy
in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security
Foundations, Verona, Italy: IEEE. https://doi.org/10.1109/CSF.2015.11'
chicago: Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy
Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. https://doi.org/10.1109/CSF.2015.11.
ieee: 'A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic
access control,” presented at the CSF: Computer Security Foundations, Verona,
Italy, 2015, pp. 46–60.'
ista: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic
access control. CSF: Computer Security Foundations, 46–60.'
mla: Ferrara, Anna, et al. Policy Privacy in Cryptographic Access Control.
IEEE, 2015, pp. 46–60, doi:10.1109/CSF.2015.11.
short: A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60.
conference:
end_date: 2015-07-17
location: Verona, Italy
name: 'CSF: Computer Security Foundations'
start_date: 2015-07-13
date_created: 2018-12-11T11:52:14Z
date_published: 2015-09-04T00:00:00Z
date_updated: 2021-01-12T06:50:59Z
day: '04'
department:
- _id: KrPi
doi: 10.1109/CSF.2015.11
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://epubs.surrey.ac.uk/808055/
month: '09'
oa: 1
oa_version: Submitted Version
page: 46-60
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: IEEE
publist_id: '5722'
quality_controlled: '1'
status: public
title: Policy privacy in cryptographic access control
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1473'
abstract:
- lang: eng
text: In this paper we survey geometric and arithmetic techniques to study the cohomology
of semiprojective hyperkähler manifolds including toric hyperkähler varieties,
Nakajima quiver varieties and moduli spaces of Higgs bundles on Riemann surfaces.
The resulting formulae for their Poincaré polynomials are combinatorial and representation
theoretical in nature. In particular we will look at their Betti numbers and will
establish some results and state some expectations on their asymptotic shape.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Fernando
full_name: Rodríguez Villegas, Fernando
last_name: Rodríguez Villegas
citation:
ama: Hausel T, Rodríguez Villegas F. Cohomology of large semiprojective hyperkähler
varieties. Asterisque. 2015;2015(370):113-156.
apa: Hausel, T., & Rodríguez Villegas, F. (2015). Cohomology of large semiprojective
hyperkähler varieties. Asterisque. Societe Mathematique de France.
chicago: Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective
Hyperkähler Varieties.” Asterisque. Societe Mathematique de France, 2015.
ieee: T. Hausel and F. Rodríguez Villegas, “Cohomology of large semiprojective hyperkähler
varieties,” Asterisque, vol. 2015, no. 370. Societe Mathematique de France,
pp. 113–156, 2015.
ista: Hausel T, Rodríguez Villegas F. 2015. Cohomology of large semiprojective hyperkähler
varieties. Asterisque. 2015(370), 113–156.
mla: Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective
Hyperkähler Varieties.” Asterisque, vol. 2015, no. 370, Societe Mathematique
de France, 2015, pp. 113–56.
short: T. Hausel, F. Rodríguez Villegas, Asterisque 2015 (2015) 113–156.
date_created: 2018-12-11T11:52:13Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:59Z
day: '01'
extern: 1
intvolume: ' 2015'
issue: '370'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1309.4914
month: '01'
oa: 1
page: 113 - 156
publication: Asterisque
publication_status: published
publisher: Societe Mathematique de France
publist_id: '5723'
quality_controlled: 0
status: public
title: Cohomology of large semiprojective hyperkähler varieties
type: review
volume: 2015
year: '2015'
...
---
_id: '1483'
abstract:
- lang: eng
text: Topological data analysis offers a rich source of valuable information to
study vision problems. Yet, so far we lack a theoretically sound connection to
popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In
this work, we establish such a connection by designing a multi-scale kernel for
persistence diagrams, a stable summary representation of topological features
in data. We show that this kernel is positive definite and prove its stability
with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets
for 3D shape classification/retrieval and texture recognition show considerable
performance gains of the proposed method compared to an alternative approach that
is based on the recently introduced persistence landscapes.
author:
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
citation:
ama: 'Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for
topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106'
apa: 'Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale
kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR:
Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106'
chicago: Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable
Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106.
ieee: 'J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel
for topological machine learning,” presented at the CVPR: Computer Vision and
Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.'
ista: 'Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel
for topological machine learning. CVPR: Computer Vision and Pattern Recognition,
4741–4748.'
mla: Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine
Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106.
short: J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.
conference:
end_date: 2015-06-12
location: Boston, MA, USA
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2015-06-07
date_created: 2018-12-11T11:52:17Z
date_published: 2015-10-14T00:00:00Z
date_updated: 2021-01-12T06:51:03Z
day: '14'
department:
- _id: HeEd
doi: 10.1109/CVPR.2015.7299106
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1412.6821
month: '10'
oa: 1
oa_version: Preprint
page: 4741 - 4748
publication_identifier:
eisbn:
- '978-1-4673-6964-0 '
publication_status: published
publisher: IEEE
publist_id: '5709'
scopus_import: 1
status: public
title: A stable multi-scale kernel for topological machine learning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1498'
abstract:
- lang: eng
text: Fault-tolerant distributed algorithms play an important role in many critical/high-availability
applications. These algorithms are notoriously difficult to implement correctly,
due to asynchronous communication and the occurrence of faults, such as the network
dropping messages or computers crashing. Nonetheless there is surprisingly little
language and verification support to build distributed systems based on fault-tolerant
algorithms. In this paper, we present some of the challenges that a designer has
to overcome to implement a fault-tolerant distributed system. Then we review different
models that have been proposed to reason about distributed algorithms and sketch
how such a model can form the basis for a domain-specific programming language.
Adopting a high-level programming model can simplify the programmer's life and
make the code amenable to automated verification, while still compiling to efficiently
executable code. We conclude by summarizing the current status of an ongoing language
design and implementation project that is based on this idea.
alternative_title:
- LIPIcs
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- 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: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant
distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90
apa: 'Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language
support for fault-tolerant distributed systems. Presented at the SNAPL: Summit
oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90'
chicago: Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for
Language Support for Fault-Tolerant Distributed Systems.” Leibniz International
Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90.
ieee: C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support
for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, pp. 90–102, 2015.
ista: Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for
fault-tolerant distributed systems. 32, 90–102.
mla: Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant
Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90.
short: C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.
conference:
end_date: 2015-05-06
location: Asilomar, CA, United States
name: 'SNAPL: Summit oN Advances in Programming Languages'
start_date: 2015-05-03
date_created: 2018-12-11T11:52:22Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2020-08-11T10:09:14Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.SNAPL.2015.90
ec_funded: 1
file:
- access_level: open_access
checksum: cf5e94baa89a2dc4c5de01abc676eda8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:02Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5050'
file_name: IST-2016-499-v1+1_9.pdf
file_size: 489362
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 32'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 90 - 102
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
isbn:
- '978-3-939897-80-4 '
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5681'
pubrep_id: '499'
quality_controlled: '1'
scopus_import: 1
series_title: Leibniz International Proceedings in Informatics
status: public
title: The need for language support for fault-tolerant distributed systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2015'
...
---
_id: '1497'
abstract:
- lang: eng
text: Detecting allelic biases from high-throughput sequencing data requires an
approach that maximises sensitivity while minimizing false positives. Here, we
present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which
uses high-throughput sequencing data from reciprocal crosses of two genetically
distinct mouse strains to detect allele-specific expression and chromatin modifications.
Allelome.PRO extends approaches used in previous studies that exclusively analyzed
imprinted expression to give a complete picture of the ‘allelome’ by automatically
categorising the allelic expression of all genes in a given cell type into imprinted,
strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity
to analyze lowly expressed transcripts, together with a robust false discovery
rate empirically calculated from variation in the sequencing data. We used RNA-seq
data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine
a biologically relevant allelic ratio cutoff, and define for the first time an
entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment
of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This
approach can be easily extended to analyze histone marks of active enhancers,
or transcription factor binding sites and therefore provides a powerful tool to
identify candidate cis regulatory elements genome wide.
acknowledgement: "Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09].
Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser
for advice during the early stages of this project. High-throughput sequencing was
conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna."
article_number: e146
author:
- first_name: Daniel
full_name: Andergassen, Daniel
last_name: Andergassen
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
- first_name: Tomasz
full_name: Kulinski, Tomasz
last_name: Kulinski
- first_name: Philipp
full_name: Guenzl, Philipp
last_name: Guenzl
- first_name: Philipp
full_name: Bammer, Philipp
last_name: Bammer
- first_name: Denise
full_name: Barlow, Denise
last_name: Barlow
- first_name: Florian
full_name: Pauler, Florian
last_name: Pauler
- first_name: Quanah
full_name: Hudson, Quanah
last_name: Hudson
citation:
ama: Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define
allele-specific genomic features from high-throughput sequencing data. Nucleic
Acids Research. 2015;43(21). doi:10.1093/nar/gkv727
apa: Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow,
D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic
features from high-throughput sequencing data. Nucleic Acids Research.
Oxford University Press. https://doi.org/10.1093/nar/gkv727
chicago: Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl,
Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO,
a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing
Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727.
ieee: D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific
genomic features from high-throughput sequencing data,” Nucleic Acids Research,
vol. 43, no. 21. Oxford University Press, 2015.
ista: Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler
F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic
features from high-throughput sequencing data. Nucleic Acids Research. 43(21),
e146.
mla: Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific
Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research,
vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727.
short: D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow,
F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).
date_created: 2018-12-11T11:52:22Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '21'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1093/nar/gkv727
file:
- access_level: open_access
checksum: 385b83854fd0eb2e4f386867da2823e2
content_type: application/pdf
creator: dernst
date_created: 2018-12-20T14:18:57Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5768'
file_name: 2015_NucleicAcidsRes_Andergassen.pdf
file_size: 6863297
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 43'
issue: '21'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '5682'
quality_controlled: '1'
scopus_import: 1
status: public
title: Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput
sequencing data
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: 43
year: '2015'
...
---
_id: '1499'
abstract:
- lang: eng
text: "We consider weighted automata with both positive and negative integer weights
on edges and\r\nstudy the problem of synchronization using adaptive strategies
that may only observe whether\r\nthe current weight-level is negative or nonnegative.
We show that the synchronization problem is decidable in polynomial time for deterministic
weighted automata."
acknowledgement: "The research leading to these results has received funding from
the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement
601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center
IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM),
the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein
Award), the Czech Science Foundation under grant agreement P202/12/G061, and People
Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme
(FP7/2007-2013) REA Grant No 291734."
alternative_title:
- LIPIcs
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Kim
full_name: Larsen, Kim
last_name: Larsen
- first_name: Simon
full_name: Laursen, Simon
last_name: Laursen
- first_name: Jiří
full_name: Srba, Jiří
last_name: Srba
citation:
ama: 'Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of
weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142'
apa: 'Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial
time decidability of weighted synchronization under partial observability (Vol.
42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142'
chicago: Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time
Decidability of Weighted Synchronization under Partial Observability,” 42:142–54.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142.
ieee: 'J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability
of weighted synchronization under partial observability,” presented at the CONCUR:
Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.'
ista: 'Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability
of weighted synchronization under partial observability. CONCUR: Concurrency Theory,
LIPIcs, vol. 42, 142–154.'
mla: Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization
under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142.
short: J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2015, pp. 142–154.
conference:
end_date: 2015-09-04
location: Madrid, Spain
name: 'CONCUR: Concurrency Theory'
start_date: 2015-09-01
date_created: 2018-12-11T11:52:22Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:10Z
day: '01'
ddc:
- '000'
- '003'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPIcs.CONCUR.2015.142
ec_funded: 1
file:
- access_level: open_access
checksum: 49eb5021caafaabe5356c65b9c5f8c9c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:12Z
date_updated: 2020-07-14T12:44:58Z
file_id: '4672'
file_name: IST-2016-498-v1+1_32.pdf
file_size: 623563
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 42'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 142 - 154
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5680'
pubrep_id: '498'
quality_controlled: '1'
scopus_import: 1
status: public
title: Polynomial time decidability of weighted synchronization under partial observability
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...
---
_id: '1495'
abstract:
- lang: eng
text: 'Motivated by biological questions, we study configurations of equal-sized
disks in the Euclidean plane that neither pack nor cover. Measuring the quality
by the probability that a random point lies in exactly one disk, we show that
the regular hexagonal grid gives the maximum among lattice configurations. '
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
- first_name: Vitaliy
full_name: Kurlin, Vitaliy
last_name: Kurlin
citation:
ama: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings
of the 27th Canadian Conference on Computational Geometry. Vol 2015-August.
Queen’s University; 2015:128-135.'
apa: 'Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk
packing. In Proceedings of the 27th Canadian Conference on Computational Geometry
(Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.'
chicago: Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed
Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational
Geometry, 2015–August:128–35. Queen’s University, 2015.
ieee: H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in
Proceedings of the 27th Canadian Conference on Computational Geometry,
Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.
ista: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings
of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference
on Computational Geometry vol. 2015–August, 128–135.'
mla: Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the
27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s
University, 2015, pp. 128–35.
short: H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th
Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.
conference:
end_date: 2015-08-12
location: Ontario, Canada
name: 'CCCG: Canadian Conference on Computational Geometry'
start_date: 2015-08-10
date_created: 2018-12-11T11:52:21Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '01'
department:
- _id: HeEd
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1505.03402
month: '08'
oa: 1
oa_version: Submitted Version
page: 128-135
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Proceedings of the 27th Canadian Conference on Computational Geometry
publication_status: published
publisher: Queen's University
publist_id: '5684'
quality_controlled: '1'
scopus_import: 1
status: public
title: Relaxed disk packing
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2015-August
year: '2015'
...
---
_id: '1504'
abstract:
- lang: eng
text: Let Q = (Q1, . . . , Qn) be a random vector drawn from the uniform distribution
on the set of all n! permutations of {1, 2, . . . , n}. Let Z = (Z1, . . . , Zn),
where Zj is the mean zero variance one random variable obtained by centralizing
and normalizing Qj , j = 1, . . . , n. Assume that Xi , i = 1, . . . ,p are i.i.d.
copies of 1/√ p Z and X = Xp,n is the p × n random matrix with Xi as its ith row.
Then Sn = XX is called the p × n Spearman's rank correlation matrix which can
be regarded as a high dimensional extension of the classical nonparametric statistic
Spearman's rank correlation coefficient between two independent random variables.
In this paper, we establish a CLT for the linear spectral statistics of this nonparametric
random matrix model in the scenario of high dimension, namely, p = p(n) and p/n→c
∈ (0,∞) as n→∞.We propose a novel evaluation scheme to estimate the core quantity
in Anderson and Zeitouni's cumulant method in [Ann. Statist. 36 (2008) 2553-2576]
to bypass the so-called joint cumulant summability. In addition, we raise a two-step
comparison approach to obtain the explicit formulae for the mean and covariance
functions in the CLT. Relying on this CLT, we then construct a distribution-free
statistic to test complete independence for components of random vectors. Owing
to the nonparametric property, we can use this test on generally distributed random
variables including the heavy-tailed ones.
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: Liang
full_name: Lin, Liang
last_name: Lin
- first_name: Guangming
full_name: Pan, Guangming
last_name: Pan
- first_name: Wang
full_name: Zhou, Wang
last_name: Zhou
citation:
ama: Bao Z, Lin L, Pan G, Zhou W. Spectral statistics of large dimensional spearman
s rank correlation matrix and its application. Annals of Statistics. 2015;43(6):2588-2623.
doi:10.1214/15-AOS1353
apa: Bao, Z., Lin, L., Pan, G., & Zhou, W. (2015). Spectral statistics of large
dimensional spearman s rank correlation matrix and its application. Annals
of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AOS1353
chicago: Bao, Zhigang, Liang Lin, Guangming Pan, and Wang Zhou. “Spectral Statistics
of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.”
Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/15-AOS1353.
ieee: Z. Bao, L. Lin, G. Pan, and W. Zhou, “Spectral statistics of large dimensional
spearman s rank correlation matrix and its application,” Annals of Statistics,
vol. 43, no. 6. Institute of Mathematical Statistics, pp. 2588–2623, 2015.
ista: Bao Z, Lin L, Pan G, Zhou W. 2015. Spectral statistics of large dimensional
spearman s rank correlation matrix and its application. Annals of Statistics.
43(6), 2588–2623.
mla: Bao, Zhigang, et al. “Spectral Statistics of Large Dimensional Spearman s Rank
Correlation Matrix and Its Application.” Annals of Statistics, vol. 43,
no. 6, Institute of Mathematical Statistics, 2015, pp. 2588–623, doi:10.1214/15-AOS1353.
short: Z. Bao, L. Lin, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 2588–2623.
date_created: 2018-12-11T11:52:24Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:14Z
day: '01'
doi: 10.1214/15-AOS1353
extern: '1'
intvolume: ' 43'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.5119
month: '12'
oa: 1
oa_version: Published Version
page: 2588 - 2623
publication: Annals of Statistics
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5674'
quality_controlled: '1'
status: public
title: Spectral statistics of large dimensional spearman s rank correlation matrix
and its application
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '1503'
abstract:
- lang: eng
text: A Herman-Avila-Bochi type formula is obtained for the average sum of the top
d Lyapunov exponents over a one-parameter family of double-struck G-cocycles,
where double-struck G is the group that leaves a certain, non-degenerate Hermitian
form of signature (c, d) invariant. The generic example of such a group is the
pseudo-unitary group U(c, d) or, in the case c = d, the Hermitian-symplectic group
HSp(2d) which naturally appears for cocycles related to Schrödinger operators.
In the case d = 1, the formula for HSp(2d) cocycles reduces to the Herman-Avila-Bochi
formula for SL(2, ℝ) cocycles.
author:
- first_name: Christian
full_name: Sadel, Christian
id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
last_name: Sadel
orcid: 0000-0001-8255-3968
citation:
ama: Sadel C. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary
and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems.
2015;35(5):1582-1591. doi:10.1017/etds.2013.103
apa: Sadel, C. (2015). A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary
and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems.
Cambridge University Press. https://doi.org/10.1017/etds.2013.103
chicago: Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional
Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical
Systems. Cambridge University Press, 2015. https://doi.org/10.1017/etds.2013.103.
ieee: C. Sadel, “A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary
and Hermitian-symplectic-cocycles,” Ergodic Theory and Dynamical Systems,
vol. 35, no. 5. Cambridge University Press, pp. 1582–1591, 2015.
ista: Sadel C. 2015. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary
and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 35(5),
1582–1591.
mla: Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary
and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems,
vol. 35, no. 5, Cambridge University Press, 2015, pp. 1582–91, doi:10.1017/etds.2013.103.
short: C. Sadel, Ergodic Theory and Dynamical Systems 35 (2015) 1582–1591.
date_created: 2018-12-11T11:52:24Z
date_published: 2015-03-14T00:00:00Z
date_updated: 2021-01-12T06:51:13Z
day: '14'
doi: 10.1017/etds.2013.103
extern: '1'
intvolume: ' 35'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1307.8414
month: '03'
oa: 1
oa_version: Preprint
page: 1582 - 1591
publication: Ergodic Theory and Dynamical Systems
publication_status: published
publisher: Cambridge University Press
publist_id: '5675'
quality_controlled: '1'
status: public
title: A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2015'
...
---
_id: '1510'
abstract:
- lang: eng
text: 'The concept of well group in a special but important case captures homological
properties of the zero set of a continuous map f from K to R^n on a compact space
K that are invariant with respect to perturbations of f. The perturbations are
arbitrary continuous maps within L_infty distance r from f for a given r >
0. The main drawback of the approach is that the computability of well groups
was shown only when dim K = n or n = 1. Our contribution to the theory of well
groups is twofold: on the one hand we improve on the computability issue, but
on the other hand we present a range of examples where the well groups are incomplete
invariants, that is, fail to capture certain important robust properties of the
zero set. For the first part, we identify a computable subgroup of the well group
that is obtained by cap product with the pullback of the orientation of R^n by
f. In other words, well groups can be algorithmically approximated from below.
When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well
group is exact. For the second part, we find examples of maps f, f'' from K to
R^n with all well groups isomorphic but whose perturbations have different zero
sets. We discuss on a possible replacement of the well groups of vector valued
maps by an invariant of a better descriptive power and computability status. '
alternative_title:
- LIPIcs
author:
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
citation:
ama: 'Franek P, Krcál M. On computability and triviality of well groups. In: Vol
34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:10.4230/LIPIcs.SOCG.2015.842'
apa: 'Franek, P., & Krcál, M. (2015). On computability and triviality of well
groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational
Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.SOCG.2015.842'
chicago: Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well
Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.842.
ieee: 'P. Franek and M. Krcál, “On computability and triviality of well groups,”
presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands,
2015, vol. 34, pp. 842–856.'
ista: 'Franek P, Krcál M. 2015. On computability and triviality of well groups.
SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.'
mla: Franek, Peter, and Marek Krcál. On Computability and Triviality of Well
Groups. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015,
pp. 842–56, doi:10.4230/LIPIcs.SOCG.2015.842.
short: P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015, pp. 842–856.
conference:
end_date: 2015-06-25
location: Eindhoven, Netherlands
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2015-06-22
date_created: 2018-12-11T11:52:26Z
date_published: 2015-06-11T00:00:00Z
date_updated: 2023-02-21T17:02:57Z
day: '11'
ddc:
- '510'
department:
- _id: UlWa
- _id: HeEd
doi: 10.4230/LIPIcs.SOCG.2015.842
ec_funded: 1
file:
- access_level: open_access
checksum: 49eb5021caafaabe5356c65b9c5f8c9c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:19Z
date_updated: 2020-07-14T12:44:59Z
file_id: '5001'
file_name: IST-2016-503-v1+1_32.pdf
file_size: 623563
relation: main_file
file_date_updated: 2020-07-14T12:44:59Z
has_accepted_license: '1'
intvolume: ' 34'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 842 - 856
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5667'
pubrep_id: '503'
quality_controlled: '1'
related_material:
record:
- id: '1408'
relation: later_version
status: public
scopus_import: 1
status: public
title: On computability and triviality of well groups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1505'
abstract:
- lang: eng
text: This paper is aimed at deriving the universality of the largest eigenvalue
of a class of high-dimensional real or complex sample covariance matrices of the
form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent
entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality,
we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic
positive-definite M × M matrices Σ , under some additional assumptions on the
distribution of xij 's, we show that the limiting behavior of the largest eigenvalue
of W N is universal, via pursuing a Green function comparison strategy raised
in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515]
by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann.
Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case
(&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing
this universality property and the results known for Gaussian matrices obtained
by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski
in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after
an appropriate normalization the largest eigenvalue of W N converges weakly to
the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show
that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom
limit TW1 holds for the normalized largest eigenvalue of W N , which extends a
result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario
of nondiagonal Σ and more generally distributed X . In summary, we establish the
Tracy-Widom type universality for the largest eigenvalue of generally distributed
sample covariance matrices under quite light assumptions on &Sigma . Applications
of these limiting results to statistical signal detection and structure recognition
of separable covariance matrices are also discussed.
acknowledgement: "B.Z. was supported in part by NSFC Grant 11071213, ZJNSF
\ Grant R6090034 and SRFDP Grant 20100101110001. P.G. was supported in part
by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported
\ in part by the Ministry of Education, Singapore, under Grant ARC 14/11,
\ and by a Grant R-155-000-131-112 at the National University of Singapore\r\n"
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: Guangming
full_name: Pan, Guangming
last_name: Pan
- first_name: Wang
full_name: Zhou, Wang
last_name: Zhou
citation:
ama: Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance
matrices with general population. Annals of Statistics. 2015;43(1):382-421.
doi:10.1214/14-AOS1281
apa: Bao, Z., Pan, G., & Zhou, W. (2015). Universality for the largest eigenvalue
of sample covariance matrices with general population. Annals of Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/14-AOS1281
chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest
Eigenvalue of Sample Covariance Matrices with General Population.” Annals of
Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/14-AOS1281.
ieee: Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample
covariance matrices with general population,” Annals of Statistics, vol.
43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.
ista: Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample
covariance matrices with general population. Annals of Statistics. 43(1), 382–421.
mla: Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance
Matrices with General Population.” Annals of Statistics, vol. 43, no. 1,
Institute of Mathematical Statistics, 2015, pp. 382–421, doi:10.1214/14-AOS1281.
short: Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.
date_created: 2018-12-11T11:52:25Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:51:14Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/14-AOS1281
intvolume: ' 43'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1304.5690
month: '02'
oa: 1
oa_version: Preprint
page: 382 - 421
publication: Annals of Statistics
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5672'
quality_controlled: '1'
status: public
title: Universality for the largest eigenvalue of sample covariance matrices with
general population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '1508'
abstract:
- lang: eng
text: We consider generalized Wigner ensembles and general β-ensembles with analytic
potentials for any β ≥ 1. The recent universality results in particular assert
that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum
are universal in the sense that they coincide with those of the corresponding
Gaussian β-ensembles. In this article, we show that local averaging is not necessary
for this result, i.e. we prove that the single gap distributions in the bulk are
universal. In fact, with an additional step, our result can be extended to any
C4(ℝ) potential.
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
citation:
ama: Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. Journal
of the European Mathematical Society. 2015;17(8):1927-2036. doi:10.4171/JEMS/548
apa: Erdös, L., & Yau, H. (2015). Gap universality of generalized Wigner and
β ensembles. Journal of the European Mathematical Society. European Mathematical
Society. https://doi.org/10.4171/JEMS/548
chicago: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and
β Ensembles.” Journal of the European Mathematical Society. European Mathematical
Society, 2015. https://doi.org/10.4171/JEMS/548.
ieee: L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,”
Journal of the European Mathematical Society, vol. 17, no. 8. European
Mathematical Society, pp. 1927–2036, 2015.
ista: Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles.
Journal of the European Mathematical Society. 17(8), 1927–2036.
mla: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β
Ensembles.” Journal of the European Mathematical Society, vol. 17, no.
8, European Mathematical Society, 2015, pp. 1927–2036, doi:10.4171/JEMS/548.
short: L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015)
1927–2036.
date_created: 2018-12-11T11:52:26Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:15Z
day: '01'
department:
- _id: LaEr
doi: 10.4171/JEMS/548
intvolume: ' 17'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1211.3786
month: '08'
oa: 1
oa_version: Preprint
page: 1927 - 2036
publication: Journal of the European Mathematical Society
publication_status: published
publisher: European Mathematical Society
publist_id: '5669'
quality_controlled: '1'
scopus_import: 1
status: public
title: Gap universality of generalized Wigner and β ensembles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2015'
...
---
_id: '1506'
abstract:
- lang: eng
text: Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i,
j = 1, . . . , n} is a collection of independent real random variables with means
zero and variances one. Under the additional moment condition supn max1≤i,j ≤n
Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞
log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: Guangming
full_name: Pan, Guangming
last_name: Pan
- first_name: Wang
full_name: Zhou, Wang
last_name: Zhou
citation:
ama: Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. Bernoulli.
2015;21(3):1600-1628. doi:10.3150/14-BEJ615
apa: Bao, Z., Pan, G., & Zhou, W. (2015). The logarithmic law of random determinant.
Bernoulli. Bernoulli Society for Mathematical Statistics and Probability.
https://doi.org/10.3150/14-BEJ615
chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random
Determinant.” Bernoulli. Bernoulli Society for Mathematical Statistics
and Probability, 2015. https://doi.org/10.3150/14-BEJ615.
ieee: Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,”
Bernoulli, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics
and Probability, pp. 1600–1628, 2015.
ista: Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli.
21(3), 1600–1628.
mla: Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” Bernoulli,
vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability,
2015, pp. 1600–28, doi:10.3150/14-BEJ615.
short: Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.
date_created: 2018-12-11T11:52:25Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:14Z
day: '01'
department:
- _id: LaEr
doi: 10.3150/14-BEJ615
intvolume: ' 21'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1208.5823
month: '08'
oa: 1
oa_version: Preprint
page: 1600 - 1628
publication: Bernoulli
publication_status: published
publisher: Bernoulli Society for Mathematical Statistics and Probability
publist_id: '5671'
quality_controlled: '1'
status: public
title: The logarithmic law of random determinant
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2015'
...
---
_id: '1513'
abstract:
- lang: eng
text: "Insects of the order Hemiptera (true bugs) use a wide range of mechanisms
of sex determination, including genetic sex determination, paternal genome elimination,
and haplodiploidy. Genetic sex determination, the prevalent mode, is generally
controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different
configurations that include additional sex chromosomes are also present. Although
this diversity of sex determining systems has been extensively studied at the
cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon
pisum has been analyzed at the genomic level, and little is known about X chromosome
biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published
DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative
analysis of the gene content and expression of the X chromosome throughout this
clade. We find that, despite showing evidence of dosage compensation, the X chromosomes
of these species show female-biased expression, and a deficit of male-biased genes,
in direct contrast to the pea aphid X. We further detect an excess of shared gene
content between these very distant species, suggesting that despite the diversity
of sex determining systems, the same chromosomal element is used as the X throughout
a large portion of the order. "
article_processing_charge: No
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage
compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268.
doi:10.1093/gbe/evv215'
apa: 'Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects:
Conservation, dosage compensation and sex-biased expression. Genome Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215'
chicago: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects:
Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology
and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.'
ieee: 'A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression,” Genome Biology and Evolution,
vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.'
ista: 'Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12),
3259–3268.'
mla: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation,
Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution,
vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.'
short: A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.
date_created: 2018-12-11T11:52:27Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:18Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evv215
ec_funded: 1
file:
- access_level: open_access
checksum: 2b56b8c2e2a1d4cc3c9cb8daba26dd9b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:29Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5284'
file_name: IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf
file_size: 858027
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 3259 - 3268
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5664'
pubrep_id: '496'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The X chromosome of hemipteran insects: Conservation, dosage compensation
and sex-biased expression'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '1517'
abstract:
- lang: eng
text: "We study the large deviation rate functional for the empirical distribution
of independent Brownian particles with drift. In one dimension, it has been shown
by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent
(in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising
in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher
dimensions, part of this statement (the lower bound) has been recently proved
by Duong, Laschos and Renger, but the upper bound remained open, since the proof
of Duong et al relies on regularity properties of optimal transport maps that
are restricted to one dimension. In this note we present a new proof of the upper
bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n"
article_number: '89'
author:
- first_name: Matthias
full_name: Erbar, Matthias
last_name: Erbar
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Michiel
full_name: Renger, Michiel
last_name: Renger
citation:
ama: Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows
in multiple dimensions. Electronic Communications in Probability. 2015;20.
doi:10.1214/ECP.v20-4315
apa: Erbar, M., Maas, J., & Renger, M. (2015). From large deviations to Wasserstein
gradient flows in multiple dimensions. Electronic Communications in Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v20-4315
chicago: Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to
Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications
in Probability. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/ECP.v20-4315.
ieee: M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient
flows in multiple dimensions,” Electronic Communications in Probability,
vol. 20. Institute of Mathematical Statistics, 2015.
ista: Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient
flows in multiple dimensions. Electronic Communications in Probability. 20, 89.
mla: Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows
in Multiple Dimensions.” Electronic Communications in Probability, vol.
20, 89, Institute of Mathematical Statistics, 2015, doi:10.1214/ECP.v20-4315.
short: M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20
(2015).
date_created: 2018-12-11T11:52:29Z
date_published: 2015-11-29T00:00:00Z
date_updated: 2021-01-12T06:51:19Z
day: '29'
ddc:
- '519'
department:
- _id: JaMa
doi: 10.1214/ECP.v20-4315
file:
- access_level: open_access
checksum: 135741c17d3e1547ca696b6fbdcd559c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:39Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4828'
file_name: IST-2016-494-v1+1_4315-23820-1-PB.pdf
file_size: 230525
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 20'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Electronic Communications in Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5660'
pubrep_id: '494'
quality_controlled: '1'
scopus_import: 1
status: public
title: From large deviations to Wasserstein gradient flows in multiple dimensions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2015'
...
---
_id: '1519'
abstract:
- lang: eng
text: Evolutionary biologists have an array of powerful theoretical techniques that
can accurately predict changes in the genetic composition of populations. Changes
in gene frequencies and genetic associations between loci can be tracked as they
respond to a wide variety of evolutionary forces. However, it is often less clear
how to decompose these various forces into components that accurately reflect
the underlying biology. Here, we present several issues that arise in the definition
and interpretation of selection and selection coefficients, focusing on insights
gained through the examination of selection coefficients in multilocus notation.
Using this notation, we discuss how its flexibility-which allows different biological
units to be identified as targets of selection-is reflected in the interpretation
of the coefficients that the notation generates. In many situations, it can be
difficult to agree on whether loci can be considered to be under "direct"
versus "indirect" selection, or to quantify this selection. We present
arguments for what the terms direct and indirect selection might best encompass,
considering a range of issues, from viability and sexual selection to kin selection.
We show how multilocus notation can discriminate between direct and indirect selection,
and describe when it can do so.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Maria
full_name: Servedio, Maria
last_name: Servedio
citation:
ama: Barton NH, Servedio M. The interpretation of selection coefficients. Evolution.
2015;69(5):1101-1112. doi:10.1111/evo.12641
apa: Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients.
Evolution. Wiley. https://doi.org/10.1111/evo.12641
chicago: Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection
Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.
ieee: N. H. Barton and M. Servedio, “The interpretation of selection coefficients,”
Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.
ista: Barton NH, Servedio M. 2015. The interpretation of selection coefficients.
Evolution. 69(5), 1101–1112.
mla: Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.”
Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.
short: N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.
date_created: 2018-12-11T11:52:29Z
date_published: 2015-03-19T00:00:00Z
date_updated: 2021-01-12T06:51:20Z
day: '19'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.12641
ec_funded: 1
file:
- access_level: open_access
checksum: fd8d23f476bc194419929b72ca265c02
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:34Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4822'
file_name: IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf
file_size: 188872
relation: main_file
- access_level: open_access
checksum: b774911e70044641d556e258efcb52ef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:35Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4823'
file_name: IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf
file_size: 577415
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 69'
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1101 - 1112
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_status: published
publisher: Wiley
publist_id: '5656'
pubrep_id: '560'
quality_controlled: '1'
scopus_import: 1
status: public
title: The interpretation of selection coefficients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2015'
...
---
_id: '1525'
abstract:
- lang: eng
text: 'Based on 16 recommendations, efforts should be made to achieve the following
goal: By 2025, all scholarly publication activity in Austria should be Open Access.
In other words, the final versions of all scholarly publications resulting from
the support of public resources must be freely accessible on the Internet without
delay (Gold Open Access). The resources required to meet this obligation shall
be provided to the authors, or the cost of the publication venues shall be borne
directly by the research organisations.'
article_processing_charge: No
article_type: original
author:
- first_name: Bruno
full_name: Bauer, Bruno
last_name: Bauer
- first_name: Guido
full_name: Blechl, Guido
last_name: Blechl
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Andreas
full_name: Ferus, Andreas
last_name: Ferus
- first_name: Anton
full_name: Graschopf, Anton
last_name: Graschopf
- first_name: Thomas
full_name: König, Thomas
last_name: König
- first_name: Katja
full_name: Mayer, Katja
last_name: Mayer
- first_name: Falk
full_name: Reckling, Falk
last_name: Reckling
- first_name: Katharina
full_name: Rieck, Katharina
last_name: Rieck
- first_name: Peter
full_name: Seitz, Peter
last_name: Seitz
- first_name: Herwig
full_name: Stöger, Herwig
last_name: Stöger
- first_name: Elvira
full_name: Welzig, Elvira
last_name: Welzig
citation:
ama: Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open
Access Network Austria OANA. VÖB Mitteilungen. 2015;68(3):580-607. doi:10.5281/zenodo.33178
apa: Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., …
Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network
Austria OANA. VÖB Mitteilungen. Verein Österreichischer Bibliothekare.
https://doi.org/10.5281/zenodo.33178
chicago: Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus,
Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des
Open Access Network Austria OANA.” VÖB Mitteilungen. Verein Österreichischer
Bibliothekare, 2015. https://doi.org/10.5281/zenodo.33178.
ieee: B. Bauer et al., “Arbeitsgruppe „Nationale Strategie“ des Open Access
Network Austria OANA,” VÖB Mitteilungen, vol. 68, no. 3. Verein Österreichischer
Bibliothekare, pp. 580–607, 2015.
ista: Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer
K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale
Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607.
mla: Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network
Austria OANA.” VÖB Mitteilungen, vol. 68, no. 3, Verein Österreichischer
Bibliothekare, 2015, pp. 580–607, doi:10.5281/zenodo.33178.
short: B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König,
K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen
68 (2015) 580–607.
date_created: 2018-12-11T11:52:31Z
date_published: 2015-11-12T00:00:00Z
date_updated: 2021-01-12T06:51:22Z
day: '12'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.5281/zenodo.33178
file:
- access_level: open_access
checksum: a495fe253bbc7615b1d60e9e85c94408
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:59Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5317'
file_name: IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf
file_size: 931707
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 68'
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 580 - 607
publication: VÖB Mitteilungen
publication_status: published
publisher: Verein Österreichischer Bibliothekare
publist_id: '5648'
pubrep_id: '720'
quality_controlled: '1'
scopus_import: 1
status: public
title: Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA
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: 68
year: '2015'
...
---
_id: '1539'
abstract:
- lang: eng
text: 'Many stochastic models of biochemical reaction networks contain some chemical
species for which the number of molecules that are present in the system can only
be finite (for instance due to conservation laws), but also other species that
can be present in arbitrarily large amounts. The prime example of such networks
are models of gene expression, which typically contain a small and finite number
of possible states for the promoter but an infinite number of possible states
for the amount of mRNA and protein. One of the main approaches to analyze such
models is through the use of equations for the time evolution of moments of the
chemical species. Recently, a new approach based on conditional moments of the
species with infinite state space given all the different possible states of the
finite species has been proposed. It was argued that this approach allows one
to capture more details about the full underlying probability distribution with
a smaller number of equations. Here, I show that the result that less moments
provide more information can only stem from an unnecessarily complicated description
of the system in the classical formulation. The foundation of this argument will
be the derivation of moment equations that describe the complete probability distribution
over the finite state space but only low-order moments over the infinite state
space. I will show that the number of equations that is needed is always less
than what was previously claimed and always less than the number of conditional
moment equations up to the same order. To support these arguments, a symbolic
algorithm is provided that can be used to derive minimal systems of unconditional
moment equations for models with partially finite state space. '
article_number: '244103'
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: Ruess J. Minimal moment equations for stochastic models of biochemical reaction
networks with partially finite state space. Journal of Chemical Physics.
2015;143(24). doi:10.1063/1.4937937
apa: Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical
reaction networks with partially finite state space. Journal of Chemical Physics.
American Institute of Physics. https://doi.org/10.1063/1.4937937
chicago: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical
Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics.
American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937.
ieee: J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction
networks with partially finite state space,” Journal of Chemical Physics,
vol. 143, no. 24. American Institute of Physics, 2015.
ista: Ruess J. 2015. Minimal moment equations for stochastic models of biochemical
reaction networks with partially finite state space. Journal of Chemical Physics.
143(24), 244103.
mla: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical
Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics,
vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937.
short: J. Ruess, Journal of Chemical Physics 143 (2015).
date_created: 2018-12-11T11:52:36Z
date_published: 2015-12-22T00:00:00Z
date_updated: 2021-01-12T06:51:28Z
day: '22'
ddc:
- '000'
department:
- _id: ToHe
- _id: GaTk
doi: 10.1063/1.4937937
ec_funded: 1
file:
- access_level: open_access
checksum: 838657118ae286463a2b7737319f35ce
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:43Z
date_updated: 2020-07-14T12:45:01Z
file_id: '4641'
file_name: IST-2016-593-v1+1_Minimal_moment_equations.pdf
file_size: 605355
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 143'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Chemical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5632'
pubrep_id: '593'
quality_controlled: '1'
scopus_import: 1
status: public
title: Minimal moment equations for stochastic models of biochemical reaction networks
with partially finite state space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2015'
...
---
_id: '1534'
abstract:
- lang: eng
text: PIN proteins are auxin export carriers that direct intercellular auxin flow
and in turn regulate many aspects of plant growth and development including responses
to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS
(FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development,
as well as female reproductive development and stress responses. Here we show
that FLP and MYB88 act redundantly but differentially in regulating the transcription
of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the
one hand, FLP is involved in responses to gravity stimulation in primary roots,
whereas on the other, FLP and MYB88 function complementarily in establishing the
gravitropic set-point angles of lateral roots. Our results support a model in
which FLP and MYB88 expression specifically determines the temporal-spatial patterns
of PIN3 and PIN7 transcription that are closely associated with their preferential
functions during root responses to gravity.
article_number: '8822'
author:
- first_name: Hongzhe
full_name: Wang, Hongzhe
last_name: Wang
- first_name: Kezhen
full_name: Yang, Kezhen
last_name: Yang
- first_name: Junjie
full_name: Zou, Junjie
last_name: Zou
- first_name: Lingling
full_name: Zhu, Lingling
last_name: Zhu
- first_name: Zidian
full_name: Xie, Zidian
last_name: Xie
- first_name: Miyoterao
full_name: Morita, Miyoterao
last_name: Morita
- first_name: Masao
full_name: Tasaka, Masao
last_name: Tasaka
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Erich
full_name: Grotewold, Erich
last_name: Grotewold
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Fred
full_name: Sack, Fred
last_name: Sack
- first_name: Jie
full_name: Le, Jie
last_name: Le
citation:
ama: Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR
LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications.
2015;6. doi:10.1038/ncomms9822
apa: Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015).
Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis
root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822
chicago: Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao
Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR
LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications.
Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822.
ieee: H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS
and MYB88 during Arabidopsis root gravitropism,” Nature Communications,
vol. 6. Nature Publishing Group, 2015.
ista: Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold
E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN
genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications.
6, 8822.
mla: Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS
and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications,
vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822.
short: H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml,
E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications
6 (2015).
date_created: 2018-12-11T11:52:34Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2021-01-12T06:51:26Z
day: '18'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1038/ncomms9822
ec_funded: 1
file:
- access_level: open_access
checksum: 3c06735fc7cd7e482ca830cbd26001bf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:07Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5259'
file_name: IST-2016-485-v1+1_ncomms9822.pdf
file_size: 1852268
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5637'
pubrep_id: '485'
quality_controlled: '1'
scopus_import: 1
status: public
title: Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis
root gravitropism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1538'
abstract:
- lang: eng
text: Systems biology rests on the idea that biological complexity can be better
unraveled through the interplay of modeling and experimentation. However, the
success of this approach depends critically on the informativeness of the chosen
experiments, which is usually unknown a priori. Here, we propose a systematic
scheme based on iterations of optimal experiment design, flow cytometry experiments,
and Bayesian parameter inference to guide the discovery process in the case of
stochastic biochemical reaction networks. To illustrate the benefit of our methodology,
we apply it to the characterization of an engineered light-inducible gene expression
circuit in yeast and compare the performance of the resulting model with models
identified from nonoptimal experiments. In particular, we compare the parameter
posterior distributions and the precision to which the outcome of future experiments
can be predicted. Moreover, we illustrate how the identified stochastic model
can be used to determine light induction patterns that make either the average
amount of protein or the variability in a population of cells follow a desired
profile. Our results show that optimal experiment design allows one to derive
models that are accurate enough to precisely predict and regulate the protein
expression in heterogeneous cell populations over extended periods of time.
acknowledgement: 'J.R., F.P., and J.L. acknowledge support from the European Commission
under the Network of Excellence HYCON2 (highly-complex and networked control systems)
and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People
Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme
FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges
support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). '
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Francesca
full_name: Parise, Francesca
last_name: Parise
- first_name: Andreas
full_name: Milias Argeitis, Andreas
last_name: Milias Argeitis
- first_name: Mustafa
full_name: Khammash, Mustafa
last_name: Khammash
- first_name: John
full_name: Lygeros, John
last_name: Lygeros
citation:
ama: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment
design guides the characterization of a light-inducible gene expression circuit.
PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112
apa: Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J.
(2015). Iterative experiment design guides the characterization of a light-inducible
gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112
chicago: Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash,
and John Lygeros. “Iterative Experiment Design Guides the Characterization of
a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences,
2015. https://doi.org/10.1073/pnas.1423947112.
ieee: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative
experiment design guides the characterization of a light-inducible gene expression
circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153,
2015.
ista: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative
experiment design guides the characterization of a light-inducible gene expression
circuit. PNAS. 112(26), 8148–8153.
mla: Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization
of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26,
National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112.
short: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112
(2015) 8148–8153.
date_created: 2018-12-11T11:52:36Z
date_published: 2015-06-30T00:00:00Z
date_updated: 2021-01-12T06:51:27Z
day: '30'
department:
- _id: ToHe
- _id: GaTk
doi: 10.1073/pnas.1423947112
ec_funded: 1
external_id:
pmid:
- '26085136'
intvolume: ' 112'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/
month: '06'
oa: 1
oa_version: Submitted Version
page: 8148 - 8153
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5633'
quality_controlled: '1'
scopus_import: 1
status: public
title: Iterative experiment design guides the characterization of a light-inducible
gene expression circuit
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1535'
abstract:
- lang: eng
text: Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open
readily at relatively low membrane potentials and allow Ca2+ to enter the cells
near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential
waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation,
hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the
adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the
pacemaking current that sustains action potential (AP) firings and part of the
catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating
BK channels and drives the resting SK currents. These latter set the inter-spike
interval duration between consecutive spikes during spontaneous firing and the
rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a
primary role in the switch from “tonic” to “burst” firing that occurs in mouse
CCs when either the availability of voltage-gated Na channels (Nav) is reduced
or the β2 subunit featuring the fast inactivating BK channels is deleted. Here,
we discuss the functional role of these “neuronlike” firing modes in CCs and how
Cav1.3 contributes to them. The open issue is to understand how these novel firing
patterns are adapted to regulate the quantity of circulating catecholamines during
resting condition or in response to acute and chronic stress.
acknowledgement: This work was supported by the Italian MIUR (PRIN 2010/2011 project
2010JFYFY2) and the University of Torino.
article_processing_charge: No
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Andrea
full_name: Marcantoni, Andrea
last_name: Marcantoni
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
citation:
ama: Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like
firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology.
2015;8(2):149-161. doi:10.2174/1874467208666150507105443
apa: Vandael, D. H., Marcantoni, A., & Carbone, E. (2015). Cav1.3 channels as
key regulators of neuron-like firings and catecholamine release in chromaffin
cells. Current Molecular Pharmacology. Bentham Science Publishers. https://doi.org/10.2174/1874467208666150507105443
chicago: Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels
as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin
Cells.” Current Molecular Pharmacology. Bentham Science Publishers, 2015.
https://doi.org/10.2174/1874467208666150507105443.
ieee: D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators
of neuron-like firings and catecholamine release in chromaffin cells,” Current
Molecular Pharmacology, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161,
2015.
ista: Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators
of neuron-like firings and catecholamine release in chromaffin cells. Current
Molecular Pharmacology. 8(2), 149–161.
mla: Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like
Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology,
vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:10.2174/1874467208666150507105443.
short: D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8
(2015) 149–161.
date_created: 2018-12-11T11:52:35Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:51:26Z
day: '01'
department:
- _id: PeJo
doi: 10.2174/1874467208666150507105443
external_id:
pmid:
- '25966692'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/
month: '10'
oa: 1
oa_version: Submitted Version
page: 149 - 161
pmid: 1
publication: Current Molecular Pharmacology
publication_status: published
publisher: Bentham Science Publishers
publist_id: '5636'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cav1.3 channels as key regulators of neuron-like firings and catecholamine
release in chromaffin cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2015'
...
---
_id: '1542'
abstract:
- lang: eng
text: 'The theory of population genetics and evolutionary computation have been
evolving separately for nearly 30 years. Many results have been independently
obtained in both fields and many others are unique to its respective field. We
aim to bridge this gap by developing a unifying framework for evolutionary processes
that allows both evolutionary algorithms and population genetics models to be
cast in the same formal framework. The framework we present here decomposes the
evolutionary process into its several components in order to facilitate the identification
of similarities between different models. In particular, we propose a classification
of evolutionary operators based on the defining properties of the different components.
We cast several commonly used operators from both fields into this common framework.
Using this, we map different evolutionary and genetic algorithms to different
evolutionary regimes and identify candidates with the most potential for the translation
of results between the fields. This provides a unified description of evolutionary
processes and represents a stepping stone towards new tools and results to both
fields. '
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Golnaz
full_name: Badkobeh, Golnaz
last_name: Badkobeh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Doğan
full_name: Çörüş, Doğan
last_name: Çörüş
- first_name: Duccuong
full_name: Dang, Duccuong
last_name: Dang
- first_name: Tobias
full_name: Friedrich, Tobias
last_name: Friedrich
- first_name: Per
full_name: Lehre, Per
last_name: Lehre
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Andrew
full_name: Sutton, Andrew
last_name: Sutton
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary
processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
apa: Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T.,
… Trubenova, B. (2015). Toward a unifying framework for evolutionary processes.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011
chicago: Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong
Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova.
“Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical
Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.
ieee: T. Paixao et al., “Toward a unifying framework for evolutionary processes,”
Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.
ista: Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt
D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal
of Theoretical Biology. 383, 28–43.
mla: Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.”
Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.
short: T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P.
Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383
(2015) 28–43.
date_created: 2018-12-11T11:52:37Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2021-01-12T06:51:29Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1016/j.jtbi.2015.07.011
ec_funded: 1
file:
- access_level: open_access
checksum: 33b60ecfea60764756a9ee9df5eb65ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:53Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5244'
file_name: IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf
file_size: 595307
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 383'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 28 - 43
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: ' Journal of Theoretical Biology'
publication_status: published
publisher: Elsevier
publist_id: '5629'
pubrep_id: '483'
quality_controlled: '1'
scopus_import: 1
status: public
title: Toward a unifying framework for evolutionary processes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 383
year: '2015'
...
---
_id: '1546'
abstract:
- lang: eng
text: Synaptic efficacy and precision are influenced by the coupling of voltage-gated
Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their
proximity to vesicles is unknown, a quantitative understanding of the determinants
of vesicular release at nanometer scale is lacking. To investigate this, we combined
freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging,
and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day
7 and 21, VGCCs formed variable sized clusters and vesicular release became less
sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally
constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular
release are located at the perimeter of VGCC clusters (<30nm) and predict that
VGCC number per cluster determines vesicular release probability without altering
release time course. This "perimeter release model" provides a unifying
framework accounting for developmental changes in both synaptic efficacy and time
course.
acknowledgement: This work was supported by the Core Research for Evolutional Science
and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.;
by the funding provided by Okinawa Institute of Science and Technology (OIST) to
T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the
Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture,
Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la
Recherche Scientifique through the Actions Thematiques et Initatives sur Programme,
Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche
sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01)
to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063)
to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413)
and Principal (095667) Research Fellowship and an ERC advance grant (294667) to
RAS.
author:
- first_name: Yukihiro
full_name: Nakamura, Yukihiro
last_name: Nakamura
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Naomi
full_name: Kamasawa, Naomi
last_name: Kamasawa
- first_name: Ko
full_name: Matsui, Ko
last_name: Matsui
- first_name: Jason
full_name: Rothman, Jason
last_name: Rothman
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: R Angus
full_name: Silver, R Angus
last_name: Silver
- first_name: David
full_name: Digregorio, David
last_name: Digregorio
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic
Ca2+ channels and its impact on vesicular release during development. Neuron.
2015;85(1):145-158. doi:10.1016/j.neuron.2014.11.019
apa: Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto,
R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels
and its impact on vesicular release during development. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2014.11.019
chicago: Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman,
Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale
Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release
during Development.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2014.11.019.
ieee: Y. Nakamura et al., “Nanoscale distribution of presynaptic Ca2+ channels
and its impact on vesicular release during development,” Neuron, vol. 85,
no. 1. Elsevier, pp. 145–158, 2015.
ista: Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver
RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+
channels and its impact on vesicular release during development. Neuron. 85(1),
145–158.
mla: Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels
and Its Impact on Vesicular Release during Development.” Neuron, vol. 85,
no. 1, Elsevier, 2015, pp. 145–58, doi:10.1016/j.neuron.2014.11.019.
short: Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto,
R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-01-07T00:00:00Z
date_updated: 2021-01-12T06:51:31Z
day: '07'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1016/j.neuron.2014.11.019
file:
- access_level: open_access
checksum: 725f4d5be2dbb44b283ce722645ef37d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:47Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5170'
file_name: IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf
file_size: 3080111
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 85'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 145 - 158
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5625'
pubrep_id: '482'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular
release during 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: 85
year: '2015'
...
---
_id: '1544'
abstract:
- lang: eng
text: 'Cell division in prokaryotes and eukaryotes is commonly initiated by the
well-controlled binding of proteins to the cytoplasmic side of the cell membrane.
However, a precise characterization of the spatiotemporal dynamics of membrane-bound
proteins is often difficult to achieve in vivo. Here, we present protocols for
the use of supported lipid bilayers to rebuild the cytokinetic machineries of
cells with greatly different dimensions: the bacterium Escherichia coli and eggs
of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence
microscopy, these experimental setups allow for precise quantitative analyses
of membrane-bound proteins. The protocols described to obtain glass-supported
membranes from bacterial and vertebrate lipids can be used as starting points
for other reconstitution experiments. We believe that similar biochemical assays
will be instrumental to study the biochemistry and biophysics underlying a variety
of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.'
author:
- first_name: Phuong
full_name: Nguyen, Phuong
last_name: Nguyen
- first_name: Christine
full_name: Field, Christine
last_name: Field
- first_name: Aaron
full_name: Groen, Aaron
last_name: Groen
- first_name: Timothy
full_name: Mitchison, Timothy
last_name: Mitchison
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers
to study the spatiotemporal organization of membrane-bound proteins. In: Building
a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007'
apa: Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using
supported bilayers to study the spatiotemporal organization of membrane-bound
proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241).
Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007
chicago: Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin
Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound
Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic
Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007.
ieee: P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported
bilayers to study the spatiotemporal organization of membrane-bound proteins,”
in Building a Cell from its Components Parts, vol. 128, Academic Press,
2015, pp. 223–241.
ista: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers
to study the spatiotemporal organization of membrane-bound proteins. In: Building
a Cell from its Components Parts. vol. 128, 223–241.'
mla: Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal
Organization of Membrane-Bound Proteins.” Building a Cell from Its Components
Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007.
short: P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell
from Its Components Parts, Academic Press, 2015, pp. 223–241.
date_created: 2018-12-11T11:52:38Z
date_published: 2015-04-08T00:00:00Z
date_updated: 2021-01-12T06:51:30Z
day: '08'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2015.01.007
external_id:
pmid:
- '25997350'
intvolume: ' 128'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/
month: '04'
oa: 1
oa_version: Submitted Version
page: 223 - 241
pmid: 1
publication: Building a Cell from its Components Parts
publication_status: published
publisher: Academic Press
publist_id: '5627'
quality_controlled: '1'
scopus_import: 1
status: public
title: Using supported bilayers to study the spatiotemporal organization of membrane-bound
proteins
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2015'
...
---
_id: '1551'
abstract:
- lang: eng
text: 'Reciprocal coevolution between host and pathogen is widely seen as a major
driver of evolution and biological innovation. Yet, to date, the underlying genetic
mechanisms and associated trait functions that are unique to rapid coevolutionary
change are generally unknown. We here combined experimental evolution of the bacterial
biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans
with large-scale phenotyping, whole genome analysis, and functional genetics to
demonstrate the selective benefit of pathogen virulence and the underlying toxin
genes during the adaptation process. We show that: (i) high virulence was specifically
favoured during pathogen–host coevolution rather than pathogen one-sided adaptation
to a nonchanging host or to an environment without host; (ii) the pathogen genotype
BT-679 with known nematocidal toxin genes and high virulence specifically swept
to fixation in all of the independent replicate populations under coevolution
but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated
populations correlated with elevated copy numbers of the plasmid containing the
nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679
isolate was reconstituted by genetic reintroduction or external addition of the
toxins.We conclude that sustained coevolution is distinct from unidirectional
selection in shaping the pathogen''s genome and life history characteristics.
To our knowledge, this study is the first to characterize the pathogen genes involved
in coevolutionary adaptation in an animal host–pathogen interaction system.'
acknowledgement: We are very grateful for funding from the German Science Foundation
(DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI
1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence
Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program
(Co-fund Marie Curie Actions of the European Commission) to LM.
author:
- first_name: Leila
full_name: El Masri, Leila
id: 349A6E66-F248-11E8-B48F-1D18A9856A87
last_name: El Masri
- first_name: Antoine
full_name: Branca, Antoine
last_name: Branca
- first_name: Anna
full_name: Sheppard, Anna
last_name: Sheppard
- first_name: Andrei
full_name: Papkou, Andrei
last_name: Papkou
- first_name: David
full_name: Laehnemann, David
last_name: Laehnemann
- first_name: Patrick
full_name: Guenther, Patrick
last_name: Guenther
- first_name: Swantje
full_name: Prahl, Swantje
last_name: Prahl
- first_name: Manja
full_name: Saebelfeld, Manja
last_name: Saebelfeld
- first_name: Jacqueline
full_name: Hollensteiner, Jacqueline
last_name: Hollensteiner
- first_name: Heiko
full_name: Liesegang, Heiko
last_name: Liesegang
- first_name: Elzbieta
full_name: Brzuszkiewicz, Elzbieta
last_name: Brzuszkiewicz
- first_name: Rolf
full_name: Daniel, Rolf
last_name: Daniel
- first_name: Nico
full_name: Michiels, Nico
last_name: Michiels
- first_name: Rebecca
full_name: Schulte, Rebecca
last_name: Schulte
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Arndt
full_name: Telschow, Arndt
last_name: Telschow
- first_name: Erich
full_name: Bornberg Bauer, Erich
last_name: Bornberg Bauer
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: 'El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective
advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS
Biology. 2015;13(6):1-30. doi:10.1371/journal.pbio.1002169'
apa: 'El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther,
P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage
of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology.
Public Library of Science. https://doi.org/10.1371/journal.pbio.1002169'
chicago: 'El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann,
Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective
Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS
Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002169.'
ieee: 'L. El Masri et al., “Host–pathogen coevolution: The selective advantage
of Bacillus thuringiensis virulence and its cry toxin genes,” PLoS Biology,
vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.'
ista: 'El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl
S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels
N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg
H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis
virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.'
mla: 'El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage
of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology,
vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:10.1371/journal.pbio.1002169.'
short: L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther,
S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R.
Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg
Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30.
date_created: 2018-12-11T11:52:40Z
date_published: 2015-06-04T00:00:00Z
date_updated: 2021-01-12T06:51:33Z
day: '04'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1371/journal.pbio.1002169
ec_funded: 1
file:
- access_level: open_access
checksum: 30dee7a2c11ed09f2f5634655c0146f8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:13Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5063'
file_name: IST-2016-481-v1+1_journal.pbio.1002169.pdf
file_size: 3468956
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1 - 30
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5620'
pubrep_id: '481'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis
virulence and its cry toxin genes'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2015'
...
---
_id: '1549'
abstract:
- lang: eng
text: Nature has incorporated small photochromic molecules, colloquially termed
'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis
and vision. While Nature's ability to employ light-responsive functionalities
has long been recognized, it was not until recently that scientists designed,
synthesized and applied synthetic photochromes to manipulate many of which open
rapidly and locally in their native cell types, biological processes with the
temporal and spatial resolution of light. Ion channels in particular have come
to the forefront of proteins that can be put under the designer control of synthetic
photochromes. Photochromic ion channel controllers are comprised of three classes,
photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and
photochromic crosslinkers (PXs), and in each class ion channel functionality is
controlled through reversible changes in photochrome structure. By acting as light-dependent
ion channel agonists, antagonist or modulators, photochromic controllers effectively
converted a wide range of ion channels, including voltage-gated ion channels,
'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive
ion channels, into man-made photoreceptors. Control by photochromes can be reversible,
unlike in the case of 'caged' compounds, and non-invasive with high spatial precision,
unlike pharmacology and electrical manipulation. Here, we introduce design principles
of emerging photochromic molecules that act on ion channels and discuss the impact
that these molecules are beginning to have on ion channel biophysics and neuronal
physiology.
author:
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels
under light control. In: Novel Chemical Tools to Study Ion Channel Biology.
Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117.
doi:10.1007/978-1-4939-2845-3_6'
apa: 'Mckenzie, C., Sanchez-Romero, I., & Janovjak, H. L. (2015). Flipping the
photoswitch: Ion channels under light control. In Novel chemical tools to study
ion channel biology (Vol. 869, pp. 101–117). Springer. https://doi.org/10.1007/978-1-4939-2845-3_6'
chicago: 'Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak.
“Flipping the Photoswitch: Ion Channels under Light Control.” In Novel Chemical
Tools to Study Ion Channel Biology, 869:101–17. Advances in Experimental Medicine
and Biology. Springer, 2015. https://doi.org/10.1007/978-1-4939-2845-3_6.'
ieee: 'C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch:
Ion channels under light control,” in Novel chemical tools to study ion channel
biology, vol. 869, Springer, 2015, pp. 101–117.'
ista: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch:
Ion channels under light control. In: Novel chemical tools to study ion channel
biology. vol. 869, 101–117.'
mla: 'Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under
Light Control.” Novel Chemical Tools to Study Ion Channel Biology, vol.
869, Springer, 2015, pp. 101–17, doi:10.1007/978-1-4939-2845-3_6.'
short: C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools
to Study Ion Channel Biology, Springer, 2015, pp. 101–117.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-09-18T00:00:00Z
date_updated: 2021-01-12T06:51:32Z
day: '18'
ddc:
- '571'
- '576'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-2845-3_6
file:
- access_level: open_access
checksum: bd1bfdf2423a0c3b6e7cabfa8b44bc0f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:02Z
date_updated: 2020-07-14T12:45:01Z
file_id: '4854'
file_name: IST-2017-839-v1+1_mckenzie.pdf
file_size: 1919655
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 869'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 101 - 117
publication: Novel chemical tools to study ion channel biology
publication_identifier:
isbn:
- 978-1-4939-2844-6
publication_status: published
publisher: Springer
publist_id: '5622'
pubrep_id: '839'
quality_controlled: '1'
scopus_import: 1
series_title: Advances in Experimental Medicine and Biology
status: public
title: 'Flipping the photoswitch: Ion channels under light control'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 869
year: '2015'
...
---
_id: '1548'
abstract:
- lang: eng
text: Reproduction within a host and transmission to the next host are crucial for
the virulence and fitness of pathogens. Nevertheless, basic knowledge about such
parameters is often missing from the literature, even for well-studied bacteria,
such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects
its hosts via the oral route. To characterize bacterial replication success, we
made use of an experimental oral infection system for the red flour beetle Tribolium
castaneum and developed a flow cytometric assay for the quantification of both
spore ingestion by the individual beetle larvae and the resulting spore load after
bacterial replication and resporulation within cadavers. On average, spore numbers
increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully
in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial
stock cultures into nutrient medium, we next investigated outgrowth characteristics
of vegetative cells and found that cadaver- derived bacteria showed reduced growth
compared to bacteria from the stock cultures. Interestingly, this reduced growth
was a consequence of inhibited spore germination, probably originating from the
host and resulting in reduced host mortality in subsequent infections by cadaver-derived
spores. Nevertheless, we further showed that Bacillus thuringiensis transmission
was possible via larval cannibalism when no other food was offered. These results
contribute to our understanding of the ecology of Bacillus thuringiensis as an
insect pathogen.
author:
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Christina
full_name: Höfling, Christina
last_name: Höfling
- first_name: Momir
full_name: Futo, Momir
last_name: Futo
- first_name: Jörn
full_name: Scharsack, Jörn
last_name: Scharsack
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium
castaneum with Bacillus thuringiensis: Quantification of bacterial replication
within cadavers, transmission via cannibalism, and inhibition of spore germination.
Applied and Environmental Microbiology. 2015;81(23):8135-8144. doi:10.1128/AEM.02051-15'
apa: 'Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., & Kurtz, J. (2015).
Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of
bacterial replication within cadavers, transmission via cannibalism, and inhibition
of spore germination. Applied and Environmental Microbiology. American
Society for Microbiology. https://doi.org/10.1128/AEM.02051-15'
chicago: 'Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and
Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis:
Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism,
and Inhibition of Spore Germination.” Applied and Environmental Microbiology.
American Society for Microbiology, 2015. https://doi.org/10.1128/AEM.02051-15.'
ieee: 'B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection
of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial
replication within cadavers, transmission via cannibalism, and inhibition of spore
germination,” Applied and Environmental Microbiology, vol. 81, no. 23.
American Society for Microbiology, pp. 8135–8144, 2015.'
ista: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of
Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication
within cadavers, transmission via cannibalism, and inhibition of spore germination.
Applied and Environmental Microbiology. 81(23), 8135–8144.'
mla: 'Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus
Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission
via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental
Microbiology, vol. 81, no. 23, American Society for Microbiology, 2015, pp.
8135–44, doi:10.1128/AEM.02051-15.'
short: B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and
Environmental Microbiology 81 (2015) 8135–8144.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:31Z
day: '01'
department:
- _id: SyCr
doi: 10.1128/AEM.02051-15
external_id:
pmid:
- '26386058'
intvolume: ' 81'
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/
month: '12'
oa: 1
oa_version: Submitted Version
page: 8135 - 8144
pmid: 1
publication: Applied and Environmental Microbiology
publication_status: published
publisher: American Society for Microbiology
publist_id: '5623'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification
of bacterial replication within cadavers, transmission via cannibalism, and inhibition
of spore germination'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2015'
...
---
_id: '1550'
abstract:
- lang: eng
text: The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain
interneurons. Here, we examine the lineage relationship among MGE-derived interneurons
using a replication-defective retroviral library containing a highly diverse set
of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor
cells enabled us to unambiguously determine their respective lineal relationship.
We found that clonal dispersion occurs across large areas of the brain and is
not restricted by anatomical divisions. As such, sibling interneurons can populate
the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons
appeared to be generated from asymmetric divisions of MGE progenitor cells, followed
by symmetric divisions within the subventricular zone. Altogether, our findings
uncover that lineage relationships do not appear to determine interneuron allocation
to particular regions. As such, it is likely that clonally related interneurons
have considerable flexibility as to the particular forebrain circuits to which
they can contribute.
acknowledgement: "Research in the G.F. laboratory is supported by NIH (NS 081297,
MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory
is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF
(1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n"
author:
- first_name: Christian
full_name: Mayer, Christian
last_name: Mayer
- first_name: Xavier
full_name: Jaglin, Xavier
last_name: Jaglin
- first_name: Lucy
full_name: Cobbs, Lucy
last_name: Cobbs
- first_name: Rachel
full_name: Bandler, Rachel
last_name: Bandler
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Constance
full_name: Cepko, Constance
last_name: Cepko
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Gord
full_name: Fishell, Gord
last_name: Fishell
citation:
ama: Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons
disperse broadly across both functional areas and structural boundaries. Neuron.
2015;87(5):989-998. doi:10.1016/j.neuron.2015.07.011
apa: Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., …
Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across
both functional areas and structural boundaries. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.07.011
chicago: Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher,
Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain
Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.”
Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.07.011.
ieee: C. Mayer et al., “Clonally related forebrain interneurons disperse
broadly across both functional areas and structural boundaries,” Neuron,
vol. 87, no. 5. Elsevier, pp. 989–998, 2015.
ista: Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S,
Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across
both functional areas and structural boundaries. Neuron. 87(5), 989–998.
mla: Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse
Broadly across Both Functional Areas and Structural Boundaries.” Neuron,
vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:10.1016/j.neuron.2015.07.011.
short: C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer,
G. Fishell, Neuron 87 (2015) 989–998.
date_created: 2018-12-11T11:52:40Z
date_published: 2015-09-02T00:00:00Z
date_updated: 2021-01-12T06:51:32Z
day: '02'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2015.07.011
external_id:
pmid:
- '26299473'
intvolume: ' 87'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/
month: '09'
oa: 1
oa_version: Submitted Version
page: 989 - 998
pmid: 1
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5621'
quality_controlled: '1'
scopus_import: 1
status: public
title: Clonally related forebrain interneurons disperse broadly across both functional
areas and structural boundaries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2015'
...
---
_id: '1547'
abstract:
- lang: eng
text: Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G),
and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals
are associated to G, the edge ideal I(G) generated by all monomials xixj with
{xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for
all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂
V(G) such that each edge has at least one vertex in C and no proper subset of
C has the same property. Indeed, the vertex cover ideal of G is the Alexander
dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we
consider the lattice of vertex covers LG and we explicitly describe the minimal
free resolution of the ideal associated to LG which is exactly the vertex cover
ideal of G. Then we compute depth, projective dimension, regularity and extremal
Betti numbers of R/I(G) in terms of the associated lattice.
author:
- first_name: Fatemeh
full_name: Mohammadi, Fatemeh
id: 2C29581E-F248-11E8-B48F-1D18A9856A87
last_name: Mohammadi
- first_name: Somayeh
full_name: Moradi, Somayeh
last_name: Moradi
citation:
ama: Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. Bulletin
of the Korean Mathematical Society. 2015;52(3):977-986. doi:10.4134/BKMS.2015.52.3.977
apa: Mohammadi, F., & Moradi, S. (2015). Resolution of unmixed bipartite graphs.
Bulletin of the Korean Mathematical Society. Korean Mathematical Society.
https://doi.org/10.4134/BKMS.2015.52.3.977
chicago: Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite
Graphs.” Bulletin of the Korean Mathematical Society. Korean Mathematical
Society, 2015. https://doi.org/10.4134/BKMS.2015.52.3.977.
ieee: F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” Bulletin
of the Korean Mathematical Society, vol. 52, no. 3. Korean Mathematical Society,
pp. 977–986, 2015.
ista: Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin
of the Korean Mathematical Society. 52(3), 977–986.
mla: Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.”
Bulletin of the Korean Mathematical Society, vol. 52, no. 3, Korean Mathematical
Society, 2015, pp. 977–86, doi:10.4134/BKMS.2015.52.3.977.
short: F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015)
977–986.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-05-31T00:00:00Z
date_updated: 2021-01-12T06:51:31Z
day: '31'
department:
- _id: CaUh
doi: 10.4134/BKMS.2015.52.3.977
intvolume: ' 52'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0901.3015
month: '05'
oa: 1
oa_version: Preprint
page: 977 - 986
publication: Bulletin of the Korean Mathematical Society
publication_identifier:
eissn:
- 2234-3016
publication_status: published
publisher: Korean Mathematical Society
publist_id: '5624'
quality_controlled: '1'
scopus_import: 1
status: public
title: Resolution of unmixed bipartite graphs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2015'
...
---
_id: '1556'
abstract:
- lang: eng
text: The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily
conserved histone acetyltransferase complex, has been shown to participate in
leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana.
Here, its role in root development was explored. Compared to the wild type, the
elp2 mutant exhibited an accelerated differentiation of its root stem cells and
cell division was more active in its quiescent centre (QC). The key transcription
factors responsible for maintaining root stem cell and QC identity, such as AP2
transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription
factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5
transcription factor WOX5, were all strongly down-regulated in the mutant. On
the other hand, expression of the G2/M transition activator CYCB1 was substantially
induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased
protein levels and PIN1 also displayed mild polarity alterations in elp2, which
resulted in a reduced auxin content in the root tip. Either the acetylation or
methylation level of each of these genes differed between the mutant and the wild
type, suggesting that the ELP2 regulation of root development involves the epigenetic
modification of a range of transcription factors and other developmental regulators.
author:
- first_name: Yuebin
full_name: Jia, Yuebin
last_name: Jia
- first_name: Huiyu
full_name: Tian, Huiyu
last_name: Tian
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Qianqian
full_name: Yu, Qianqian
last_name: Yu
- first_name: Lei
full_name: Wang, Lei
last_name: Wang
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
citation:
ama: Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit
2 epigenetically affects root development. Journal of Experimental Botany.
2015;66(15):4631-4642. doi:10.1093/jxb/erv230
apa: Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015).
The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root
development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230
chicago: Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml,
and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically
Affects Root Development.” Journal of Experimental Botany. Oxford University
Press, 2015. https://doi.org/10.1093/jxb/erv230.
ieee: Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit
2 epigenetically affects root development,” Journal of Experimental Botany,
vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015.
ista: Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis
thaliana elongator complex subunit 2 epigenetically affects root development.
Journal of Experimental Botany. 66(15), 4631–4642.
mla: Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically
Affects Root Development.” Journal of Experimental Botany, vol. 66, no.
15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230.
short: Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental
Botany 66 (2015) 4631–4642.
date_created: 2018-12-11T11:52:42Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:35Z
day: '01'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1093/jxb/erv230
file:
- access_level: open_access
checksum: 257919be0ce3d306185d3891ad7acf39
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:02Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5051'
file_name: IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf
file_size: 7753043
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 66'
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 4631 - 4642
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5615'
pubrep_id: '480'
quality_controlled: '1'
scopus_import: 1
status: public
title: The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects
root 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: 66
year: '2015'
...
---
_id: '1555'
abstract:
- lang: eng
text: We show that incorporating spatial dispersal of individuals into a simple
vaccination epidemic model may give rise to a model that exhibits rich dynamical
behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as
a basis, we describe the spread of an infectious disease in a population split
into two regions. In each subpopulation, both forward and backward bifurcations
can occur. This implies that for disconnected regions the two-patch system may
admit several steady states. We consider traveling between the regions and investigate
the impact of spatial dispersal of individuals on the model dynamics. We establish
conditions for the existence of multiple nontrivial steady states in the system,
and we study the structure of the equilibria. The mathematical analysis reveals
an unusually rich dynamical behavior, not normally found in the simple epidemic
models. In addition to the disease-free equilibrium, eight endemic equilibria
emerge from backward transcritical and saddle-node bifurcation points, forming
an interesting bifurcation diagram. Stability of steady states, their bifurcations,
and the global dynamics are investigated with analytical tools, numerical simulations,
and rigorous set-oriented numerical computations.
acknowledgement: Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg,
Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported
by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de
Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de
Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia
e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645
(ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559
in the framework of the EPIDELAY project.
article_processing_charge: No
article_type: original
author:
- first_name: Diána
full_name: Knipl, Diána
last_name: Knipl
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Gergely
full_name: Röst, Gergely
last_name: Röst
citation:
ama: Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination
model. SIAM Journal on Applied Dynamical Systems. 2015;14(2):980-1017.
doi:10.1137/140993934
apa: Knipl, D., Pilarczyk, P., & Röst, G. (2015). Rich bifurcation structure
in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems.
Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140993934
chicago: Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure
in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems.
Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140993934.
ieee: D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two
patch vaccination model,” SIAM Journal on Applied Dynamical Systems, vol.
14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015.
ista: Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch
vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017.
mla: Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination
Model.” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2, Society
for Industrial and Applied Mathematics , 2015, pp. 980–1017, doi:10.1137/140993934.
short: D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems
14 (2015) 980–1017.
date_created: 2018-12-11T11:52:42Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:34Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1137/140993934
ec_funded: 1
intvolume: ' 14'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://discovery.ucl.ac.uk/1473750/1/99393.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 980 - 1017
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication: SIAM Journal on Applied Dynamical Systems
publication_identifier:
eissn:
- 1536-0040
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '5616'
quality_controlled: '1'
scopus_import: 1
status: public
title: Rich bifurcation structure in a two patch vaccination model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2015'
...
---
_id: '1559'
abstract:
- lang: eng
text: 'There are deep, yet largely unexplored, connections between computer science
and biology. Both disciplines examine how information proliferates in time and
space. Central results in computer science describe the complexity of algorithms
that solve certain classes of problems. An algorithm is deemed efficient if it
can solve a problem in polynomial time, which means the running time of the algorithm
is a polynomial function of the length of the input. There are classes of harder
problems for which the fastest possible algorithm requires exponential time. Another
criterion is the space requirement of the algorithm. There is a crucial distinction
between algorithms that can find a solution, verify a solution, or list several
distinct solutions in given time and space. The complexity hierarchy that is generated
in this way is the foundation of theoretical computer science. Precise complexity
results can be notoriously difficult. The famous question whether polynomial time
equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open
problems in computer science and all of mathematics. Here, we consider simple
processes of ecological and evolutionary spatial dynamics. The basic question
is: What is the probability that a new invader (or a new mutant)will take over
a resident population?We derive precise complexity results for a variety of scenarios.
We therefore show that some fundamental questions in this area cannot be answered
by simple equations (assuming that P is not equal to NP).'
author:
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological
and evolutionary spatial dynamics. PNAS. 2015;112(51):15636-15641. doi:10.1073/pnas.1511366112
apa: Ibsen-Jensen, R., Chatterjee, K., & Nowak, M. (2015). Computational complexity
of ecological and evolutionary spatial dynamics. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1511366112
chicago: Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational
Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS. National
Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511366112.
ieee: R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of
ecological and evolutionary spatial dynamics,” PNAS, vol. 112, no. 51.
National Academy of Sciences, pp. 15636–15641, 2015.
ista: Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological
and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641.
mla: Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary
Spatial Dynamics.” PNAS, vol. 112, no. 51, National Academy of Sciences,
2015, pp. 15636–41, doi:10.1073/pnas.1511366112.
short: R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641.
date_created: 2018-12-11T11:52:43Z
date_published: 2015-12-22T00:00:00Z
date_updated: 2021-01-12T06:51:36Z
day: '22'
department:
- _id: KrCh
doi: 10.1073/pnas.1511366112
external_id:
pmid:
- '26644569'
intvolume: ' 112'
issue: '51'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/
month: '12'
oa: 1
oa_version: Submitted Version
page: 15636 - 15641
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5612'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computational complexity of ecological and evolutionary spatial dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1554'
abstract:
- lang: eng
text: The visualization of hormonal signaling input and output is key to understanding
how multicellular development is regulated. The plant signaling molecule auxin
triggers many growth and developmental responses, but current tools lack the sensitivity
or precision to visualize these. We developed a set of fluorescent reporters that
allow sensitive and semiquantitative readout of auxin responses at cellular resolution
in Arabidopsis thaliana. These generic tools are suitable for any transformable
plant species.
author:
- first_name: Cheyang
full_name: Liao, Cheyang
last_name: Liao
- first_name: Wouter
full_name: Smet, Wouter
last_name: Smet
- first_name: Géraldine
full_name: Brunoud, Géraldine
last_name: Brunoud
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Teva
full_name: Vernoux, Teva
last_name: Vernoux
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
citation:
ama: Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive
and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210.
doi:10.1038/nmeth.3279
apa: Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D.
(2015). Reporters for sensitive and quantitative measurement of auxin response.
Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279
chicago: Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux,
and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin
Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279.
ieee: C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters
for sensitive and quantitative measurement of auxin response,” Nature Methods,
vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.
ista: Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters
for sensitive and quantitative measurement of auxin response. Nature Methods.
12(3), 207–210.
mla: Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement
of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group,
2015, pp. 207–10, doi:10.1038/nmeth.3279.
short: C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature
Methods 12 (2015) 207–210.
date_created: 2018-12-11T11:52:41Z
date_published: 2015-02-26T00:00:00Z
date_updated: 2021-01-12T06:51:34Z
day: '26'
department:
- _id: JiFr
doi: 10.1038/nmeth.3279
external_id:
pmid:
- '25643149'
intvolume: ' 12'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/
month: '02'
oa: 1
oa_version: Submitted Version
page: 207 - 210
pmid: 1
publication: Nature Methods
publication_status: published
publisher: Nature Publishing Group
publist_id: '5617'
quality_controlled: '1'
scopus_import: 1
status: public
title: Reporters for sensitive and quantitative measurement of auxin response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2015'
...
---
_id: '1565'
abstract:
- lang: eng
text: Leptin is an adipokine produced by the adipose tissue regulating body weight
through its appetite-suppressing effect. Besides being expressed in the hypothalamus
and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells
of the adrenal medulla. In the present study, we report the effect of leptin on
mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine
secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused
a slowly developing membrane hyperpolarization followed by complete blockade of
action potential (AP) firing. This inhibitory effect at rest was abolished by
the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium
channels. Single-channel recordings in 'perforated microvesicles' confirmed that
leptin increased BK channel open probability without altering its unitary conductance.
BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K)
signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully
prevented BK current increase. We also tested the effect of leptin on evoked AP
firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains
of lower frequency, APs are broader and depolarization-evoked exocytosis is increased
as a result of the larger size of the ready-releasable pool and higher frequency
of vesicle release. The kinetics and quantal size of single secretory events remained
unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking
the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual
action on MCC activity. It dampens AP firing at rest but preserves AP firing and
increases catecholamine secretion during sustained stimulation, highlighting the
importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic
tone and catecholamine release.
acknowledgement: "This work was supported by the Compagnia di San Paolo Foundation
‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank
Dr Claudio Franchino for cell preparation and for providing excellent technical
support."
author:
- first_name: Daniela
full_name: Gavello, Daniela
last_name: Gavello
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Sara
full_name: Gosso, Sara
last_name: Gosso
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
- first_name: Valentina
full_name: Carabelli, Valentina
last_name: Carabelli
citation:
ama: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin
on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven
BK channel up-regulation in mouse chromaffin cells. Journal of Physiology.
2015;593(22):4835-4853. doi:10.1113/JP271078
apa: Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015).
Dual action of leptin on rest-firing and stimulated catecholamine release via
phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells.
Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078
chicago: Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina
Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine
Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse
Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078.
ieee: D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action
of leptin on rest-firing and stimulated catecholamine release via phosphoinositide
3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal
of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015.
ista: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action
of leptin on rest-firing and stimulated catecholamine release via phosphoinositide
3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of
Physiology. 593(22), 4835–4853.
mla: Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated
Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation
in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell,
2015, pp. 4835–53, doi:10.1113/JP271078.
short: D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of
Physiology 593 (2015) 4835–4853.
date_created: 2018-12-11T11:52:45Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2021-01-12T06:51:38Z
day: '15'
department:
- _id: PeJo
doi: 10.1113/JP271078
external_id:
pmid:
- '26282459'
intvolume: ' 593'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/
month: '11'
oa: 1
oa_version: Submitted Version
page: 4835 - 4853
pmid: 1
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5606'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dual action of leptin on rest-firing and stimulated catecholamine release via
phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 593
year: '2015'
...
---
_id: '1564'
article_number: '145'
author:
- first_name: Matthieu
full_name: Gilson, Matthieu
last_name: Gilson
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Friedemann
full_name: Zenke, Friedemann
last_name: Zenke
citation:
ama: 'Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the
interaction of different forms of plasticity. Frontiers in Computational Neuroscience.
2015;9(11). doi:10.3389/fncom.2015.00145'
apa: 'Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural
computation from the interaction of different forms of plasticity. Frontiers
in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145'
chicago: 'Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent
Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers
in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.'
ieee: 'M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation
from the interaction of different forms of plasticity,” Frontiers in Computational
Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.'
ista: 'Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation
from the interaction of different forms of plasticity. Frontiers in Computational
Neuroscience. 9(11), 145.'
mla: 'Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the
Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience,
vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.'
short: M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9
(2015).
date_created: 2018-12-11T11:52:45Z
date_published: 2015-11-30T00:00:00Z
date_updated: 2021-01-12T06:51:37Z
day: '30'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.3389/fncom.2015.00145
ec_funded: 1
file:
- access_level: open_access
checksum: cea73b6d3ef1579f32da10b82f4de4fd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:09Z
date_updated: 2020-07-14T12:45:02Z
file_id: '4927'
file_name: IST-2016-479-v1+1_fncom-09-00145.pdf
file_size: 187038
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Frontiers in Computational Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '5607'
pubrep_id: '479'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Editorial: Emergent neural computation from the interaction of different forms
of plasticity'
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: 9
year: '2015'
...
---
_id: '1574'
abstract:
- lang: eng
text: Multiple plant developmental processes, such as lateral root development,
depend on auxin distribution patterns that are in part generated by the PIN-formed
family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7
(ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly
form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription
in planta to steer the early steps of lateral root formation. This regulatory
mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli,
potentially maintaining and enhancing the robustness of the auxin flux directionality
during lateral root development. The cooperative action between canonical auxin
signalling and other transcription factors might constitute a general mechanism
by which transcriptional auxin-sensitivity can be regulated at a tissue-specific
level.
acknowledgement: 'of the European Research Council (project ERC-2011-StG-20101109-PSDP)
(to J.F.), a FEBS long-term fellowship (to P.M.) '
article_number: '8821'
author:
- first_name: Qian
full_name: Chen, Qian
last_name: Chen
- first_name: Yang
full_name: Liu, Yang
last_name: Liu
- first_name: Steven
full_name: Maere, Steven
last_name: Maere
- first_name: Eunkyoung
full_name: Lee, Eunkyoung
last_name: Lee
- first_name: Gert
full_name: Van Isterdael, Gert
last_name: Van Isterdael
- first_name: Zidian
full_name: Xie, Zidian
last_name: Xie
- first_name: Wei
full_name: Xuan, Wei
last_name: Xuan
- first_name: Jessica
full_name: Lucas, Jessica
last_name: Lucas
- first_name: Valya
full_name: Vassileva, Valya
last_name: Vassileva
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Niko
full_name: Geldner, Niko
last_name: Geldner
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jie
full_name: Le, Jie
last_name: Le
- first_name: Hidehiro
full_name: Fukaki, Hidehiro
last_name: Fukaki
- first_name: Erich
full_name: Grotewold, Erich
last_name: Grotewold
- first_name: Chuanyou
full_name: Li, Chuanyou
last_name: Li
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Fred
full_name: Sack, Fred
last_name: Sack
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
citation:
ama: Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif
model for mediating auxin-sensitive PIN3 expression during lateral root development.
Nature Communications. 2015;6. doi:10.1038/ncomms9821
apa: Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste,
S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive
PIN3 expression during lateral root development. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms9821
chicago: Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael,
Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model
for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.”
Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.
ieee: Q. Chen et al., “A coherent transcriptional feed-forward motif model
for mediating auxin-sensitive PIN3 expression during lateral root development,”
Nature Communications, vol. 6. Nature Publishing Group, 2015.
ista: Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva
V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold
E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional
feed-forward motif model for mediating auxin-sensitive PIN3 expression during
lateral root development. Nature Communications. 6, 8821.
mla: Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for
Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature
Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.
short: Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J.
Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková,
J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste,
Nature Communications 6 (2015).
date_created: 2018-12-11T11:52:48Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2021-01-12T06:51:42Z
day: '18'
ddc:
- '580'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/ncomms9821
file:
- access_level: open_access
checksum: 8ff5c108899b548806e1cb7a302fe76d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:32Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5085'
file_name: IST-2016-477-v1+1_ncomms9821.pdf
file_size: 1701815
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5597'
pubrep_id: '477'
quality_controlled: '1'
scopus_import: 1
status: public
title: A coherent transcriptional feed-forward motif model for mediating auxin-sensitive
PIN3 expression during lateral root 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: 6
year: '2015'
...
---
_id: '1575'
abstract:
- lang: eng
text: The immune response relies on the migration of leukocytes and on their ability
to stop in precise anatomical locations to fulfil their task. How leukocyte migration
and function are coordinated is unknown. Here we show that in immature dendritic
cells, which patrol their environment by engulfing extracellular material, cell
migration and antigen capture are antagonistic. This antagonism results from transient
enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient
of the motor protein, slowing down locomotion but promoting antigen capture. We
further highlight that myosin IIA enrichment at the cell front requires the MHC
class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization,
Ii imposes on dendritic cells an intermittent antigen capture behaviour that might
facilitate environment patrolling. We propose that the requirement for myosin
II in both cell migration and specific cell functions may provide a general mechanism
for their coordination in time and space.
acknowledgement: M.C. and M.L.H. were supported by fellowships from the Fondation
pour la Recherche Médicale and the Association pour la Recherche contre le Cancer,
respectively. This work was funded by grants from the City of Paris and the European
Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour
la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico)
to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL*
and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an
ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934,
Institut Curie).
article_number: '7526'
author:
- first_name: Mélanie
full_name: Chabaud, Mélanie
last_name: Chabaud
- first_name: Mélina
full_name: Heuzé, Mélina
last_name: Heuzé
- first_name: Marine
full_name: Bretou, Marine
last_name: Bretou
- first_name: Pablo
full_name: Vargas, Pablo
last_name: Vargas
- first_name: Paolo
full_name: Maiuri, Paolo
last_name: Maiuri
- first_name: Paola
full_name: Solanes, Paola
last_name: Solanes
- first_name: Mathieu
full_name: Maurin, Mathieu
last_name: Maurin
- first_name: Emmanuel
full_name: Terriac, Emmanuel
last_name: Terriac
- first_name: Maël
full_name: Le Berre, Maël
last_name: Le Berre
- first_name: Danielle
full_name: Lankar, Danielle
last_name: Lankar
- first_name: Tristan
full_name: Piolot, Tristan
last_name: Piolot
- first_name: Robert
full_name: Adelstein, Robert
last_name: Adelstein
- first_name: Yingfan
full_name: Zhang, Yingfan
last_name: Zhang
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Jordan
full_name: Jacobelli, Jordan
last_name: Jacobelli
- first_name: Olivier
full_name: Bénichou, Olivier
last_name: Bénichou
- first_name: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
- first_name: Matthieu
full_name: Piel, Matthieu
last_name: Piel
- first_name: Ana
full_name: Lennon Duménil, Ana
last_name: Lennon Duménil
citation:
ama: Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are
antagonistic processes coupled by myosin II in dendritic cells. Nature Communications.
2015;6. doi:10.1038/ncomms8526
apa: Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., …
Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic
processes coupled by myosin II in dendritic cells. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms8526
chicago: Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri,
Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are
Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications.
Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526.
ieee: M. Chabaud et al., “Cell migration and antigen capture are antagonistic
processes coupled by myosin II in dendritic cells,” Nature Communications,
vol. 6. Nature Publishing Group, 2015.
ista: Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac
E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J,
Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen
capture are antagonistic processes coupled by myosin II in dendritic cells. Nature
Communications. 6, 7526.
mla: Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic
Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications,
vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526.
short: M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin,
E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt,
J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications
6 (2015).
date_created: 2018-12-11T11:52:48Z
date_published: 2015-06-25T00:00:00Z
date_updated: 2021-01-12T06:51:42Z
day: '25'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1038/ncomms8526
file:
- access_level: open_access
checksum: bae12e86be2adb28253f890b8bba8315
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:58Z
date_updated: 2020-07-14T12:45:02Z
file_id: '4915'
file_name: IST-2016-476-v1+1_ncomms8526.pdf
file_size: 4530215
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5596'
pubrep_id: '476'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cell migration and antigen capture are antagonistic processes coupled by myosin
II in dendritic 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: 6
year: '2015'
...
---
_id: '1569'
abstract:
- lang: eng
text: Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin)
is essential for plant development. Auxin gradient establishment is mediated by
polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their
localization and abundance at the plasma membrane are tightly regulated by endomembrane
machinery, especially the endocytic and recycling pathways mediated by the ADP
ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed
the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis
thaliana by pharmacological and genetic approaches. We identified the compound
endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without
altering the polarity of apical proteins. ES8 alters the auxin distribution pattern
in the root and induces a strong developmental phenotype, including reduced root
length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7)
are significantly resistant to ES8. The compound does not affect recycling or
vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting
in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role
for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated
early secretory pathway selectively regulates PIN1 basal polarity establishment
in a manner essential for normal plant development.
acknowledgement: 'This work was supported by Vetenskapsrådet and Vinnova (Verket för
Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs
Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers
Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP
(to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National
Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). '
author:
- first_name: Siamsa
full_name: Doyle, Siamsa
last_name: Doyle
- first_name: Ash
full_name: Haegera, Ash
last_name: Haegera
- first_name: Thomas
full_name: Vain, Thomas
last_name: Vain
- first_name: Adeline
full_name: Rigala, Adeline
last_name: Rigala
- first_name: Corrado
full_name: Viotti, Corrado
last_name: Viotti
- first_name: Małgorzata
full_name: Łangowskaa, Małgorzata
last_name: Łangowskaa
- first_name: Qian
full_name: Maa, Qian
last_name: Maa
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Natasha
full_name: Raikhel, Natasha
last_name: Raikhel
- first_name: Glenn
full_name: Hickse, Glenn
last_name: Hickse
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
citation:
ama: Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like
1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana.
PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112
apa: Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., …
Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom
is essential for basal polarity establishment in Arabidopsis thaliana. PNAS.
National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112
chicago: Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti,
Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by
Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis
Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112.
ieee: S. Doyle et al., “An early secretory pathway mediated by gnom-like
1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,”
PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.
ista: Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml
J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by
gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis
thaliana. PNAS. 112(7), E806–E815.
mla: Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and
Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS,
vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112.
short: S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa,
J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.
date_created: 2018-12-11T11:52:46Z
date_published: 2015-02-17T00:00:00Z
date_updated: 2021-01-12T06:51:39Z
day: '17'
department:
- _id: JiFr
doi: 10.1073/pnas.1424856112
ec_funded: 1
intvolume: ' 112'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/
month: '02'
oa: 1
oa_version: Published Version
page: E806 - E815
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5602'
quality_controlled: '1'
scopus_import: 1
status: public
title: An early secretory pathway mediated by gnom-like 1 and gnom is essential for
basal polarity establishment in Arabidopsis thaliana
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1570'
abstract:
- lang: eng
text: Grounding autonomous behavior in the nervous system is a fundamental challenge
for neuroscience. In particular, self-organized behavioral development provides
more questions than answers. Are there special functional units for curiosity,
motivation, and creativity? This paper argues that these features can be grounded
in synaptic plasticity itself, without requiring any higher-level constructs.
We propose differential extrinsic plasticity (DEP) as a new synaptic rule for
self-learning systems and apply it to a number of complex robotic systems as a
test case. Without specifying any purpose or goal, seemingly purposeful and adaptive
rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence.
These surprising results require no systemspecific modifications of the DEP rule.
They rather arise from the underlying mechanism of spontaneous symmetry breaking,which
is due to the tight brain body environment coupling. The new synaptic rule is
biologically plausible and would be an interesting target for neurobiological
investigation. We also argue that this neuronal mechanism may have been a catalyst
in natural evolution.
author:
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
citation:
ama: Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor
intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112
apa: Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the
development of sensorimotor intelligence. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1508400112
chicago: Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the
Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences,
2015. https://doi.org/10.1073/pnas.1508400112.
ieee: R. Der and G. S. Martius, “Novel plasticity rule can explain the development
of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy
of Sciences, pp. E6224–E6232, 2015.
ista: Der R, Martius GS. 2015. Novel plasticity rule can explain the development
of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.
mla: Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development
of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy
of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112.
short: R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.
date_created: 2018-12-11T11:52:47Z
date_published: 2015-11-10T00:00:00Z
date_updated: 2021-01-12T06:51:40Z
day: '10'
department:
- _id: ChLa
- _id: GaTk
doi: 10.1073/pnas.1508400112
ec_funded: 1
external_id:
pmid:
- '26504200'
intvolume: ' 112'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/
month: '11'
oa: 1
oa_version: Submitted Version
page: E6224 - E6232
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5601'
quality_controlled: '1'
scopus_import: 1
status: public
title: Novel plasticity rule can explain the development of sensorimotor intelligence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1572'
abstract:
- lang: eng
text: "We consider the quantum ferromagnetic Heisenberg model in three dimensions,
for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation
for the excitation spectrum, at the level of the first non-trivial contribution
to the free energy at low temperatures. Our proof comes with explicit, constructive
upper and lower bounds on the error term. It uses in an essential way the bosonic
formulation of the model in terms of the Holstein-Primakoff representation. In
this language, the model describes interacting bosons with a hard-core on-site
repulsion and a nearest-neighbor attraction. This attractive interaction makes
the lower bound on the free energy particularly tricky: the key idea there is
to prove a differential inequality for the two-particle density, which is thereby
shown to be smaller than the probability density of a suitably weighted two-particle
random process on the lattice.\r\n"
author:
- first_name: Michele
full_name: Correggi, Michele
last_name: Correggi
- first_name: Alessandro
full_name: Giuliani, Alessandro
last_name: Giuliani
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation
for the free energy of the Heisenberg ferromagnet. Communications in Mathematical
Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0
apa: Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave
approximation for the free energy of the Heisenberg ferromagnet. Communications
in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0
chicago: Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity
of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.”
Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0.
ieee: M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation
for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical
Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015.
ista: Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation
for the free energy of the Heisenberg ferromagnet. Communications in Mathematical
Physics. 339(1), 279–307.
mla: Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the
Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical
Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0.
short: M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics
339 (2015) 279–307.
date_created: 2018-12-11T11:52:47Z
date_published: 2015-06-23T00:00:00Z
date_updated: 2021-01-12T06:51:41Z
day: '23'
department:
- _id: RoSe
doi: 10.1007/s00220-015-2402-0
intvolume: ' 339'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1312.7873
month: '06'
oa: 1
oa_version: Preprint
page: 279 - 307
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '5599'
quality_controlled: '1'
scopus_import: 1
status: public
title: Validity of the spin-wave approximation for the free energy of the Heisenberg
ferromagnet
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2015'
...
---
_id: '1573'
abstract:
- lang: eng
text: We present a new, simpler proof of the unconditional uniqueness of solutions
to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis
is the quantum de Finetti theorem. Our uniqueness result is equivalent to the
one established in the celebrated works of Erdos, Schlein, and Yau.
author:
- first_name: Thomas
full_name: Chen, Thomas
last_name: Chen
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Nataša
full_name: Pavlović, Nataša
last_name: Pavlović
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the
cubic gross pitaevskii hierarchy via quantum de finetti. Communications on
Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552
apa: Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional
uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications
on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552
chicago: Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer.
“Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum
de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015.
https://doi.org/10.1002/cpa.21552.
ieee: T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness
for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications
on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015.
ista: Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness
for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications
on Pure and Applied Mathematics. 68(10), 1845–1884.
mla: Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii
Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics,
vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552.
short: T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and
Applied Mathematics 68 (2015) 1845–1884.
date_created: 2018-12-11T11:52:48Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:51:41Z
day: '01'
department:
- _id: RoSe
doi: 10.1002/cpa.21552
intvolume: ' 68'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.3168
month: '10'
oa: 1
oa_version: Preprint
page: 1845 - 1884
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Communications on Pure and Applied Mathematics
publication_status: published
publisher: Wiley
publist_id: '5598'
quality_controlled: '1'
scopus_import: 1
status: public
title: Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum
de finetti
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2015'
...
---
_id: '1580'
abstract:
- lang: eng
text: Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins
crucial for the fine-tuning of synaptic function. A large amount of experimental
evidences has shown that Syns are involved in the development of epileptic phenotypes
and several mutations in Syn genes have been associated with epilepsy in humans
and animal models. Syn mutations induce alterations in circuitry and neurotransmitter
release, differentially affecting excitatory and inhibitory synapses, thus causing
an excitation/inhibition imbalance in network excitability toward hyperexcitability
that may be a determinant with regard to the development of epilepsy. Another
approach to investigate epileptogenic mechanisms is to understand how silencing
Syn affects the cellular behavior of single neurons and is associated with the
hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional
effects of antisense-RNA inhibition of Syn expression on individually identified
and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin
silencing increases cell excitability characterized by a slightly depolarized
resting membrane potential, decreases the rheobase, reduces the threshold for
action potential (AP) firing and increases the mean and instantaneous firing rates,
with respect to control cells. The observed increase of Ca2+ and BK currents in
Syn-silenced cells seems to be related to changes in the shape of the AP waveform.
These currents sustain the faster spiking in Syn-deficient cells by increasing
the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation
during repetitive firing. This in turn speeds up the depolarization phase by reaching
the AP threshold faster. Our results provide evidence that Syn silencing increases
intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent
BK currents in the absence of excitatory or inhibitory inputs.
article_processing_charge: No
article_type: original
author:
- first_name: Oscar
full_name: Brenes, Oscar
last_name: Brenes
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
- first_name: Pier
full_name: Montarolo, Pier
last_name: Montarolo
- first_name: Mirella
full_name: Ghirardi, Mirella
last_name: Ghirardi
citation:
ama: Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin
alters cell excitability and action potential waveform by potentiating BK and
voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience.
2015;311:430-443. doi:10.1016/j.neuroscience.2015.10.046
apa: Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., & Ghirardi, M.
(2015). Knock-down of synapsin alters cell excitability and action potential waveform
by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons.
Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2015.10.046
chicago: Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella
Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential
Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic
Neurons.” Neuroscience. Elsevier, 2015. https://doi.org/10.1016/j.neuroscience.2015.10.046.
ieee: O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down
of synapsin alters cell excitability and action potential waveform by potentiating
BK and voltage gated Ca2 currents in Helix serotonergic neurons,” Neuroscience,
vol. 311. Elsevier, pp. 430–443, 2015.
ista: Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down
of synapsin alters cell excitability and action potential waveform by potentiating
BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience.
311, 430–443.
mla: Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and
Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in
Helix Serotonergic Neurons.” Neuroscience, vol. 311, Elsevier, 2015, pp.
430–43, doi:10.1016/j.neuroscience.2015.10.046.
short: O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience
311 (2015) 430–443.
date_created: 2018-12-11T11:52:50Z
date_published: 2015-12-17T00:00:00Z
date_updated: 2021-01-12T06:51:44Z
day: '17'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuroscience.2015.10.046
file:
- access_level: open_access
checksum: af2c4c994718c7be417eba0dc746aac9
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T06:50:20Z
date_updated: 2020-07-14T12:45:02Z
file_id: '7849'
file_name: 2015_Neuroscience_Brenes.pdf
file_size: 5563015
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 311'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 430 - 443
publication: Neuroscience
publication_status: published
publisher: Elsevier
publist_id: '5591'
quality_controlled: '1'
scopus_import: 1
status: public
title: Knock-down of synapsin alters cell excitability and action potential waveform
by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 311
year: '2015'
...
---
_id: '1577'
abstract:
- lang: eng
text: Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked
genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be
unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y
transposition must be the main source of Drosophila Y-linked genes. Here we show
how these genes were acquired. We found a previously unidentified gene (flagrante
delicto Y, FDY) that originated from a recent duplication of the autosomal gene
vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were
duplicated along with vig2, but they became pseudogenes through the accumulation
of deletions and transposable element insertions, whereas FDY remained functional,
acquired testis-specific expression, and now accounts for ∼20% of the vig2-like
mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and
DNA sequence divergence indicates that the duplication to the Y chromosome occurred
∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the
establishment of a Y-linked gene and demonstrates how the Drosophila Y has been
accumulating autosomal genes.
acknowledgement: "This work was supported by grants from Conselho Nacional de Desenvolvimento
Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes
of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski,
C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished
data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski,
B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for
help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members
of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments
on the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Antonio
full_name: Carvalho, Antonio
last_name: Carvalho
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Claudia
full_name: Russo, Claudia
last_name: Russo
- first_name: Bonnielin
full_name: Swenor, Bonnielin
last_name: Swenor
- first_name: Andrew
full_name: Clark, Andrew
last_name: Clark
citation:
ama: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the
Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455.
doi:10.1073/pnas.1516543112
apa: Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth
of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1516543112
chicago: Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and
Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.”
PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112.
ieee: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new
gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no.
40. National Academy of Sciences, pp. 12450–12455, 2015.
ista: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene
on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.
mla: Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila
Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015,
pp. 12450–55, doi:10.1073/pnas.1516543112.
short: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.
date_created: 2018-12-11T11:52:49Z
date_published: 2015-10-06T00:00:00Z
date_updated: 2021-01-12T06:51:43Z
day: '06'
department:
- _id: BeVi
doi: 10.1073/pnas.1516543112
external_id:
pmid:
- '26385968'
intvolume: ' 112'
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/
month: '10'
oa: 1
oa_version: Published Version
page: 12450 - 12455
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5594'
quality_controlled: '1'
scopus_import: 1
status: public
title: Birth of a new gene on the Y chromosome of Drosophila melanogaster
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1579'
abstract:
- lang: eng
text: We show that the Galois group of any Schubert problem involving lines in projective
space contains the alternating group. This constitutes the largest family of enumerative
problems whose Galois groups have been largely determined. Using a criterion of
Vakil and a special position argument due to Schubert, our result follows from
a particular inequality among Kostka numbers of two-rowed tableaux. In most cases,
a combinatorial injection proves the inequality. For the remaining cases, we use
the Weyl integral formulas to obtain an integral formula for these Kostka numbers.
This rewrites the inequality as an integral, which we estimate to establish the
inequality.
acknowledgement: "This research was supported in part by NSF grant DMS-915211 and
the Institut Mittag-Leffler.\r\n"
article_processing_charge: No
author:
- first_name: Christopher
full_name: Brooks, Christopher
last_name: Brooks
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin Del Campo Sanchez
- first_name: Frank
full_name: Sottile, Frank
last_name: Sottile
citation:
ama: Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert
problems of lines are at least alternating. Transactions of the American Mathematical
Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8
apa: Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois
groups of Schubert problems of lines are at least alternating. Transactions
of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8
chicago: Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile.
“Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions
of the American Mathematical Society. American Mathematical Society, 2015.
https://doi.org/10.1090/S0002-9947-2014-06192-8.
ieee: C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of
Schubert problems of lines are at least alternating,” Transactions of the American
Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp.
4183–4206, 2015.
ista: Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert
problems of lines are at least alternating. Transactions of the American Mathematical
Society. 367(6), 4183–4206.
mla: Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are
at Least Alternating.” Transactions of the American Mathematical Society,
vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8.
short: C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American
Mathematical Society 367 (2015) 4183–4206.
date_created: 2018-12-11T11:52:50Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:43Z
day: '01'
department:
- _id: CaUh
doi: 10.1090/S0002-9947-2014-06192-8
intvolume: ' 367'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.4280
month: '06'
oa: 1
oa_version: Preprint
page: 4183 - 4206
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '5592'
quality_controlled: '1'
scopus_import: 1
status: public
title: Galois groups of Schubert problems of lines are at least alternating
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 367
year: '2015'
...
---
_id: '1589'
abstract:
- lang: eng
text: We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating
Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant
azimuthal modes. Without external magnetic field flows are stable and pro-grade
with respect to the rotation of the inner cylinder. More complex behaviors can
arise when an axial or a transverse magnetic field is applied. Depending on the
direction and strength of the field, multi-stable wavy states and bifurcations
can occur. We uncover the phenomenon of flow pattern reversal as the strength
of the magnetic field is increased through a critical value. In between the regimes
of pro-grade and retrograde flow rotations, standing waves with zero angular velocities
can emerge. A striking finding is that, under a transverse magnetic field, a second
reversal in the flow pattern direction can occur, where the flow pattern evolves
into pro-grade rotation again from a retrograde state. Flow reversal is relevant
to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest
that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic
field in a controlled manner, which can be realized in laboratory experiments
with potential applications in the development of modern fluid devices.
article_number: '18589'
article_type: original
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
- first_name: Younghae
full_name: Do, Younghae
last_name: Do
- first_name: Ying
full_name: Lai, Ying
last_name: Lai
citation:
ama: Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a
ferrofluidic Taylor-Couette system. Scientific Reports. 2015;5. doi:10.1038/srep18589
apa: Altmeyer, S., Do, Y., & Lai, Y. (2015). Magnetic field induced flow pattern
reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/srep18589
chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced
Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific
Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep18589.
ieee: S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal
in a ferrofluidic Taylor-Couette system,” Scientific Reports, vol. 5. Nature
Publishing Group, 2015.
ista: Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal
in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589.
mla: Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in
a Ferrofluidic Taylor-Couette System.” Scientific Reports, vol. 5, 18589,
Nature Publishing Group, 2015, doi:10.1038/srep18589.
short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).
date_created: 2018-12-11T11:52:53Z
date_published: 2015-12-21T00:00:00Z
date_updated: 2021-01-12T06:51:48Z
day: '21'
ddc:
- '530'
- '540'
department:
- _id: BjHo
doi: 10.1038/srep18589
file:
- access_level: open_access
checksum: 927e151674347661ce36eae2818dafdc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:49Z
date_updated: 2020-07-14T12:45:03Z
file_id: '5036'
file_name: IST-2016-472-v1+1_srep18589.pdf
file_size: 2771236
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '5582'
pubrep_id: '472'
quality_controlled: '1'
scopus_import: 1
status: public
title: Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette
system
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: 5
year: '2015'
...
---
_id: '1584'
abstract:
- lang: eng
text: We investigate weighted straight skeletons from a geometric, graph-theoretical,
and combinatorial point of view. We start with a thorough definition and shed
light on some ambiguity issues in the procedural definition. We investigate the
geometry, combinatorics, and topology of faces and the roof model, and we discuss
in which cases a weighted straight skeleton is connected. Finally, we show that
the weighted straight skeleton of even a simple polygon may be non-planar and
may contain cycles, and we discuss under which restrictions on the weights and/or
the input polygon the weighted straight skeleton still behaves similar to its
unweighted counterpart. In particular, we obtain a non-procedural description
and a linear-time construction algorithm for the straight skeleton of strictly
convex polygons with arbitrary weights.
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Dominik
full_name: Kaaser, Dominik
last_name: Kaaser
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Reprint of: Weighted straight
skeletons in the plane. Computational Geometry: Theory and Applications.
2015;48(5):429-442. doi:10.1016/j.comgeo.2015.01.004'
apa: 'Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Reprint
of: Weighted straight skeletons in the plane. Computational Geometry: Theory
and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2015.01.004'
chicago: 'Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader.
“Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry:
Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.01.004.'
ieee: 'T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Reprint of: Weighted
straight skeletons in the plane,” Computational Geometry: Theory and Applications,
vol. 48, no. 5. Elsevier, pp. 429–442, 2015.'
ista: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Reprint of: Weighted
straight skeletons in the plane. Computational Geometry: Theory and Applications.
48(5), 429–442.'
mla: 'Biedl, Therese, et al. “Reprint of: Weighted Straight Skeletons in the Plane.”
Computational Geometry: Theory and Applications, vol. 48, no. 5, Elsevier,
2015, pp. 429–42, doi:10.1016/j.comgeo.2015.01.004.'
short: 'T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry:
Theory and Applications 48 (2015) 429–442.'
date_created: 2018-12-11T11:52:51Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T10:05:22Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2015.01.004
file:
- access_level: open_access
checksum: 5b33719a86f7f4c8e5dc62c1b6893f49
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:36Z
date_updated: 2020-07-14T12:45:03Z
file_id: '5292'
file_name: IST-2016-475-v1+1_1-s2.0-S092577211500005X-main.pdf
file_size: 508379
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 48'
issue: '5'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 429 - 442
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '5587'
pubrep_id: '475'
quality_controlled: '1'
related_material:
record:
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relation: other
status: public
scopus_import: 1
status: public
title: 'Reprint of: Weighted straight skeletons in the plane'
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: 48
year: '2015'
...
---
_id: '1582'
abstract:
- lang: eng
text: We investigate weighted straight skeletons from a geometric, graph-theoretical,
and combinatorial point of view. We start with a thorough definition and shed
light on some ambiguity issues in the procedural definition. We investigate the
geometry, combinatorics, and topology of faces and the roof model, and we discuss
in which cases a weighted straight skeleton is connected. Finally, we show that
the weighted straight skeleton of even a simple polygon may be non-planar and
may contain cycles, and we discuss under which restrictions on the weights and/or
the input polygon the weighted straight skeleton still behaves similar to its
unweighted counterpart. In particular, we obtain a non-procedural description
and a linear-time construction algorithm for the straight skeleton of strictly
convex polygons with arbitrary weights.
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Dominik
full_name: Kaaser, Dominik
last_name: Kaaser
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Weighted straight skeletons
in the plane. Computational Geometry: Theory and Applications. 2015;48(2):120-133.
doi:10.1016/j.comgeo.2014.08.006'
apa: 'Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Weighted
straight skeletons in the plane. Computational Geometry: Theory and Applications.
Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.006'
chicago: 'Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader.
“Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory
and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.006.'
ieee: 'T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Weighted straight
skeletons in the plane,” Computational Geometry: Theory and Applications,
vol. 48, no. 2. Elsevier, pp. 120–133, 2015.'
ista: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Weighted straight
skeletons in the plane. Computational Geometry: Theory and Applications. 48(2),
120–133.'
mla: 'Biedl, Therese, et al. “Weighted Straight Skeletons in the Plane.” Computational
Geometry: Theory and Applications, vol. 48, no. 2, Elsevier, 2015, pp. 120–33,
doi:10.1016/j.comgeo.2014.08.006.'
short: 'T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry:
Theory and Applications 48 (2015) 120–133.'
date_created: 2018-12-11T11:52:51Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2023-02-23T10:05:27Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2014.08.006
file:
- access_level: open_access
checksum: c1ef67f6ec925e12f73a96b8fe285ab4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:28Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5215'
file_name: IST-2016-474-v1+1_1-s2.0-S0925772114000807-main.pdf
file_size: 505987
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 48'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 120 - 133
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '5589'
pubrep_id: '474'
quality_controlled: '1'
related_material:
record:
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relation: other
status: public
scopus_import: 1
status: public
title: Weighted straight skeletons in the plane
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: 48
year: '2015'
...
---
_id: '1583'
abstract:
- lang: eng
text: We study the characteristics of straight skeletons of monotone polygonal chains
and use them to devise an algorithm for computing positively weighted straight
skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space,
where n denotes the number of vertices of the polygon.
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Dominik
full_name: Kaaser, Dominik
last_name: Kaaser
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: Biedl T, Held M, Huber S, Kaaser D, Palfrader P. A simple algorithm for computing
positively weighted straight skeletons of monotone polygons. Information Processing
Letters. 2015;115(2):243-247. doi:10.1016/j.ipl.2014.09.021
apa: Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). A simple
algorithm for computing positively weighted straight skeletons of monotone polygons.
Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.021
chicago: Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader.
“A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone
Polygons.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.021.
ieee: T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “A simple algorithm
for computing positively weighted straight skeletons of monotone polygons,” Information
Processing Letters, vol. 115, no. 2. Elsevier, pp. 243–247, 2015.
ista: Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. A simple algorithm
for computing positively weighted straight skeletons of monotone polygons. Information
Processing Letters. 115(2), 243–247.
mla: Biedl, Therese, et al. “A Simple Algorithm for Computing Positively Weighted
Straight Skeletons of Monotone Polygons.” Information Processing Letters,
vol. 115, no. 2, Elsevier, 2015, pp. 243–47, doi:10.1016/j.ipl.2014.09.021.
short: T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Information Processing
Letters 115 (2015) 243–247.
date_created: 2018-12-11T11:52:51Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:51:45Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.ipl.2014.09.021
file:
- access_level: open_access
checksum: 2779a648610c9b5c86d0b51a62816d23
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:45Z
date_updated: 2020-07-14T12:45:03Z
file_id: '5367'
file_name: IST-2016-473-v1+1_1-s2.0-S0020019014001987-main.pdf
file_size: 270137
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 243 - 247
publication: Information Processing Letters
publication_status: published
publisher: Elsevier
publist_id: '5588'
pubrep_id: '473'
quality_controlled: '1'
scopus_import: 1
status: public
title: A simple algorithm for computing positively weighted straight skeletons of
monotone polygons
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: 115
year: '2015'
...
---
_id: '1587'
abstract:
- lang: eng
text: We investigate the quantum interference shifts between energetically close
states, where the state structure is observed by laser spectroscopy. We report
a compact and analytical expression that models the quantum interference induced
shift for any admixture of circular polarization of the incident laser and angle
of observation. An experimental scenario free of quantum interference can thus
be predicted with this formula. Although this study is exemplified here for muonic
deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p
frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme.
article_number: '062506'
article_processing_charge: No
article_type: original
author:
- first_name: Pedro
full_name: Amaro, Pedro
last_name: Amaro
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Aldo
full_name: Antognini, Aldo
last_name: Antognini
- first_name: Paul
full_name: Indelicato, Paul
last_name: Indelicato
- first_name: Randolf
full_name: Pohl, Randolf
last_name: Pohl
- first_name: José
full_name: Santos, José
last_name: Santos
citation:
ama: Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy
with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical
Physics. 2015;92(6). doi:10.1103/PhysRevA.92.062506
apa: Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R.,
& Santos, J. (2015). Quantum interference shifts in laser spectroscopy with
elliptical polarization. Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.92.062506
chicago: Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato,
Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy
with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.062506.
ieee: P. Amaro et al., “Quantum interference shifts in laser spectroscopy
with elliptical polarization,” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 92, no. 6. American Physical Society, 2015.
ista: Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J.
2015. Quantum interference shifts in laser spectroscopy with elliptical polarization.
Physical Review A - Atomic, Molecular, and Optical Physics. 92(6), 062506.
mla: Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with
Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:10.1103/PhysRevA.92.062506.
short: P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J.
Santos, Physical Review A - Atomic, Molecular, and Optical Physics 92 (2015).
date_created: 2018-12-11T11:52:53Z
date_published: 2015-12-31T00:00:00Z
date_updated: 2021-01-12T06:51:47Z
day: '31'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.92.062506
ec_funded: 1
external_id:
arxiv:
- '1511.03585'
intvolume: ' 92'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03585
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5584'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantum interference shifts in laser spectroscopy with elliptical polarization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2015'
...
---
_id: '1593'
abstract:
- lang: eng
text: 'Plants are sessile organisms that are permanently restricted to their site
of germination. To compensate for their lack of mobility, plants evolved unique
mechanisms enabling them to rapidly react to ever changing environmental conditions
and flexibly adapt their postembryonic developmental program. A prominent demonstration
of this developmental plasticity is their ability to bend organs in order to reach
the position most optimal for growth and utilization of light, nutrients, and
other resources. Shortly after germination, dicotyledonous seedlings form a bended
structure, the so-called apical hook, to protect the delicate shoot meristem and
cotyledons from damage when penetrating through the soil. Upon perception of a
light stimulus, the apical hook rapidly opens and the photomorphogenic developmental
program is activated. After germination, plant organs are able to align their
growth with the light source and adopt the most favorable orientation through
bending, in a process named phototropism. On the other hand, when roots and shoots
are diverted from their upright orientation, they immediately detect a change
in the gravity vector and bend to maintain a vertical growth direction. Noteworthy,
despite the diversity of external stimuli perceived by different plant organs,
all plant tropic movements share a common mechanistic basis: differential cell
growth. In our review, we will discuss the molecular principles underlying various
tropic responses with the focus on mechanisms mediating the perception of external
signals, transduction cascades and downstream responses that regulate differential
cell growth and consequently, organ bending. In particular, we highlight common
and specific features of regulatory pathways in control of the bending of organs
and a role for the plant hormone auxin as a key regulatory component.'
author:
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Dajo
full_name: Smet, Dajo
last_name: Smet
- first_name: Qiang
full_name: Zhu, Qiang
id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87
last_name: Zhu
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings
to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant
Science. 2015;6(4). doi:10.3389/fpls.2015.00218'
apa: 'Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., & Benková, E.
(2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility
control. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.00218'
chicago: 'Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and
Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin
in Mobility Control.” Frontiers in Plant Science. Frontiers Research Foundation,
2015. https://doi.org/10.3389/fpls.2015.00218.'
ieee: 'P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies
of seedlings to overcome their sessile nature: Auxin in mobility control,” Frontiers
in Plant Science, vol. 6, no. 4. Frontiers Research Foundation, 2015.'
ista: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies
of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers
in Plant Science. 6(4).'
mla: 'Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile
Nature: Auxin in Mobility Control.” Frontiers in Plant Science, vol. 6,
no. 4, Frontiers Research Foundation, 2015, doi:10.3389/fpls.2015.00218.'
short: P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers
in Plant Science 6 (2015).
date_created: 2018-12-11T11:52:55Z
date_published: 2015-04-14T00:00:00Z
date_updated: 2021-01-12T06:51:50Z
day: '14'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.3389/fpls.2015.00218
ec_funded: 1
file:
- access_level: open_access
checksum: c454d642e18dfa86820b97a86cd6d3cc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:23Z
date_updated: 2020-07-14T12:45:03Z
file_id: '5142'
file_name: IST-2016-471-v1+1_fpls-06-00218.pdf
file_size: 965690
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '4'
language:
- iso: eng
month: '04'
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
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '5578'
pubrep_id: '471'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Strategies of seedlings to overcome their sessile nature: Auxin in mobility
control'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1595'
abstract:
- lang: eng
text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric
circles C1, . . . , Ck with common center c, and edges are drawn radially: every
edge intersects every circle centered at c at most once. G is radial planar if
it has a radial embedding, that is, a crossing- free radial drawing. If the vertices
of G are ordered or partitioned into ordered levels (as they are for leveled graphs),
we require that the assignment of vertices to circles corresponds to the given
ordering or leveling. We show that a graph G is radial planar if G has a radial
drawing in which every two edges cross an even number of times; the radial embedding
has the same leveling as the radial drawing. In other words, we establish the
weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes
a result by Pach and Tóth.'
acknowledgement: The research leading to these results has received funding from the
People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreement no [291734].
alternative_title:
- LNCS
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Michael
full_name: Pelsmajer, Michael
last_name: Pelsmajer
- first_name: Marcus
full_name: Schaefer, Marcus
last_name: Schaefer
citation:
ama: 'Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol
9411. Springer; 2015:99-110. doi:10.1007/978-3-319-27261-0_9'
apa: 'Fulek, R., Pelsmajer, M., & Schaefer, M. (2015). Hanani-Tutte for radial
planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network
Visualization, Los Angeles, CA, USA: Springer. https://doi.org/10.1007/978-3-319-27261-0_9'
chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte
for Radial Planarity,” 9411:99–110. Springer, 2015. https://doi.org/10.1007/978-3-319-27261-0_9.
ieee: 'R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,”
presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA,
USA, 2015, vol. 9411, pp. 99–110.'
ista: 'Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity.
GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.'
mla: Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity. Vol. 9411,
Springer, 2015, pp. 99–110, doi:10.1007/978-3-319-27261-0_9.
short: R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110.
conference:
end_date: 2015-09-26
location: Los Angeles, CA, USA
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2015-09-24
date_created: 2018-12-11T11:52:55Z
date_published: 2015-11-27T00:00:00Z
date_updated: 2023-02-21T16:23:36Z
day: '27'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/978-3-319-27261-0_9
ec_funded: 1
file:
- access_level: open_access
checksum: 685f91bd077a951ba067d42cce75409e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:36Z
date_updated: 2020-07-14T12:45:03Z
file_id: '4697'
file_name: IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf
file_size: 330135
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 9411'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 99 - 110
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5576'
pubrep_id: '594'
quality_controlled: '1'
related_material:
record:
- id: '1113'
relation: later_version
status: public
- id: '1164'
relation: later_version
status: public
scopus_import: 1
status: public
title: Hanani-Tutte for radial planarity
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9411
year: '2015'
...
---
_id: '1590'
abstract:
- lang: eng
text: 'The straight skeleton of a polygon is the geometric graph obtained by tracing
the vertices during a mitered offsetting process. It is known that the straight
skeleton of a simple polygon is a tree, and one can naturally derive directions
on the edges of the tree from the propagation of the shrinking process. In this
paper, we ask the reverse question: Given a tree with directed edges, can it be
the straight skeleton of a polygon? And if so, can we find a suitable simple polygon?
We answer these questions for all directed trees where the order of edges around
each node is fixed.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Oswin
full_name: Aichholzer, Oswin
last_name: Aichholzer
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Thomas
full_name: Hackl, Thomas
last_name: Hackl
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
- first_name: Birgit
full_name: Vogtenhuber, Birgit
last_name: Vogtenhuber
citation:
ama: 'Aichholzer O, Biedl T, Hackl T, et al. Representing directed trees as straight
skeletons. In: Graph Drawing and Network Visualization. Vol 9411. Springer
Nature; 2015:335-347. doi:10.1007/978-3-319-27261-0_28'
apa: 'Aichholzer, O., Biedl, T., Hackl, T., Held, M., Huber, S., Palfrader, P.,
& Vogtenhuber, B. (2015). Representing directed trees as straight skeletons.
In Graph Drawing and Network Visualization (Vol. 9411, pp. 335–347). Los
Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_28'
chicago: Aichholzer, Oswin, Therese Biedl, Thomas Hackl, Martin Held, Stefan Huber,
Peter Palfrader, and Birgit Vogtenhuber. “Representing Directed Trees as Straight
Skeletons.” In Graph Drawing and Network Visualization, 9411:335–47. Springer
Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_28.
ieee: O. Aichholzer et al., “Representing directed trees as straight skeletons,”
in Graph Drawing and Network Visualization, vol. 9411, Springer Nature,
2015, pp. 335–347.
ista: 'Aichholzer O, Biedl T, Hackl T, Held M, Huber S, Palfrader P, Vogtenhuber
B. 2015.Representing directed trees as straight skeletons. In: Graph Drawing and
Network Visualization. LNCS, vol. 9411, 335–347.'
mla: Aichholzer, Oswin, et al. “Representing Directed Trees as Straight Skeletons.”
Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015,
pp. 335–47, doi:10.1007/978-3-319-27261-0_28.
short: O. Aichholzer, T. Biedl, T. Hackl, M. Held, S. Huber, P. Palfrader, B. Vogtenhuber,
in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 335–347.
conference:
end_date: 2015-09-26
location: Los Angeles, CA, United States
name: 'GD: International Symposium on Graph Drawing'
start_date: 2015-09-24
date_created: 2018-12-11T11:52:54Z
date_published: 2015-11-27T00:00:00Z
date_updated: 2022-01-28T09:10:37Z
day: '27'
department:
- _id: HeEd
doi: 10.1007/978-3-319-27261-0_28
intvolume: ' 9411'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1508.01076
month: '11'
oa: 1
oa_version: Preprint
page: 335 - 347
publication: Graph Drawing and Network Visualization
publication_identifier:
eisbn:
- 978-3-319-27261-0
isbn:
- 978-3-319-27260-3
publication_status: published
publisher: Springer Nature
publist_id: '5581'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Representing directed trees as straight skeletons
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9411
year: '2015'
...
---
_id: '1596'
abstract:
- lang: eng
text: Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon
in the plane with the stacking order. The collection C forms a visibility clique
if for everyi < j the intersection Ci and (Ci ∩ Cj)\⋃i<l<jCl =∅.elements
that are stacked between them, i.e., We show that if C forms a visibility clique
its size is bounded from above by O(k4) thereby improving the upper bound of 22k
from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the
size of a visibility clique for homothetes of a convex (not necessarily regular)
k-gon.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Radoš
full_name: Radoičić, Radoš
last_name: Radoičić
citation:
ama: 'Fulek R, Radoičić R. Vertical visibility among parallel polygons in three
dimensions. In: Graph Drawing and Network Visualization. Vol 9411. Springer
Nature; 2015:373-379. doi:10.1007/978-3-319-27261-0_31'
apa: 'Fulek, R., & Radoičić, R. (2015). Vertical visibility among parallel polygons
in three dimensions. In Graph Drawing and Network Visualization (Vol. 9411,
pp. 373–379). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_31'
chicago: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel
Polygons in Three Dimensions.” In Graph Drawing and Network Visualization,
9411:373–79. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_31.
ieee: R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in
three dimensions,” in Graph Drawing and Network Visualization, vol. 9411,
Springer Nature, 2015, pp. 373–379.
ista: 'Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in
three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411,
373–379.'
mla: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons
in Three Dimensions.” Graph Drawing and Network Visualization, vol. 9411,
Springer Nature, 2015, pp. 373–79, doi:10.1007/978-3-319-27261-0_31.
short: R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer
Nature, 2015, pp. 373–379.
conference:
end_date: 2015-09-26
location: Los Angeles, CA, United States
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2015-09-24
date_created: 2018-12-11T11:52:56Z
date_published: 2015-11-27T00:00:00Z
date_updated: 2022-01-28T09:20:50Z
day: '27'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1007/978-3-319-27261-0_31
ec_funded: 1
file:
- access_level: open_access
checksum: eec04f86c5921d04f025d5791db9b965
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:06Z
date_updated: 2020-07-14T12:45:04Z
file_id: '5258'
file_name: IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf
file_size: 312992
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 9411'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 373 - 379
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Graph Drawing and Network Visualization
publication_identifier:
isbn:
- 978-3-319-27260-3
publication_status: published
publisher: Springer Nature
publist_id: '5575'
pubrep_id: '595'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Vertical visibility among parallel polygons in three dimensions
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9411
year: '2015'
...
---
_id: '1601'
abstract:
- lang: eng
text: We propose a flexible exchange format for ω-automata, as typically used in
formal verification, and implement support for it in a range of established tools.
Our aim is to simplify the interaction of tools, helping the research community
to build upon other people’s work. A key feature of the format is the use of very
generic acceptance conditions, specified by Boolean combinations of acceptance
primitives, rather than being limited to common cases such as Büchi, Streett,
or Rabin. Such flexibility in the choice of acceptance conditions can be exploited
in applications, for example in probabilistic model checking, and furthermore
encourages the development of acceptance-agnostic tools for automata manipulations.
The format allows acceptance conditions that are either state-based or transition-based,
and also supports alternating automata.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Tomáš
full_name: Babiak, Tomáš
last_name: Babiak
- first_name: František
full_name: Blahoudek, František
last_name: Blahoudek
- first_name: Alexandre
full_name: Duret Lutz, Alexandre
last_name: Duret Lutz
- first_name: Joachim
full_name: Klein, Joachim
last_name: Klein
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
- first_name: David
full_name: Parker, David
last_name: Parker
- first_name: Jan
full_name: Strejček, Jan
last_name: Strejček
citation:
ama: 'Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format.
In: Vol 9206. Springer; 2015:479-486. doi:10.1007/978-3-319-21690-4_31'
apa: 'Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller,
D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486).
Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States:
Springer. https://doi.org/10.1007/978-3-319-21690-4_31'
chicago: Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein,
Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata
Format,” 9206:479–86. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_31.
ieee: 'T. Babiak et al., “The Hanoi omega-automata format,” presented at
the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015,
vol. 9206, pp. 479–486.'
ista: 'Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker
D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification,
LNCS, vol. 9206, 479–486.'
mla: Babiak, Tomáš, et al. The Hanoi Omega-Automata Format. Vol. 9206, Springer,
2015, pp. 479–86, doi:10.1007/978-3-319-21690-4_31.
short: T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller,
D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486.
conference:
end_date: 2015-07-24
location: San Francisco, CA, United States
name: 'CAV: Computer Aided Verification'
start_date: 2015-07-18
date_created: 2018-12-11T11:52:57Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2021-01-12T06:51:54Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-319-21690-4_31
ec_funded: 1
file:
- access_level: open_access
checksum: 5885236fa88a439baba9ac6f3e801e93
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T08:38:12Z
date_updated: 2020-07-14T12:45:04Z
file_id: '7850'
file_name: 2015_CAV_Babiak.pdf
file_size: 1651779
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 9206'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 479 - 486
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5566'
quality_controlled: '1'
scopus_import: 1
status: public
title: The Hanoi omega-automata format
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '1605'
abstract:
- lang: eng
text: Multiaffine hybrid automata (MHA) represent a powerful formalism to model
complex dynamical systems. This formalism is particularly suited for the representation
of biological systems which often exhibit highly non-linear behavior. In this
paper, we consider the problem of parameter identification for MHA. We present
an abstraction of MHA based on linear hybrid automata, which can be analyzed by
the SpaceEx model checker. This abstraction enables a precise handling of time-dependent
properties. We demonstrate the potential of our approach on a model of a genetic
regulatory network and a myocyte model.
acknowledgement: This work was partly supported by the European Research Council (ERC)
under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23,
S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by
the German Research Foundation (DFG) as part of the Transregional Collaborative
Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR
14 AVACS, http://www.avacs.org/).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Grégory
full_name: Batt, Grégory
last_name: Batt
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based
parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35.
doi:10.1007/978-3-319-26287-1_2'
apa: 'Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., & Grosu,
R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol.
9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa,
Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_2'
chicago: Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui
Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,”
9434:19–35. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_2.
ieee: 'S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu,
“Abstraction-based parameter synthesis for multiaffine systems,” presented at
the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.'
ista: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based
parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference,
LNCS, vol. 9434, 19–35.'
mla: Bogomolov, Sergiy, et al. Abstraction-Based Parameter Synthesis for Multiaffine
Systems. Vol. 9434, Springer, 2015, pp. 19–35, doi:10.1007/978-3-319-26287-1_2.
short: S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:,
Springer, 2015, pp. 19–35.
conference:
end_date: 2015-11-19
location: Haifa, Israel
name: 'HVC: Haifa Verification Conference'
start_date: 2015-11-17
date_created: 2018-12-11T11:52:59Z
date_published: 2015-11-28T00:00:00Z
date_updated: 2021-01-12T06:51:56Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-26287-1_2
ec_funded: 1
file:
- access_level: open_access
checksum: 3aab260f3f34641d622030ba22645b3e
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T08:43:19Z
date_updated: 2020-07-14T12:45:05Z
file_id: '7851'
file_name: 2015_LNCS_Bogomolov.pdf
file_size: 1053207
relation: main_file
file_date_updated: 2020-07-14T12:45:05Z
has_accepted_license: '1'
intvolume: ' 9434'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 19 - 35
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5561'
quality_controlled: '1'
scopus_import: 1
status: public
title: Abstraction-based parameter synthesis for multiaffine systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9434
year: '2015'
...
---
_id: '1609'
abstract:
- lang: eng
text: The synthesis problem asks for the automatic construction of a system from
its specification. In the traditional setting, the system is “constructed from
scratch” rather than composed from reusable components. However, this is rare
in practice, and almost every non-trivial software system relies heavily on the
use of libraries of reusable components. Recently, Lustig and Vardi introduced
dataflow and controlflow synthesis from libraries of reusable components. They
proved that dataflow synthesis is undecidable, while controlflow synthesis is
decidable. The problem of controlflow synthesis from libraries of probabilistic
components was considered by Nain, Lustig and Vardi, and was shown to be decidable
for qualitative analysis (that asks that the specification be satisfied with probability
1). Our main contribution for controlflow synthesis from probabilistic components
is to establish better complexity bounds for the qualitative analysis problem,
and to show that the more general quantitative problem is undecidable. For the
qualitative analysis, we show that the problem (i) is EXPTIME-complete when the
specification is given as a deterministic parity word automaton, improving the
previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games
hard, when the specification is given directly as a parity condition on the components,
improving the previously known EXPTIME upper bound.
acknowledgement: 'This research was supported by Austrian Science Fund (FWF) Grant
No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph
Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF
Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program
Engineering”, by BSF grant 9800096, and by gift from Intel.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Moshe
full_name: Vardi, Moshe
last_name: Vardi
citation:
ama: 'Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic
components. In: 42nd International Colloquium. Vol 9135. Springer Nature;
2015:108-120. doi:10.1007/978-3-662-47666-6_9'
apa: 'Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis
from probabilistic components. In 42nd International Colloquium (Vol. 9135,
pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity
of Synthesis from Probabilistic Components.” In 42nd International Colloquium,
9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9.
ieee: K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic
components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol.
9135, pp. 108–120.
ista: 'Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic
components. 42nd International Colloquium. ICALP: Automata, Languages and Programming,
LNCS, vol. 9135, 108–120.'
mla: Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic
Components.” 42nd International Colloquium, vol. 9135, Springer Nature,
2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9.
short: K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer
Nature, 2015, pp. 108–120.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: Automata, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:00Z
date_published: 2015-06-20T00:00:00Z
date_updated: 2022-02-01T15:04:44Z
day: '20'
department:
- _id: KrCh
doi: 10.1007/978-3-662-47666-6_9
ec_funded: 1
intvolume: ' 9135'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.04844
month: '06'
oa: 1
oa_version: Preprint
page: 108 - 120
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'
publication: 42nd International Colloquium
publication_identifier:
isbn:
- 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5557'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The complexity of synthesis from probabilistic components
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '1615'
abstract:
- lang: eng
text: Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are
among the most common genetic abnormalities associated with autism spectrum disorders,
but little is known about the function of Neuroligin-4 and the consequences of
its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout
mice, focusing on the hippocampus as a model brain region with a critical role
in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects
of the protein composition and function of GABAergic synapses in the hippocampal
CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced
perturbations of γ-oscillatory network activity, which has been implicated in
cognitive function and is altered in multiple psychiatric and neurodevelopmental
disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent
GABAergic synapses may contribute to autism phenotypes and indicate new strategies
for therapeutic approaches.
acknowledgement: This work was supported by the Max Planck Society (N.B. and H.E.),
the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.),
the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von
Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen
Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular
Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody.
We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler
for valuable advice and excellent technical support. We are grateful to the staff
at the animal facility of the Max Planck Institute of Experimental Medicine for
mouse husbandry.
author:
- first_name: Matthieu
full_name: Hammer, Matthieu
last_name: Hammer
- first_name: Dilja
full_name: Krueger Burg, Dilja
last_name: Krueger Burg
- first_name: Liam
full_name: Tuffy, Liam
last_name: Tuffy
- first_name: Benjamin
full_name: Cooper, Benjamin
last_name: Cooper
- first_name: Holger
full_name: Taschenberger, Holger
last_name: Taschenberger
- first_name: Sarit
full_name: Goswami, Sarit
id: 3A578F32-F248-11E8-B48F-1D18A9856A87
last_name: Goswami
- first_name: Hannelore
full_name: Ehrenreich, Hannelore
last_name: Ehrenreich
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Frederique
full_name: Varoqueaux, Frederique
last_name: Varoqueaux
- first_name: Jeong
full_name: Rhee, Jeong
last_name: Rhee
- first_name: Nils
full_name: Brose, Nils
last_name: Brose
citation:
ama: Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition
and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports.
2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011
apa: Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami,
S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations
in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press.
https://doi.org/10.1016/j.celrep.2015.09.011
chicago: Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger
Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal
Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model
of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011.
ieee: M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations
in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13,
no. 3. Cell Press, pp. 516–523, 2015.
ista: Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich
H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic
inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism.
Cell Reports. 13(3), 516–523.
mla: Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations
in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13,
no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011.
short: M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami,
H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015)
516–523.
date_created: 2018-12-11T11:53:02Z
date_published: 2015-10-20T00:00:00Z
date_updated: 2021-01-12T06:52:01Z
day: '20'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2015.09.011
file:
- access_level: open_access
checksum: 44d30fbb543774b076b4938bd36af9d7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:23Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5005'
file_name: IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf
file_size: 2314406
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '3'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 516 - 523
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '5551'
pubrep_id: '470'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4
knockout mouse model of autism
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: '2015'
...
---
_id: '1614'
abstract:
- lang: eng
text: 'GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively
control the activity of large neuron populations by their wide axonal arborizations.
It is generally assumed that the output of one PII to its target cells is strong
and rapid. Here, we show that, unexpectedly, both strength and time course of
PII-mediated perisomatic inhibition change with distance between synaptically
connected partners in the rodent hippocampus. Synaptic signals become weaker due
to lower contact numbers and decay more slowly with distance, very likely resulting
from changes in GABAA receptor subunit composition. When distance-dependent synaptic
inhibition is introduced to a rhythmically active neuronal network model, randomly
driven principal cell assemblies are strongly synchronized by the PIIs, leading
to higher precision in principal cell spike times than in a network with uniform
synaptic inhibition. '
author:
- first_name: Michael
full_name: Strüber, Michael
last_name: Strüber
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic
inhibition depend on distance between synaptically connected cells. PNAS.
2015;112(4):1220-1225. doi:10.1073/pnas.1412996112
apa: Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of
perisomatic GABAergic inhibition depend on distance between synaptically connected
cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112
chicago: Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration
of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected
Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112.
ieee: M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic
GABAergic inhibition depend on distance between synaptically connected cells,”
PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.
ista: Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic
GABAergic inhibition depend on distance between synaptically connected cells.
PNAS. 112(4), 1220–1225.
mla: Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition
Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112,
no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112.
short: M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.
date_created: 2018-12-11T11:53:02Z
date_published: 2015-01-27T00:00:00Z
date_updated: 2021-01-12T06:52:01Z
day: '27'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1073/pnas.1412996112
ec_funded: 1
external_id:
pmid:
- '25583495'
file:
- access_level: open_access
checksum: 6703309a1f58493cf5a704211fb6ebed
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T07:52:40Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5838'
file_name: 2015_PNAS_Strueber.pdf
file_size: 1280860
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1220 - 1225
pmid: 1
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5552'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strength and duration of perisomatic GABAergic inhibition depend on distance
between synaptically connected cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1611'
abstract:
- lang: eng
text: Biosensors for signaling molecules allow the study of physiological processes
by bringing together the fields of protein engineering, fluorescence imaging,
and cell biology. Construction of genetically encoded biosensors generally relies
on the availability of a binding "core" that is both specific and stable,
which can then be combined with fluorescent molecules to create a sensor. However,
binding proteins with the desired properties are often not available in nature
and substantial improvement to sensors can be required, particularly with regard
to their durability. Ancestral protein reconstruction is a powerful protein-engineering
tool able to generate highly stable and functional proteins. In this work, we
sought to establish the utility of ancestral protein reconstruction to biosensor
development, beginning with the construction of an l-arginine biosensor. l-arginine,
as the immediate precursor to nitric oxide, is an important molecule in many physiological
contexts including brain function. Using a combination of ancestral reconstruction
and circular permutation, we constructed a Förster resonance energy transfer (FRET)
biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity,
with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was
highly robust, enabling accurate l-arginine measurement at physiological temperatures.
We established that cpFLIPR is compatible with two-photon excitation fluorescence
microscopy and report l-arginine concentrations in brain tissue.
author:
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Ben
full_name: Clifton, Ben
last_name: Clifton
- first_name: Johanna
full_name: Radziejewski, Johanna
last_name: Radziejewski
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive
arginine biosensor through ancestral protein reconstruction. Protein Science.
2015;24(9):1412-1422. doi:10.1002/pro.2721
apa: Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak,
H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor
through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721
chicago: Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski,
Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of
a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.”
Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721.
ieee: J. Whitfield et al., “Construction of a robust and sensitive arginine
biosensor through ancestral protein reconstruction,” Protein Science, vol.
24, no. 9. Wiley, pp. 1412–1422, 2015.
ista: Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger
C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor
through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.
mla: Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor
through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no.
9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721.
short: J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak,
C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.
date_created: 2018-12-11T11:53:01Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:52:00Z
day: '01'
department:
- _id: HaJa
doi: 10.1002/pro.2721
external_id:
pmid:
- '26061224'
intvolume: ' 24'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/
month: '09'
oa: 1
oa_version: Submitted Version
page: 1412 - 1422
pmid: 1
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Protein Science
publication_status: published
publisher: Wiley
publist_id: '5555'
quality_controlled: '1'
scopus_import: 1
status: public
title: Construction of a robust and sensitive arginine biosensor through ancestral
protein reconstruction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '1624'
abstract:
- lang: eng
text: Population structure can facilitate evolution of cooperation. In a structured
population, cooperators can form clusters which resist exploitation by defectors.
Recently, it was observed that a shift update rule is an extremely strong amplifier
of cooperation in a one dimensional spatial model. For the shift update rule,
an individual is chosen for reproduction proportional to fecundity; the offspring
is placed next to the parent; a random individual dies. Subsequently, the population
is rearranged (shifted) until all individual cells are again evenly spaced out.
For large population size and a one dimensional population structure, the shift
update rule favors cooperation for any benefit-to-cost ratio greater than one.
But every attempt to generalize shift updating to higher dimensions while maintaining
its strong effect has failed. The reason is that in two dimensions the clusters
are fragmented by the movements caused by rearranging the cells. Here we introduce
the natural phenomenon of a repulsive force between cells of different types.
After a birth and death event, the cells are being rearranged minimizing the overall
energy expenditure. If the repulsive force is sufficiently high, shift becomes
a strong promoter of cooperation in two dimensions.
acknowledgement: 'The research was supported by the Austrian Science Fund (FWF) Grant
No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307:
Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton
foundation is gratefully acknowledged.'
article_number: '17147'
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift
updating and repulsion. Scientific Reports. 2015;5. doi:10.1038/srep17147
apa: Pavlogiannis, A., Chatterjee, K., Adlam, B., & Nowak, M. (2015). Cellular
cooperation with shift updating and repulsion. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/srep17147
chicago: Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak.
“Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports.
Nature Publishing Group, 2015. https://doi.org/10.1038/srep17147.
ieee: A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation
with shift updating and repulsion,” Scientific Reports, vol. 5. Nature
Publishing Group, 2015.
ista: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation
with shift updating and repulsion. Scientific Reports. 5, 17147.
mla: Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and
Repulsion.” Scientific Reports, vol. 5, 17147, Nature Publishing Group,
2015, doi:10.1038/srep17147.
short: A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5
(2015).
date_created: 2018-12-11T11:53:06Z
date_published: 2015-11-25T00:00:00Z
date_updated: 2021-01-12T06:52:05Z
day: '25'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/srep17147
ec_funded: 1
file:
- access_level: open_access
checksum: 38e06d8310d2087cae5f6d4d4bfe082b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:29Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4947'
file_name: IST-2016-466-v1+1_srep17147.pdf
file_size: 1021931
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '5536'
pubrep_id: '466'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cellular cooperation with shift updating and repulsion
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: 5
year: '2015'
...
---
_id: '1623'
abstract:
- lang: eng
text: "Background\r\nPhotosynthetic cyanobacteria are attractive for a range of
biotechnological applications including biofuel production. However, due to slow
growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe
present a method for high-throughput, single-cell analysis and sorting of genetically
engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic
device is used to encapsulate single cells in picoliter droplets, assay the droplets
for l-lactate production, and sort strains with high productivity. We demonstrate
the separation of low- and high-producing reference strains, as well as enrichment
of a more productive l-lactate-synthesizing population after UV-induced mutagenesis.
The droplet platform also revealed population heterogeneity in photosynthetic
growth and lactate production, as well as the presence of metabolically stalled
cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and
directed evolution studies and will be useful in studies of cyanobacteria biochemistry
and physiology.\r\n"
article_number: '193'
author:
- first_name: Petter
full_name: Hammar, Petter
last_name: Hammar
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Staffan
full_name: Sjostrom, Staffan
last_name: Sjostrom
- first_name: Josefin
full_name: Van Der Meer, Josefin
last_name: Van Der Meer
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
- first_name: Elton
full_name: Hudson, Elton
last_name: Hudson
- first_name: Hakaan
full_name: Joensson, Hakaan
last_name: Joensson
citation:
ama: Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic
growth and lactate production by cyanobacteria. Biotechnology for Biofuels.
2015;8(1). doi:10.1186/s13068-015-0380-2
apa: Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K.,
Hudson, E., & Joensson, H. (2015). Single-cell screening of photosynthetic
growth and lactate production by cyanobacteria. Biotechnology for Biofuels.
BioMed Central. https://doi.org/10.1186/s13068-015-0380-2
chicago: Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer,
Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of
Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology
for Biofuels. BioMed Central, 2015. https://doi.org/10.1186/s13068-015-0380-2.
ieee: P. Hammar et al., “Single-cell screening of photosynthetic growth and
lactate production by cyanobacteria,” Biotechnology for Biofuels, vol.
8, no. 1. BioMed Central, 2015.
ista: Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E,
Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production
by cyanobacteria. Biotechnology for Biofuels. 8(1), 193.
mla: Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and
Lactate Production by Cyanobacteria.” Biotechnology for Biofuels, vol.
8, no. 1, 193, BioMed Central, 2015, doi:10.1186/s13068-015-0380-2.
short: P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E.
Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015).
date_created: 2018-12-11T11:53:05Z
date_published: 2015-11-25T00:00:00Z
date_updated: 2021-01-12T06:52:04Z
day: '25'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1186/s13068-015-0380-2
file:
- access_level: open_access
checksum: 172b0b6f4eb2e5c22b7cec1d57dc0107
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:11Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4796'
file_name: IST-2016-467-v1+1_s13068-015-0380-2.pdf
file_size: 2914089
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Biotechnology for Biofuels
publication_status: published
publisher: BioMed Central
publist_id: '5537'
pubrep_id: '467'
quality_controlled: '1'
scopus_import: 1
status: public
title: Single-cell screening of photosynthetic growth and lactate production by cyanobacteria
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: '2015'
...
---
_id: '1628'
abstract:
- lang: eng
text: We propose a method for fabricating deformable objects with spatially varying
elasticity using 3D printing. Using a single, relatively stiff printer material,
our method designs an assembly of smallscale microstructures that have the effect
of a softer material at the object scale, with properties depending on the microstructure
used in each part of the object. We build on work in the area of metamaterials,
using numerical optimization to design tiled microstructures with desired properties,
but with the key difference that our method designs families of related structures
that can be interpolated to smoothly vary the material properties over a wide
range. To create an object with spatially varying elastic properties, we tile
the object's interior with microstructures drawn from these families, generating
a different microstructure for each cell using an efficient algorithm to select
compatible structures for neighboring cells. We show results computed for both
2D and 3D objects, validating several 2D and 3D printed structures using standard
material tests as well as demonstrating various example applications.
article_number: '136'
article_processing_charge: No
author:
- first_name: Christian
full_name: Schumacher, Christian
last_name: Schumacher
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Jan
full_name: Rys, Jan
last_name: Rys
- first_name: Steve
full_name: Marschner, Steve
last_name: Marschner
- first_name: Chiara
full_name: Daraio, Chiara
last_name: Daraio
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
citation:
ama: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. Microstructures
to control elasticity in 3D printing. In: Vol 34. ACM; 2015. doi:10.1145/2766926'
apa: 'Schumacher, C., Bickel, B., Rys, J., Marschner, S., Daraio, C., & Gross,
M. (2015). Microstructures to control elasticity in 3D printing (Vol. 34). Presented
at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766926'
chicago: Schumacher, Christian, Bernd Bickel, Jan Rys, Steve Marschner, Chiara Daraio,
and Markus Gross. “Microstructures to Control Elasticity in 3D Printing,” Vol.
34. ACM, 2015. https://doi.org/10.1145/2766926.
ieee: 'C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, and M. Gross,
“Microstructures to control elasticity in 3D printing,” presented at the SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles,
CA, USA, 2015, vol. 34, no. 4.'
ista: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. 2015. Microstructures
to control elasticity in 3D printing. SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques vol. 34, 136.'
mla: Schumacher, Christian, et al. Microstructures to Control Elasticity in 3D
Printing. Vol. 34, no. 4, 136, ACM, 2015, doi:10.1145/2766926.
short: C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, M. Gross, in:,
ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, USA
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:07Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:52:06Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/2766926
intvolume: ' 34'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/2766926
month: '08'
oa: 1
oa_version: Published Version
publication_status: published
publisher: ACM
publist_id: '5529'
quality_controlled: '1'
scopus_import: 1
status: public
title: Microstructures to control elasticity in 3D printing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1634'
abstract:
- lang: eng
text: Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally
required the use of a fully three-dimensional many-phase Navier-Stokes solver,
even though their visual appearance is completely dominated by the thin liquid
surface. We depart from earlier work on soap bubbles and foams by noting that
their dynamics are naturally described by a Lagrangian vortex sheet model in which
circulation is the primary variable. This leads us to derive a novel circulation-preserving
surface-only discretization of foam dynamics driven by surface tension on a non-manifold
triangle mesh. We represent the surface using a mesh-based multimaterial surface
tracker which supports complex bubble topology changes, and evolve the surface
according to the ambient air flow induced by a scalar circulation field stored
on the mesh. Surface tension forces give rise to a simple update rule for circulation,
even at non-manifold Plateau borders, based on a discrete measure of signed scalar
mean curvature. We further incorporate vertex constraints to enable the interaction
of soap films with wires. The result is a method that is at once simple, robust,
and efficient, yet able to capture an array of soap films behaviors including
foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being
pulled apart.
article_number: '149'
author:
- first_name: Fang
full_name: Da, Fang
last_name: Da
- first_name: Christopher
full_name: Batty, Christopher
last_name: Batty
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Eitan
full_name: Grinspun, Eitan
last_name: Grinspun
citation:
ama: 'Da F, Batty C, Wojtan C, Grinspun E. Double bubbles sans toil and trouble:
discrete circulation-preserving vortex sheets for soap films and foams. In: Vol
34. ACM; 2015. doi:10.1145/2767003'
apa: 'Da, F., Batty, C., Wojtan, C., & Grinspun, E. (2015). Double bubbles sans
toil and trouble: discrete circulation-preserving vortex sheets for soap films
and foams (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2767003'
chicago: 'Da, Fang, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Double
Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for
Soap Films and Foams,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2767003.'
ieee: 'F. Da, C. Batty, C. Wojtan, and E. Grinspun, “Double bubbles sans toil and
trouble: discrete circulation-preserving vortex sheets for soap films and foams,”
presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.'
ista: 'Da F, Batty C, Wojtan C, Grinspun E. 2015. Double bubbles sans toil and trouble:
discrete circulation-preserving vortex sheets for soap films and foams. SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques vol. 34,
149.'
mla: 'Da, Fang, et al. Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving
Vortex Sheets for Soap Films and Foams. Vol. 34, no. 4, 149, ACM, 2015, doi:10.1145/2767003.'
short: F. Da, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2023-02-23T10:07:42Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2767003
ec_funded: 1
file:
- access_level: open_access
checksum: 57b07d78d2d612a8052744b37d4a71fa
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:14Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4867'
file_name: IST-2016-608-v1+1_doublebubbles.pdf
file_size: 8973215
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5521'
pubrep_id: '608'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Double bubbles sans toil and trouble: discrete circulation-preserving vortex
sheets for soap films and foams'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1636'
abstract:
- lang: eng
text: "Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem
that appears in many areas of Computer Science. It can be equivalently stated
as computing a homomorphism R→ΓΓ between two relational structures, e.g. between
two directed graphs. Analyzing its complexity has been a prominent research direction,
especially for the fixed template CSPs where the right side ΓΓ is fixed and the
left side R is unconstrained.\r\n\r\nFar fewer results are known for the hybrid
setting that restricts both sides simultaneously. It assumes that R belongs to
a certain class of relational structures (called a structural restriction in this
paper). We study which structural restrictions are effective, i.e. there exists
a fixed template ΓΓ (from a certain class of languages) for which the problem
is tractable when R is restricted, and NP-hard otherwise. We provide a characterization
for structural restrictions that are closed under inverse homomorphisms. The criterion
is based on the chromatic number of a relational structure defined in this paper;
it generalizes the standard chromatic number of a graph.\r\n\r\nAs our main tool,
we use the algebraic machinery developed for fixed template CSPs. To apply it
to our case, we introduce a new construction called a “lifted language”. We also
give a characterization for structural restrictions corresponding to minor-closed
families of graphs, extend results to certain Valued CSPs (namely conservative
valued languages), and state implications for (valued) CSPs with ordered variables
and for the maximum weight independent set problem on some restricted families
of graphs."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
- first_name: Rustem
full_name: Takhanov, Rustem
last_name: Takhanov
citation:
ama: 'Kolmogorov V, Rolinek M, Takhanov R. Effectiveness of structural restrictions
for hybrid CSPs. In: 26th International Symposium. Vol 9472. Springer Nature;
2015:566-577. doi:10.1007/978-3-662-48971-0_48'
apa: 'Kolmogorov, V., Rolinek, M., & Takhanov, R. (2015). Effectiveness of structural
restrictions for hybrid CSPs. In 26th International Symposium (Vol. 9472,
pp. 566–577). Nagoya, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-48971-0_48'
chicago: Kolmogorov, Vladimir, Michal Rolinek, and Rustem Takhanov. “Effectiveness
of Structural Restrictions for Hybrid CSPs.” In 26th International Symposium,
9472:566–77. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48971-0_48.
ieee: V. Kolmogorov, M. Rolinek, and R. Takhanov, “Effectiveness of structural restrictions
for hybrid CSPs,” in 26th International Symposium, Nagoya, Japan, 2015,
vol. 9472, pp. 566–577.
ista: 'Kolmogorov V, Rolinek M, Takhanov R. 2015. Effectiveness of structural restrictions
for hybrid CSPs. 26th International Symposium. ISAAC: International Symposium
on Algorithms and Computation, LNCS, vol. 9472, 566–577.'
mla: Kolmogorov, Vladimir, et al. “Effectiveness of Structural Restrictions for
Hybrid CSPs.” 26th International Symposium, vol. 9472, Springer Nature,
2015, pp. 566–77, doi:10.1007/978-3-662-48971-0_48.
short: V. Kolmogorov, M. Rolinek, R. Takhanov, in:, 26th International Symposium,
Springer Nature, 2015, pp. 566–577.
conference:
end_date: 2015-12-11
location: Nagoya, Japan
name: 'ISAAC: International Symposium on Algorithms and Computation'
start_date: 2015-12-09
date_created: 2018-12-11T11:53:10Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2022-02-01T15:12:35Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/978-3-662-48971-0_48
ec_funded: 1
external_id:
arxiv:
- '1504.07067'
intvolume: ' 9472'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.07067
month: '12'
oa: 1
oa_version: Preprint
page: 566 - 577
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: 26th International Symposium
publication_identifier:
isbn:
- 978-3-662-48970-3
publication_status: published
publisher: Springer Nature
publist_id: '5519'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effectiveness of structural restrictions for hybrid CSPs
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9472
year: '2015'
...
---
_id: '1632'
abstract:
- lang: eng
text: "This paper presents a liquid simulation technique that enforces the incompressibility
condition using a stream function solve instead of a pressure projection. Previous
methods have used stream function techniques for the simulation of detailed single-phase
flows, but a formulation for liquid simulation has proved elusive in part due
to the free surface boundary conditions. In this paper, we introduce a stream
function approach to liquid simulations with novel boundary conditions for free
surfaces, solid obstacles, and solid-fluid coupling.\r\n\r\nAlthough our approach
increases the dimension of the linear system necessary to enforce incompressibility,
it provides interesting and surprising benefits. First, the resulting flow is
guaranteed to be divergence-free regardless of the accuracy of the solve. Second,
our free-surface boundary conditions guarantee divergence-free motion even in
the un-simulated air phase, which enables two-phase flow simulation by only computing
a single phase. We implemented this method using a variant of FLIP simulation
which only samples particles within a narrow band of the liquid surface, and we
illustrate the effectiveness of our method for detailed two-phase flow simulations
with complex boundaries, detailed bubble interactions, and two-way solid-fluid
coupling."
acknowledgement: The first author was supported by a JSPS Postdoctoral Fellowship
for Research Abroad. This work was also supported by the ERC projects ERC-2014-StG-637014
realFlow and ERC-2014- StG-638176 BigSplash.
alternative_title:
- ACM Transactions on Graphics
article_number: '53'
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. A stream function solver for liquid simulations.
In: Vol 34. ACM; 2015. doi:10.1145/2766935'
apa: 'Ando, R., Thuerey, N., & Wojtan, C. (2015). A stream function solver for
liquid simulations (Vol. 34). Presented at the SIGGRAPH: Special Interest Group
on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766935'
chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “A Stream Function Solver
for Liquid Simulations,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766935.
ieee: 'R. Ando, N. Thuerey, and C. Wojtan, “A stream function solver for liquid
simulations,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics
and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.'
ista: 'Ando R, Thuerey N, Wojtan C. 2015. A stream function solver for liquid simulations.
SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
ACM Transactions on Graphics, vol. 34, 53.'
mla: Ando, Ryoichi, et al. A Stream Function Solver for Liquid Simulations.
Vol. 34, no. 4, 53, ACM, 2015, doi:10.1145/2766935.
short: R. Ando, N. Thuerey, C. Wojtan, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, USA
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2023-02-23T10:07:37Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766935
file:
- access_level: open_access
checksum: 7a9afdfaba9209157ce19376e15bc90b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:52Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4909'
file_name: IST-2016-610-v1+1_vecpotential.pdf
file_size: 21831121
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: ACM
publist_id: '5523'
pubrep_id: '610'
quality_controlled: '1'
scopus_import: 1
status: public
title: A stream function solver for liquid simulations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1630'
abstract:
- lang: eng
text: We present a method to learn and propagate shape placements in 2D polygonal
scenes from a few examples provided by a user. The placement of a shape is modeled
as an oriented bounding box. Simple geometric relationships between this bounding
box and nearby scene polygons define a feature set for the placement. The feature
sets of all example placements are then used to learn a probabilistic model over
all possible placements and scenes. With this model, we can generate a new set
of placements with similar geometric relationships in any given scene. We introduce
extensions that enable propagation and generation of shapes in 3D scenes, as
well as the application of a learned modeling session to large scenes without
additional user interaction. These concepts allow us to generate complex scenes
with thousands of objects with relatively little user interaction.
acknowledgement: This publication is based upon work supported by the KAUST Office
of Competitive Research Funds (OCRF) under Award No. 62140401, the KAUST Visual
Computing Center and the Austrian Science Fund (FWF) projects DEEP PICTURES (no.
P24352-N23) and Data-Driven Procedural Modeling of Interiors (no. P24600-N23).
article_number: '108'
author:
- first_name: Paul
full_name: Guerrero, Paul
last_name: Guerrero
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
- first_name: Peter
full_name: Wonka, Peter
last_name: Wonka
citation:
ama: 'Guerrero P, Jeschke S, Wimmer M, Wonka P. Learning shape placements by example.
In: Vol 34. ACM; 2015. doi:10.1145/2766933'
apa: 'Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2015). Learning shape
placements by example (Vol. 34). Presented at the SIGGRAPH: Special Interest Group
on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States:
ACM. https://doi.org/10.1145/2766933'
chicago: Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Learning
Shape Placements by Example,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766933.
ieee: 'P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Learning shape placements
by example,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics
and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no.
4.'
ista: 'Guerrero P, Jeschke S, Wimmer M, Wonka P. 2015. Learning shape placements
by example. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques vol. 34, 108.'
mla: Guerrero, Paul, et al. Learning Shape Placements by Example. Vol. 34,
no. 4, 108, ACM, 2015, doi:10.1145/2766933.
short: P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:08Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2021-01-12T06:52:07Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766933
file:
- access_level: open_access
checksum: 8b05a51e372c9b0b5af9a00098a9538b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:49Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4647'
file_name: IST-2016-576-v1+1_guerrero-2015-lsp-paper.pdf
file_size: 11902290
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25357BD2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 24352-N23
name: 'Deep Pictures: Creating Visual and Haptic Vector Images'
publication_status: published
publisher: ACM
publist_id: '5525'
pubrep_id: '576'
quality_controlled: '1'
scopus_import: 1
status: public
title: Learning shape placements by example
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1640'
abstract:
- lang: eng
text: Auxin and cytokinin are key endogenous regulators of plant development. Although
cytokinin-mediated modulation of auxin distribution is a developmentally crucial
hormonal interaction, its molecular basis is largely unknown. Here we show a direct
regulatory link between cytokinin signalling and the auxin transport machinery
uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that
the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin
perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters
at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory
element effectively uncouples PIN transcription from the CRF-mediated cytokinin
regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent
a missing cross-talk component that fine-tunes auxin transport capacity downstream
of cytokinin signalling to control plant development.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: This work was supported by the European Research Council Starting
Independent Research grant (ERC-2007-Stg-207362-HCPO to E.B., M.S., C.C.), by the
Ghent University Multidisciplinary Research Partnership ‘Biotechnology for a Sustainable
Economy’ no.01MRB510W, by the Research Foundation—Flanders (grant 3G033711 to J.-A.O.),
by the Austrian Science Fund (FWF01_I1774S) to K.Ö.,E.B., and by the Interuniversity
Attraction Poles Programme (IUAP P7/29 ‘MARS’) initiated by the Belgian Science
Policy Office. I.D.C. and S.V. are post-doctoral fellows of the Research Foundation—Flanders
(FWO). This research was supported by the Scientific Service Units (SSU) of IST-Austria
through resources provided by the Bioimaging Facility (BIF), the Life Science Facility
(LSF).
article_number: '8717'
author:
- first_name: Mária
full_name: Šimášková, Mária
last_name: Šimášková
- first_name: José
full_name: O'Brien, José
last_name: O'Brien
- first_name: Mamoona
full_name: Khan-Djamei, Mamoona
id: 391B5BBC-F248-11E8-B48F-1D18A9856A87
last_name: Khan-Djamei
- first_name: Giel
full_name: Van Noorden, Giel
last_name: Van Noorden
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Anne
full_name: Vieten, Anne
last_name: Vieten
- first_name: Inge
full_name: De Clercq, Inge
last_name: De Clercq
- first_name: Johanna
full_name: Van Haperen, Johanna
last_name: Van Haperen
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Klára
full_name: Hoyerová, Klára
last_name: Hoyerová
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Frank
full_name: Van Breusegem, Frank
last_name: Van Breusegem
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
- first_name: Angus
full_name: Murphy, Angus
last_name: Murphy
- first_name: Jiřĺ
full_name: Friml, Jiřĺ
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Šimášková M, O’Brien J, Khan-Djamei M, et al. Cytokinin response factors regulate
PIN-FORMED auxin transporters. Nature Communications. 2015;6. doi:10.1038/ncomms9717
apa: Šimášková, M., O’Brien, J., Khan-Djamei, M., Van Noorden, G., Ötvös, K., Vieten,
A., … Benková, E. (2015). Cytokinin response factors regulate PIN-FORMED auxin
transporters. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9717
chicago: Šimášková, Mária, José O’Brien, Mamoona Khan-Djamei, Giel Van Noorden,
Krisztina Ötvös, Anne Vieten, Inge De Clercq, et al. “Cytokinin Response Factors
Regulate PIN-FORMED Auxin Transporters.” Nature Communications. Nature
Publishing Group, 2015. https://doi.org/10.1038/ncomms9717.
ieee: M. Šimášková et al., “Cytokinin response factors regulate PIN-FORMED
auxin transporters,” Nature Communications, vol. 6. Nature Publishing Group,
2015.
ista: Šimášková M, O’Brien J, Khan-Djamei M, Van Noorden G, Ötvös K, Vieten A, De
Clercq I, Van Haperen J, Cuesta C, Hoyerová K, Vanneste S, Marhavý P, Wabnik KT,
Van Breusegem F, Nowack M, Murphy A, Friml J, Weijers D, Beeckman T, Benková E.
2015. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature
Communications. 6, 8717.
mla: Šimášková, Mária, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin
Transporters.” Nature Communications, vol. 6, 8717, Nature Publishing Group,
2015, doi:10.1038/ncomms9717.
short: M. Šimášková, J. O’Brien, M. Khan-Djamei, G. Van Noorden, K. Ötvös, A. Vieten,
I. De Clercq, J. Van Haperen, C. Cuesta, K. Hoyerová, S. Vanneste, P. Marhavý,
K.T. Wabnik, F. Van Breusegem, M. Nowack, A. Murphy, J. Friml, D. Weijers, T.
Beeckman, E. Benková, Nature Communications 6 (2015).
date_created: 2018-12-11T11:53:12Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:11Z
day: '01'
ddc:
- '580'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/ncomms9717
ec_funded: 1
file:
- access_level: open_access
checksum: c2c84bca37401435fedf76bad0ba0579
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:36Z
date_updated: 2020-07-14T12:45:08Z
file_id: '5358'
file_name: IST-2018-1020-v1+1_Simaskova_et_al_NatCom_2015.pdf
file_size: 1471217
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5513'
pubrep_id: '1020'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinin response factors regulate PIN-FORMED auxin transporters
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1642'
abstract:
- lang: eng
text: The Hanani-Tutte theorem is a classical result proved for the first time in
the 1930s that characterizes planar graphs as graphs that admit a drawing in the
plane in which every pair of edges not sharing a vertex cross an even number of
times. We generalize this result to clustered graphs with two disjoint clusters,
and show that a straightforward extension to flat clustered graphs with three
or more disjoint clusters is not possible. For general clustered graphs we show
a variant of the Hanani-Tutte theorem in the case when each cluster induces a
connected subgraph. Di Battista and Frati proved that clustered planarity of embedded
clustered graphs whose every face is incident to at most five vertices can be
tested in polynomial time. We give a new and short proof of this result, using
the matroid intersection algorithm.
acknowledgement: e research leading to these results has received funding fromthe
People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme(FP7/2007-2013) under REA grant agreement no [291734], and ESF Eurogiga
project GraDR as GAˇCRGIG/11/E023.
article_number: 'P4.24 '
article_processing_charge: No
article_type: original
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
- first_name: Igor
full_name: Malinovič, Igor
last_name: Malinovič
- first_name: Dömötör
full_name: Pálvölgyi, Dömötör
last_name: Pálvölgyi
citation:
ama: Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. Clustered planarity testing revisited.
Electronic Journal of Combinatorics. 2015;22(4). doi:10.37236/5002
apa: Fulek, R., Kynčl, J., Malinovič, I., & Pálvölgyi, D. (2015). Clustered
planarity testing revisited. Electronic Journal of Combinatorics. Electronic
Journal of Combinatorics. https://doi.org/10.37236/5002
chicago: Fulek, Radoslav, Jan Kynčl, Igor Malinovič, and Dömötör Pálvölgyi. “Clustered
Planarity Testing Revisited.” Electronic Journal of Combinatorics. Electronic
Journal of Combinatorics, 2015. https://doi.org/10.37236/5002.
ieee: R. Fulek, J. Kynčl, I. Malinovič, and D. Pálvölgyi, “Clustered planarity testing
revisited,” Electronic Journal of Combinatorics, vol. 22, no. 4. Electronic
Journal of Combinatorics, 2015.
ista: Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. 2015. Clustered planarity testing
revisited. Electronic Journal of Combinatorics. 22(4), P4.24.
mla: Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” Electronic
Journal of Combinatorics, vol. 22, no. 4, P4.24, Electronic Journal of Combinatorics,
2015, doi:10.37236/5002.
short: R. Fulek, J. Kynčl, I. Malinovič, D. Pálvölgyi, Electronic Journal of Combinatorics
22 (2015).
date_created: 2018-12-11T11:53:12Z
date_published: 2015-11-13T00:00:00Z
date_updated: 2023-02-21T16:03:02Z
day: '13'
ddc:
- '514'
- '516'
department:
- _id: UlWa
doi: 10.37236/5002
ec_funded: 1
external_id:
arxiv:
- '1305.4519'
file:
- access_level: open_access
checksum: 40b5920b49ee736694f59f39588ee206
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:03Z
date_updated: 2020-07-14T12:45:08Z
file_id: '5120'
file_name: IST-2016-714-v1+1_5002-15499-3-PB.pdf
file_size: 443655
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
publist_id: '5511'
pubrep_id: '714'
quality_controlled: '1'
related_material:
record:
- id: '10793'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Clustered planarity testing revisited
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2015'
...
---
_id: '1639'
abstract:
- lang: eng
text: In this paper the optimal transport and the metamorphosis perspectives are
combined. For a pair of given input images geodesic paths in the space of images
are defined as minimizers of a resulting path energy. To this end, the underlying
Riemannian metric measures the rate of transport cost and the rate of viscous
dissipation. Furthermore, the model is capable to deal with strongly varying image
contrast and explicitly allows for sources and sinks in the transport equations
which are incorporated in the metric related to the metamorphosis approach by
Trouvé and Younes. In the non-viscous case with source term existence of geodesic
paths is proven in the space of measures. The proposed model is explored on the
range from merely optimal transport to strongly dissipative dynamics. For this
model a robust and effective variational time discretization of geodesic paths
is proposed. This requires to minimize a discrete path energy consisting of a
sum of consecutive image matching functionals. These functionals are defined on
corresponding pairs of intensity functions and on associated pairwise matching
deformations. Existence of time discrete geodesics is demonstrated. Furthermore,
a finite element implementation is proposed and applied to instructive test cases
and to real images. In the non-viscous case this is compared to the algorithm
proposed by Benamou and Brenier including a discretization of the source term.
Finally, the model is generalized to define discrete weighted barycentres with
applications to textures and objects.
acknowledgement: The authors acknowledge support of the Collaborative Research Centre
1060 funded by the German Science foundation. This work is further supported by
the King Abdullah University for Science and Technology (KAUST) Award No. KUK-I1-007-43
and the EPSRC grant Nr. EP/M00483X/1.
author:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Martin
full_name: Rumpf, Martin
last_name: Rumpf
- first_name: Carola
full_name: Schönlieb, Carola
last_name: Schönlieb
- first_name: Stefan
full_name: Simon, Stefan
last_name: Simon
citation:
ama: 'Maas J, Rumpf M, Schönlieb C, Simon S. A generalized model for optimal transport
of images including dissipation and density modulation. ESAIM: Mathematical
Modelling and Numerical Analysis. 2015;49(6):1745-1769. doi:10.1051/m2an/2015043'
apa: 'Maas, J., Rumpf, M., Schönlieb, C., & Simon, S. (2015). A generalized
model for optimal transport of images including dissipation and density modulation.
ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2015043'
chicago: 'Maas, Jan, Martin Rumpf, Carola Schönlieb, and Stefan Simon. “A Generalized
Model for Optimal Transport of Images Including Dissipation and Density Modulation.”
ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences, 2015.
https://doi.org/10.1051/m2an/2015043.'
ieee: 'J. Maas, M. Rumpf, C. Schönlieb, and S. Simon, “A generalized model for optimal
transport of images including dissipation and density modulation,” ESAIM: Mathematical
Modelling and Numerical Analysis, vol. 49, no. 6. EDP Sciences, pp. 1745–1769,
2015.'
ista: 'Maas J, Rumpf M, Schönlieb C, Simon S. 2015. A generalized model for optimal
transport of images including dissipation and density modulation. ESAIM: Mathematical
Modelling and Numerical Analysis. 49(6), 1745–1769.'
mla: 'Maas, Jan, et al. “A Generalized Model for Optimal Transport of Images Including
Dissipation and Density Modulation.” ESAIM: Mathematical Modelling and Numerical
Analysis, vol. 49, no. 6, EDP Sciences, 2015, pp. 1745–69, doi:10.1051/m2an/2015043.'
short: 'J. Maas, M. Rumpf, C. Schönlieb, S. Simon, ESAIM: Mathematical Modelling
and Numerical Analysis 49 (2015) 1745–1769.'
date_created: 2018-12-11T11:53:11Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2021-01-12T06:52:10Z
day: '01'
department:
- _id: JaMa
doi: 10.1051/m2an/2015043
external_id:
arxiv:
- '1504.01988'
intvolume: ' 49'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.01988
month: '11'
oa: 1
oa_version: Preprint
page: 1745 - 1769
publication: 'ESAIM: Mathematical Modelling and Numerical Analysis'
publication_status: published
publisher: EDP Sciences
publist_id: '5514'
quality_controlled: '1'
scopus_import: 1
status: public
title: A generalized model for optimal transport of images including dissipation and
density modulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2015'
...
---
_id: '1646'
abstract:
- lang: eng
text: 'A pseudorandom function (PRF) is a keyed function F : K × X → Y where, for
a random key k ∈ K, the function F(k, ·) is indistinguishable from a uniformly
random function, given black-box access. A key-homomorphic PRF has the additional
feature that for any keys k, k'' and any input x, we have F(k+k'', x) = F(k, x)⊕F(k'',
x) for some group operations +,⊕ on K and Y, respectively. A constrained PRF for
a family of setsS ⊆ P(X) has the property that, given any key k and set S ∈ S,
one can efficiently compute a “constrained” key kS that enables evaluation of
F(k, x) on all inputs x ∈ S, while the values F(k, x) for x /∈ S remain pseudorandom
even given kS. In this paper we construct PRFs that are simultaneously constrained
and key homomorphic, where the homomorphic property holds even for constrained
keys. We first show that the multilinear map-based bit-fixing and circuit-constrained
PRFs of Boneh and Waters (Asiacrypt 2013) can be modified to also be keyhomomorphic.
We then show that the LWE-based key-homomorphic PRFs of Banerjee and Peikert (Crypto
2014) are essentially already prefix-constrained PRFs, using a (non-obvious) definition
of constrained keys and associated group operation. Moreover, the constrained
keys themselves are pseudorandom, and the constraining and evaluation functions
can all be computed in low depth. As an application of key-homomorphic constrained
PRFs,we construct a proxy re-encryption schemewith fine-grained access control.
This scheme allows storing encrypted data on an untrusted server, where each file
can be encrypted relative to some attributes, so that only parties whose constrained
keys match the attributes can decrypt. Moreover, the server can re-key (arbitrary
subsets of) the ciphertexts without learning anything about the plaintexts, thus
permitting efficient and finegrained revocation.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Abishek
full_name: Banerjee, Abishek
last_name: Banerjee
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Chris
full_name: Peikert, Chris
last_name: Peikert
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Sophie
full_name: Stevens, Sophie
last_name: Stevens
citation:
ama: 'Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. Key-homomorphic
constrained pseudorandom functions. In: 12th Theory of Cryptography Conference.
Vol 9015. Springer Nature; 2015:31-60. doi:10.1007/978-3-662-46497-7_2'
apa: 'Banerjee, A., Fuchsbauer, G., Peikert, C., Pietrzak, K. Z., & Stevens,
S. (2015). Key-homomorphic constrained pseudorandom functions. In 12th Theory
of Cryptography Conference (Vol. 9015, pp. 31–60). Warsaw, Poland: Springer
Nature. https://doi.org/10.1007/978-3-662-46497-7_2'
chicago: Banerjee, Abishek, Georg Fuchsbauer, Chris Peikert, Krzysztof Z Pietrzak,
and Sophie Stevens. “Key-Homomorphic Constrained Pseudorandom Functions.” In 12th
Theory of Cryptography Conference, 9015:31–60. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-46497-7_2.
ieee: A. Banerjee, G. Fuchsbauer, C. Peikert, K. Z. Pietrzak, and S. Stevens, “Key-homomorphic
constrained pseudorandom functions,” in 12th Theory of Cryptography Conference,
Warsaw, Poland, 2015, vol. 9015, pp. 31–60.
ista: 'Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. 2015. Key-homomorphic
constrained pseudorandom functions. 12th Theory of Cryptography Conference. TCC:
Theory of Cryptography Conference, LNCS, vol. 9015, 31–60.'
mla: Banerjee, Abishek, et al. “Key-Homomorphic Constrained Pseudorandom Functions.”
12th Theory of Cryptography Conference, vol. 9015, Springer Nature, 2015,
pp. 31–60, doi:10.1007/978-3-662-46497-7_2.
short: A. Banerjee, G. Fuchsbauer, C. Peikert, K.Z. Pietrzak, S. Stevens, in:, 12th
Theory of Cryptography Conference, Springer Nature, 2015, pp. 31–60.
conference:
end_date: 2015-03-25
location: Warsaw, Poland
name: 'TCC: Theory of Cryptography Conference'
start_date: 2015-03-23
date_created: 2018-12-11T11:53:14Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2022-02-03T08:41:46Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-662-46497-7_2
ec_funded: 1
file:
- access_level: open_access
checksum: 3c5093bda5783c89beaacabf1aa0e60e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:17Z
date_updated: 2020-07-14T12:45:08Z
file_id: '5136'
file_name: IST-2016-679-v1+1_180.pdf
file_size: 450665
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9015'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2015/180
month: '03'
oa: 1
oa_version: Submitted Version
page: 31 - 60
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: 12th Theory of Cryptography Conference
publication_identifier:
isbn:
- 978-3-662-46496-0
publication_status: published
publisher: Springer Nature
publist_id: '5505'
pubrep_id: '679'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Key-homomorphic constrained pseudorandom functions
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9015
year: '2015'
...
---
_id: '1648'
abstract:
- lang: eng
text: Generalized Selective Decryption (GSD), introduced by Panjwani [TCC’07], is
a game for a symmetric encryption scheme Enc that captures the difficulty of proving
adaptive security of certain protocols, most notably the Logical Key Hierarchy
(LKH) multicast encryption protocol. In the GSD game there are n keys k1,...,
kn, which the adversary may adaptively corrupt (learn); moreover, it can ask for
encryptions Encki (kj) of keys under other keys. The adversary’s task is to distinguish
keys (which it cannot trivially compute) from random. Proving the hardness of
GSD assuming only IND-CPA security of Enc is surprisingly hard. Using “complexity
leveraging” loses a factor exponential in n, which makes the proof practically
meaningless. We can think of the GSD game as building a graph on n vertices, where
we add an edge i → j when the adversary asks for an encryption of kj under ki.
If restricted to graphs of depth ℓ, Panjwani gave a reduction that loses only
a factor exponential in ℓ (not n). To date, this is the only non-trivial result
known for GSD. In this paper we give almost-polynomial reductions for large classes
of graphs. Most importantly, we prove the security of the GSD game restricted
to trees losing only a quasi-polynomial factor n3 log n+5. Trees are an important
special case capturing real-world protocols like the LKH protocol. Our new bound
improves upon Panjwani’s on some LKH variants proposed in the literature where
the underlying tree is not balanced. Our proof builds on ideas from the “nested
hybrids” technique recently introduced by Fuchsbauer et al. [Asiacrypt’14] for
proving the adaptive security of constrained PRFs.
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Zahra
full_name: Jafargholi, Zahra
last_name: Jafargholi
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Fuchsbauer G, Jafargholi Z, Pietrzak KZ. A quasipolynomial reduction for generalized
selective decryption on trees. In: Vol 9215. Springer; 2015:601-620. doi:10.1007/978-3-662-47989-6_29'
apa: 'Fuchsbauer, G., Jafargholi, Z., & Pietrzak, K. Z. (2015). A quasipolynomial
reduction for generalized selective decryption on trees (Vol. 9215, pp. 601–620).
Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA,
USA: Springer. https://doi.org/10.1007/978-3-662-47989-6_29'
chicago: Fuchsbauer, Georg, Zahra Jafargholi, and Krzysztof Z Pietrzak. “A Quasipolynomial
Reduction for Generalized Selective Decryption on Trees,” 9215:601–20. Springer,
2015. https://doi.org/10.1007/978-3-662-47989-6_29.
ieee: 'G. Fuchsbauer, Z. Jafargholi, and K. Z. Pietrzak, “A quasipolynomial reduction
for generalized selective decryption on trees,” presented at the CRYPTO: International
Cryptology Conference, Santa Barbara, CA, USA, 2015, vol. 9215, pp. 601–620.'
ista: 'Fuchsbauer G, Jafargholi Z, Pietrzak KZ. 2015. A quasipolynomial reduction
for generalized selective decryption on trees. CRYPTO: International Cryptology
Conference, LNCS, vol. 9215, 601–620.'
mla: Fuchsbauer, Georg, et al. A Quasipolynomial Reduction for Generalized Selective
Decryption on Trees. Vol. 9215, Springer, 2015, pp. 601–20, doi:10.1007/978-3-662-47989-6_29.
short: G. Fuchsbauer, Z. Jafargholi, K.Z. Pietrzak, in:, Springer, 2015, pp. 601–620.
conference:
end_date: 2015-08-20
location: Santa Barbara, CA, USA
name: 'CRYPTO: International Cryptology Conference'
start_date: 2015-08-16
date_created: 2018-12-11T11:53:14Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:52:14Z
day: '01'
ddc:
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-662-47989-6_29
ec_funded: 1
file:
- access_level: open_access
checksum: 99b76b3263d5082554d0a9cbdeca3a22
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:31Z
date_updated: 2020-07-14T12:45:08Z
file_id: '5015'
file_name: IST-2016-674-v1+1_389.pdf
file_size: 505618
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9215'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 601 - 620
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5502'
pubrep_id: '674'
quality_controlled: '1'
scopus_import: 1
status: public
title: A quasipolynomial reduction for generalized selective decryption on trees
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9215
year: '2015'
...
---
_id: '1649'
abstract:
- lang: eng
text: 'We extend a commitment scheme based on the learning with errors over rings
(RLWE) problem, and present efficient companion zeroknowledge proofs of knowledge.
Our scheme maps elements from the ring (or equivalently, n elements from '
alternative_title:
- LNCS
author:
- first_name: Fabrice
full_name: Benhamouda, Fabrice
last_name: Benhamouda
- first_name: Stephan
full_name: Krenn, Stephan
last_name: Krenn
- first_name: Vadim
full_name: Lyubashevsky, Vadim
last_name: Lyubashevsky
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. Efficient zero-knowledge
proofs for commitments from learning with errors over rings. 2015;9326:305-325.
doi:10.1007/978-3-319-24174-6_16
apa: 'Benhamouda, F., Krenn, S., Lyubashevsky, V., & Pietrzak, K. Z. (2015).
Efficient zero-knowledge proofs for commitments from learning with errors over
rings. Presented at the ESORICS: European Symposium on Research in Computer Security,
Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-24174-6_16'
chicago: Benhamouda, Fabrice, Stephan Krenn, Vadim Lyubashevsky, and Krzysztof Z
Pietrzak. “Efficient Zero-Knowledge Proofs for Commitments from Learning with
Errors over Rings.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-24174-6_16.
ieee: F. Benhamouda, S. Krenn, V. Lyubashevsky, and K. Z. Pietrzak, “Efficient zero-knowledge
proofs for commitments from learning with errors over rings,” vol. 9326. Springer,
pp. 305–325, 2015.
ista: Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. 2015. Efficient zero-knowledge
proofs for commitments from learning with errors over rings. 9326, 305–325.
mla: Benhamouda, Fabrice, et al. Efficient Zero-Knowledge Proofs for Commitments
from Learning with Errors over Rings. Vol. 9326, Springer, 2015, pp. 305–25,
doi:10.1007/978-3-319-24174-6_16.
short: F. Benhamouda, S. Krenn, V. Lyubashevsky, K.Z. Pietrzak, 9326 (2015) 305–325.
conference:
end_date: 2015-09-25
location: Vienna, Austria
name: 'ESORICS: European Symposium on Research in Computer Security'
start_date: 2015-09-21
date_created: 2018-12-11T11:53:15Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:14Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-319-24174-6_16
ec_funded: 1
file:
- access_level: open_access
checksum: 6eac4a485b2aa644b2d3f753ed0b280b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:28Z
date_updated: 2020-07-14T12:45:08Z
file_id: '4883'
file_name: IST-2016-678-v1+1_889.pdf
file_size: 494239
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9326'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 305 - 325
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5501'
pubrep_id: '678'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Efficient zero-knowledge proofs for commitments from learning with errors over
rings
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9326
year: '2015'
...
---
_id: '1644'
abstract:
- lang: eng
text: Increasing the computational complexity of evaluating a hash function, both
for the honest users as well as for an adversary, is a useful technique employed
for example in password-based cryptographic schemes to impede brute-force attacks,
and also in so-called proofs of work (used in protocols like Bitcoin) to show
that a certain amount of computation was performed by a legitimate user. A natural
approach to adjust the complexity of a hash function is to iterate it c times,
for some parameter c, in the hope that any query to the scheme requires c evaluations
of the underlying hash function. However, results by Dodis et al. (Crypto 2012)
imply that plain iteration falls short of achieving this goal, and designing schemes
which provably have such a desirable property remained an open problem. This paper
formalizes explicitly what it means for a given scheme to amplify the query complexity
of a hash function. In the random oracle model, the goal of a secure query-complexity
amplifier (QCA) scheme is captured as transforming, in the sense of indifferentiability,
a random oracle allowing R queries (for the adversary) into one provably allowing
only r < R queries. Turned around, this means that making r queries to the
scheme requires at least R queries to the actual random oracle. Second, a new
scheme, called collision-free iteration, is proposed and proven to achieve c-fold
QCA for both the honest parties and the adversary, for any fixed parameter c.
alternative_title:
- LNCS
author:
- first_name: Grégory
full_name: Demay, Grégory
last_name: Demay
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Ueli
full_name: Maurer, Ueli
last_name: Maurer
- first_name: Björn
full_name: Tackmann, Björn
last_name: Tackmann
citation:
ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Query-complexity amplification for
random oracles. In: Vol 9063. Springer; 2015:159-180. doi:10.1007/978-3-319-17470-9_10'
apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2015). Query-complexity
amplification for random oracles (Vol. 9063, pp. 159–180). Presented at the ICITS:
International Conference on Information Theoretic Security, Lugano, Switzerland:
Springer. https://doi.org/10.1007/978-3-319-17470-9_10'
chicago: Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Query-Complexity
Amplification for Random Oracles,” 9063:159–80. Springer, 2015. https://doi.org/10.1007/978-3-319-17470-9_10.
ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Query-complexity amplification
for random oracles,” presented at the ICITS: International Conference on Information
Theoretic Security, Lugano, Switzerland, 2015, vol. 9063, pp. 159–180.'
ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2015. Query-complexity amplification
for random oracles. ICITS: International Conference on Information Theoretic Security,
LNCS, vol. 9063, 159–180.'
mla: Demay, Grégory, et al. Query-Complexity Amplification for Random Oracles.
Vol. 9063, Springer, 2015, pp. 159–80, doi:10.1007/978-3-319-17470-9_10.
short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, Springer, 2015, pp. 159–180.
conference:
end_date: 2015-05-05
location: Lugano, Switzerland
name: 'ICITS: International Conference on Information Theoretic Security'
start_date: 2015-05-02
date_created: 2018-12-11T11:53:13Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:13Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-17470-9_10
ec_funded: 1
intvolume: ' 9063'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2015/315
month: '01'
oa: 1
oa_version: Submitted Version
page: 159 - 180
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5507'
quality_controlled: '1'
scopus_import: 1
status: public
title: Query-complexity amplification for random oracles
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9063
year: '2015'
...
---
_id: '1647'
abstract:
- lang: eng
text: Round-optimal blind signatures are notoriously hard to construct in the standard
model, especially in the malicious-signer model, where blindness must hold under
adversarially chosen keys. This is substantiated by several impossibility results.
The only construction that can be termed theoretically efficient, by Garg and
Gupta (Eurocrypt’14), requires complexity leveraging, inducing an exponential
security loss. We present a construction of practically efficient round-optimal
blind signatures in the standard model. It is conceptually simple and builds on
the recent structure-preserving signatures on equivalence classes (SPSEQ) from
Asiacrypt’14. While the traditional notion of blindness follows from standard
assumptions, we prove blindness under adversarially chosen keys under an interactive
variant of DDH. However, we neither require non-uniform assumptions nor complexity
leveraging. We then show how to extend our construction to partially blind signatures
and to blind signatures on message vectors, which yield a construction of one-show
anonymous credentials à la “anonymous credentials light” (CCS’13) in the standard
model. Furthermore, we give the first SPS-EQ construction under noninteractive
assumptions and show how SPS-EQ schemes imply conventional structure-preserving
signatures, which allows us to apply optimality results for the latter to SPS-EQ.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Christian
full_name: Hanser, Christian
last_name: Hanser
- first_name: Daniel
full_name: Slamanig, Daniel
last_name: Slamanig
citation:
ama: 'Fuchsbauer G, Hanser C, Slamanig D. Practical round-optimal blind signatures
in the standard model. In: Vol 9216. Springer; 2015:233-253. doi:10.1007/978-3-662-48000-7_12'
apa: 'Fuchsbauer, G., Hanser, C., & Slamanig, D. (2015). Practical round-optimal
blind signatures in the standard model (Vol. 9216, pp. 233–253). Presented at
the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States:
Springer. https://doi.org/10.1007/978-3-662-48000-7_12'
chicago: Fuchsbauer, Georg, Christian Hanser, and Daniel Slamanig. “Practical Round-Optimal
Blind Signatures in the Standard Model,” 9216:233–53. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_12.
ieee: 'G. Fuchsbauer, C. Hanser, and D. Slamanig, “Practical round-optimal blind
signatures in the standard model,” presented at the CRYPTO: International Cryptology
Conference, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 233–253.'
ista: 'Fuchsbauer G, Hanser C, Slamanig D. 2015. Practical round-optimal blind signatures
in the standard model. CRYPTO: International Cryptology Conference, LNCS, vol.
9216, 233–253.'
mla: Fuchsbauer, Georg, et al. Practical Round-Optimal Blind Signatures in the
Standard Model. Vol. 9216, Springer, 2015, pp. 233–53, doi:10.1007/978-3-662-48000-7_12.
short: G. Fuchsbauer, C. Hanser, D. Slamanig, in:, Springer, 2015, pp. 233–253.
conference:
end_date: 2015-08-20
location: Santa Barbara, CA, United States
name: 'CRYPTO: International Cryptology Conference'
start_date: 2015-08-16
date_created: 2018-12-11T11:53:14Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2023-02-21T16:44:51Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-662-48000-7_12
ec_funded: 1
intvolume: ' 9216'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2015/626.pdf
month: '08'
oa: 1
oa_version: Submitted Version
page: 233 - 253
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5503'
quality_controlled: '1'
related_material:
record:
- id: '1225'
relation: later_version
status: public
scopus_import: 1
status: public
title: Practical round-optimal blind signatures in the standard model
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9216
year: '2015'
...
---
_id: '1654'
abstract:
- lang: eng
text: "HMAC and its variant NMAC are the most popular approaches to deriving a MAC
(and more generally, a PRF) from a cryptographic hash function. Despite nearly
two decades of research, their exact security still remains far from understood
in many different contexts. Indeed, recent works have re-surfaced interest for
{\\em generic} attacks, i.e., attacks that treat the compression function of the
underlying hash function as a black box.\r\n\r\nGeneric security can be proved
in a model where the underlying compression function is modeled as a random function
-- yet, to date, the question of proving tight, non-trivial bounds on the generic
security of HMAC/NMAC even as a PRF remains a challenging open question.\r\n\r\nIn
this paper, we ask the question of whether a small modification to HMAC and NMAC
can allow us to exactly characterize the security of the resulting constructions,
while only incurring little penalty with respect to efficiency. To this end, we
present simple variants of NMAC and HMAC, for which we prove tight bounds on the
generic PRF security, expressed in terms of numbers of construction and compression
function queries necessary to break the construction. All of our constructions
are obtained via a (near) {\\em black-box} modification of NMAC and HMAC, which
can be interpreted as an initial step of key-dependent message pre-processing.\r\n\r\nWhile
our focus is on PRF security, a further attractive feature of our new constructions
is that they clearly defeat all recent generic attacks against properties such
as state recovery and universal forgery. These exploit properties of the so-called
``functional graph'' which are not directly accessible in our new constructions. "
alternative_title:
- LNCS
author:
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Stefano
full_name: Tessaro, Stefano
last_name: Tessaro
citation:
ama: Gazi P, Pietrzak KZ, Tessaro S. Generic security of NMAC and HMAC with input
whitening. 2015;9453:85-109. doi:10.1007/978-3-662-48800-3_4
apa: 'Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). Generic security of NMAC
and HMAC with input whitening. Presented at the ASIACRYPT: Theory and Application
of Cryptology and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48800-3_4'
chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “Generic Security
of NMAC and HMAC with Input Whitening.” Lecture Notes in Computer Science. Springer,
2015. https://doi.org/10.1007/978-3-662-48800-3_4.
ieee: P. Gazi, K. Z. Pietrzak, and S. Tessaro, “Generic security of NMAC and HMAC
with input whitening,” vol. 9453. Springer, pp. 85–109, 2015.
ista: Gazi P, Pietrzak KZ, Tessaro S. 2015. Generic security of NMAC and HMAC with
input whitening. 9453, 85–109.
mla: Gazi, Peter, et al. Generic Security of NMAC and HMAC with Input Whitening.
Vol. 9453, Springer, 2015, pp. 85–109, doi:10.1007/978-3-662-48800-3_4.
short: P. Gazi, K.Z. Pietrzak, S. Tessaro, 9453 (2015) 85–109.
conference:
end_date: 2015-12-03
location: Auckland, New Zealand
name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security'
start_date: 2015-11-29
date_created: 2018-12-11T11:53:17Z
date_published: 2015-12-30T00:00:00Z
date_updated: 2021-01-12T06:52:16Z
day: '30'
ddc:
- '004'
- '005'
department:
- _id: KrPi
doi: 10.1007/978-3-662-48800-3_4
ec_funded: 1
file:
- access_level: open_access
checksum: d1e53203db2d8573a560995ccdffac62
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:09Z
date_updated: 2020-07-14T12:45:08Z
file_id: '4732'
file_name: IST-2016-676-v1+1_881.pdf
file_size: 512071
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9453'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 85 - 109
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5496'
pubrep_id: '676'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Generic security of NMAC and HMAC with input whitening
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9453
year: '2015'
...
---
_id: '1650'
abstract:
- lang: eng
text: "We consider the task of deriving a key with high HILL entropy (i.e., being
computationally indistinguishable from a key with high min-entropy) from an unpredictable
source.\r\n\r\nPrevious to this work, the only known way to transform unpredictability
into a key that was ϵ indistinguishable from having min-entropy was via pseudorandomness,
for example by Goldreich-Levin (GL) hardcore bits. This approach has the inherent
limitation that from a source with k bits of unpredictability entropy one can
derive a key of length (and thus HILL entropy) at most k−2log(1/ϵ) bits. In many
settings, e.g. when dealing with biometric data, such a 2log(1/ϵ) bit entropy
loss in not an option. Our main technical contribution is a theorem that states
that in the high entropy regime, unpredictability implies HILL entropy. Concretely,
any variable K with |K|−d bits of unpredictability entropy has the same amount
of so called metric entropy (against real-valued, deterministic distinguishers),
which is known to imply the same amount of HILL entropy. The loss in circuit size
in this argument is exponential in the entropy gap d, and thus this result only
applies for small d (i.e., where the size of distinguishers considered is exponential
in d).\r\n\r\nTo overcome the above restriction, we investigate if it’s possible
to first “condense” unpredictability entropy and make the entropy gap small. We
show that any source with k bits of unpredictability can be condensed into a source
of length k with k−3 bits of unpredictability entropy. Our condenser simply “abuses"
the GL construction and derives a k bit key from a source with k bits of unpredicatibily.
The original GL theorem implies nothing when extracting that many bits, but we
show that in this regime, GL still behaves like a “condenser" for unpredictability.
This result comes with two caveats (1) the loss in circuit size is exponential
in k and (2) we require that the source we start with has no HILL entropy (equivalently,
one can efficiently check if a guess is correct). We leave it as an intriguing
open problem to overcome these restrictions or to prove they’re inherent."
alternative_title:
- LNCS
author:
- first_name: Maciej
full_name: Skórski, Maciej
last_name: Skórski
- first_name: Alexander
full_name: Golovnev, Alexander
last_name: Golovnev
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Skórski M, Golovnev A, Pietrzak KZ. Condensed unpredictability . In: Vol 9134.
Springer; 2015:1046-1057. doi:10.1007/978-3-662-47672-7_85'
apa: 'Skórski, M., Golovnev, A., & Pietrzak, K. Z. (2015). Condensed unpredictability (Vol.
9134, pp. 1046–1057). Presented at the ICALP: Automata, Languages and Programming,
Kyoto, Japan: Springer. https://doi.org/10.1007/978-3-662-47672-7_85'
chicago: Skórski, Maciej, Alexander Golovnev, and Krzysztof Z Pietrzak. “Condensed
Unpredictability ,” 9134:1046–57. Springer, 2015. https://doi.org/10.1007/978-3-662-47672-7_85.
ieee: 'M. Skórski, A. Golovnev, and K. Z. Pietrzak, “Condensed unpredictability
,” presented at the ICALP: Automata, Languages and Programming, Kyoto, Japan,
2015, vol. 9134, pp. 1046–1057.'
ista: 'Skórski M, Golovnev A, Pietrzak KZ. 2015. Condensed unpredictability . ICALP:
Automata, Languages and Programming, LNCS, vol. 9134, 1046–1057.'
mla: Skórski, Maciej, et al. Condensed Unpredictability . Vol. 9134, Springer,
2015, pp. 1046–57, doi:10.1007/978-3-662-47672-7_85.
short: M. Skórski, A. Golovnev, K.Z. Pietrzak, in:, Springer, 2015, pp. 1046–1057.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: Automata, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:15Z
date_published: 2015-06-20T00:00:00Z
date_updated: 2021-01-12T06:52:15Z
day: '20'
ddc:
- '000'
- '005'
department:
- _id: KrPi
doi: 10.1007/978-3-662-47672-7_85
ec_funded: 1
file:
- access_level: open_access
checksum: e808c7eecb631336fc9f9bf2e8d4ecae
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:32Z
date_updated: 2020-07-14T12:45:08Z
file_id: '4693'
file_name: IST-2016-675-v1+1_384.pdf
file_size: 525503
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9134'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1046 - 1057
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5500'
pubrep_id: '675'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Condensed unpredictability '
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9134
year: '2015'
...
---
_id: '1651'
abstract:
- lang: eng
text: Cryptographic e-cash allows off-line electronic transactions between a bank,
users and merchants in a secure and anonymous fashion. A plethora of e-cash constructions
has been proposed in the literature; however, these traditional e-cash schemes
only allow coins to be transferred once between users and merchants. Ideally,
we would like users to be able to transfer coins between each other multiple times
before deposit, as happens with physical cash. “Transferable” e-cash schemes are
the solution to this problem. Unfortunately, the currently proposed schemes are
either completely impractical or do not achieve the desirable anonymity properties
without compromises, such as assuming the existence of a trusted “judge” who can
trace all coins and users in the system. This paper presents the first efficient
and fully anonymous transferable e-cash scheme without any trusted third parties.
We start by revising the security and anonymity properties of transferable e-cash
to capture issues that were previously overlooked. For our construction we use
the recently proposed malleable signatures by Chase et al. to allow the secure
and anonymous transfer of coins, combined with a new efficient double-spending
detection mechanism. Finally, we discuss an instantiation of our construction.
acknowledgement: Work done as an intern in Microsoft Research Redmond and as a student
at Brown University, where supported by NSF grant 0964379. Supported by the European
Research Council, ERC Starting Grant (259668-PSPC).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Foteini
full_name: Baldimtsi, Foteini
last_name: Baldimtsi
- first_name: Melissa
full_name: Chase, Melissa
last_name: Chase
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Markulf
full_name: Kohlweiss, Markulf
last_name: Kohlweiss
citation:
ama: 'Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. Anonymous transferable e-cash.
In: Public-Key Cryptography - PKC 2015. Vol 9020. Springer; 2015:101-124.
doi:10.1007/978-3-662-46447-2_5'
apa: 'Baldimtsi, F., Chase, M., Fuchsbauer, G., & Kohlweiss, M. (2015). Anonymous
transferable e-cash. In Public-Key Cryptography - PKC 2015 (Vol. 9020,
pp. 101–124). Gaithersburg, MD, United States: Springer. https://doi.org/10.1007/978-3-662-46447-2_5'
chicago: Baldimtsi, Foteini, Melissa Chase, Georg Fuchsbauer, and Markulf Kohlweiss.
“Anonymous Transferable E-Cash.” In Public-Key Cryptography - PKC 2015,
9020:101–24. Springer, 2015. https://doi.org/10.1007/978-3-662-46447-2_5.
ieee: F. Baldimtsi, M. Chase, G. Fuchsbauer, and M. Kohlweiss, “Anonymous transferable
e-cash,” in Public-Key Cryptography - PKC 2015, Gaithersburg, MD, United
States, 2015, vol. 9020, pp. 101–124.
ista: 'Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. 2015. Anonymous transferable
e-cash. Public-Key Cryptography - PKC 2015. PKC: Public Key Crypography, LNCS,
vol. 9020, 101–124.'
mla: Baldimtsi, Foteini, et al. “Anonymous Transferable E-Cash.” Public-Key Cryptography
- PKC 2015, vol. 9020, Springer, 2015, pp. 101–24, doi:10.1007/978-3-662-46447-2_5.
short: F. Baldimtsi, M. Chase, G. Fuchsbauer, M. Kohlweiss, in:, Public-Key Cryptography
- PKC 2015, Springer, 2015, pp. 101–124.
conference:
end_date: 2015-04-01
location: Gaithersburg, MD, United States
name: 'PKC: Public Key Crypography'
start_date: 2015-03-30
date_created: 2018-12-11T11:53:15Z
date_published: 2015-03-17T00:00:00Z
date_updated: 2022-05-23T10:08:37Z
day: '17'
department:
- _id: KrPi
doi: 10.1007/978-3-662-46447-2_5
ec_funded: 1
intvolume: ' 9020'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/978-3-662-46447-2_5
month: '03'
oa: 1
oa_version: Published Version
page: 101 - 124
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Public-Key Cryptography - PKC 2015
publication_identifier:
isbn:
- 978-3-662-46446-5
publication_status: published
publisher: Springer
publist_id: '5499'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anonymous transferable e-cash
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9020
year: '2015'
...
---
_id: '1652'
abstract:
- lang: eng
text: We develop new theoretical tools for proving lower-bounds on the (amortized)
complexity of certain functions in models of parallel computation. We apply the
tools to construct a class of functions with high amortized memory complexity
in the parallel Random Oracle Model (pROM); a variant of the standard ROM allowing
for batches of simultaneous queries. In particular we obtain a new, more robust,
type of Memory-Hard Functions (MHF); a security primitive which has recently been
gaining acceptance in practice as an effective means of countering brute-force
attacks on security relevant functions. Along the way we also demonstrate an important
shortcoming of previous definitions of MHFs and give a new definition addressing
the problem. The tools we develop represent an adaptation of the powerful pebbling
paradigm (initially introduced by Hewitt and Paterson [HP70] and Cook [Coo73])
to a simple and intuitive parallel setting. We define a simple pebbling game Gp
over graphs which aims to abstract parallel computation in an intuitive way. As
a conceptual contribution we define a measure of pebbling complexity for graphs
called cumulative complexity (CC) and show how it overcomes a crucial shortcoming
(in the parallel setting) exhibited by more traditional complexity measures used
in the past. As a main technical contribution we give an explicit construction
of a constant in-degree family of graphs whose CC in Gp approaches maximality
to within a polylogarithmic factor for any graph of equal size (analogous to the
graphs of Tarjan et. al. [PTC76, LT82] for sequential pebbling games). Finally,
for a given graph G and related function fG, we derive a lower-bound on the amortized
memory complexity of fG in the pROM in terms of the CC of G in the game Gp.
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Vladimir
full_name: Serbinenko, Vladimir
last_name: Serbinenko
citation:
ama: 'Alwen JF, Serbinenko V. High parallel complexity graphs and memory-hard functions.
In: Proceedings of the 47th Annual ACM Symposium on Theory of Computing.
ACM; 2015:595-603. doi:10.1145/2746539.2746622'
apa: 'Alwen, J. F., & Serbinenko, V. (2015). High parallel complexity graphs
and memory-hard functions. In Proceedings of the 47th annual ACM symposium
on Theory of computing (pp. 595–603). Portland, OR, United States: ACM. https://doi.org/10.1145/2746539.2746622'
chicago: Alwen, Joel F, and Vladimir Serbinenko. “High Parallel Complexity Graphs
and Memory-Hard Functions.” In Proceedings of the 47th Annual ACM Symposium
on Theory of Computing, 595–603. ACM, 2015. https://doi.org/10.1145/2746539.2746622.
ieee: J. F. Alwen and V. Serbinenko, “High parallel complexity graphs and memory-hard
functions,” in Proceedings of the 47th annual ACM symposium on Theory of computing,
Portland, OR, United States, 2015, pp. 595–603.
ista: 'Alwen JF, Serbinenko V. 2015. High parallel complexity graphs and memory-hard
functions. Proceedings of the 47th annual ACM symposium on Theory of computing.
STOC: Symposium on the Theory of Computing, 595–603.'
mla: Alwen, Joel F., and Vladimir Serbinenko. “High Parallel Complexity Graphs and
Memory-Hard Functions.” Proceedings of the 47th Annual ACM Symposium on Theory
of Computing, ACM, 2015, pp. 595–603, doi:10.1145/2746539.2746622.
short: J.F. Alwen, V. Serbinenko, in:, Proceedings of the 47th Annual ACM Symposium
on Theory of Computing, ACM, 2015, pp. 595–603.
conference:
end_date: 2015-06-17
location: Portland, OR, United States
name: 'STOC: Symposium on the Theory of Computing'
start_date: 2015-06-14
date_created: 2018-12-11T11:53:16Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:52:16Z
day: '01'
department:
- _id: KrPi
doi: 10.1145/2746539.2746622
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2014/238
month: '06'
oa: 1
oa_version: Submitted Version
page: 595 - 603
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Proceedings of the 47th annual ACM symposium on Theory of computing
publication_status: published
publisher: ACM
publist_id: '5498'
quality_controlled: '1'
scopus_import: 1
status: public
title: High parallel complexity graphs and memory-hard functions
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1660'
abstract:
- lang: eng
text: We study the pattern frequency vector for runs in probabilistic Vector Addition
Systems with States (pVASS). Intuitively, each configuration of a given pVASS
is assigned one of finitely many patterns, and every run can thus be seen as an
infinite sequence of these patterns. The pattern frequency vector assigns to each
run the limit of pattern frequencies computed for longer and longer prefixes of
the run. If the limit does not exist, then the vector is undefined. We show that
for one-counter pVASS, the pattern frequency vector is defined and takes one of
finitely many values for almost all runs. Further, these values and their associated
probabilities can be approximated up to an arbitrarily small relative error in
polynomial time. For stable two-counter pVASS, we show the same result, but we
do not provide any upper complexity bound. As a byproduct of our study, we discover
counterexamples falsifying some classical results about stochastic Petri nets
published in the 80s.
alternative_title:
- LICS
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Stefan
full_name: Kiefer, Stefan
last_name: Kiefer
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
citation:
ama: 'Brázdil T, Kiefer S, Kučera A, Novotný P. Long-run average behaviour of probabilistic
vector addition systems. In: IEEE; 2015:44-55. doi:10.1109/LICS.2015.15'
apa: 'Brázdil, T., Kiefer, S., Kučera, A., & Novotný, P. (2015). Long-run average
behaviour of probabilistic vector addition systems (pp. 44–55). Presented at the
LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.15'
chicago: Brázdil, Tomáš, Stefan Kiefer, Antonín Kučera, and Petr Novotný. “Long-Run
Average Behaviour of Probabilistic Vector Addition Systems,” 44–55. IEEE, 2015.
https://doi.org/10.1109/LICS.2015.15.
ieee: 'T. Brázdil, S. Kiefer, A. Kučera, and P. Novotný, “Long-run average behaviour
of probabilistic vector addition systems,” presented at the LICS: Logic in Computer
Science, Kyoto, Japan, 2015, pp. 44–55.'
ista: 'Brázdil T, Kiefer S, Kučera A, Novotný P. 2015. Long-run average behaviour
of probabilistic vector addition systems. LICS: Logic in Computer Science, LICS,
, 44–55.'
mla: Brázdil, Tomáš, et al. Long-Run Average Behaviour of Probabilistic Vector
Addition Systems. IEEE, 2015, pp. 44–55, doi:10.1109/LICS.2015.15.
short: T. Brázdil, S. Kiefer, A. Kučera, P. Novotný, in:, IEEE, 2015, pp. 44–55.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:19Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2021-01-12T06:52:20Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/LICS.2015.15
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1505.02655
month: '07'
oa: 1
oa_version: Preprint
page: 44 - 55
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: IEEE
publist_id: '5490'
quality_controlled: '1'
scopus_import: 1
status: public
title: Long-run average behaviour of probabilistic vector addition systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1665'
abstract:
- lang: eng
text: Which genetic alterations drive tumorigenesis and how they evolve over the
course of disease and therapy are central questions in cancer biology. Here we
identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations
through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and
matched germline DNA samples, 278 of which were collected in a prospective clinical
trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3),
and collectively identify RNA processing and export, MYC activity, and MAPK signalling
as central pathways involved in CLL. Clonality analysis of this large data set
further enabled reconstruction of temporal relationships between driver events.
Direct comparison between matched pre-treatment and relapse samples from 59 patients
demonstrated highly frequent clonal evolution. Thus, large sequencing data sets
of clinically informative samples enable the discovery of novel genes associated
with cancer, the network of relationships between the driver events, and their
impact on disease relapse and clinical outcome.
article_processing_charge: No
article_type: original
author:
- first_name: Dan
full_name: Landau, Dan
last_name: Landau
- first_name: Eugen
full_name: Tausch, Eugen
last_name: Tausch
- first_name: Amaro
full_name: Taylor Weiner, Amaro
last_name: Taylor Weiner
- first_name: Chip
full_name: Stewart, Chip
last_name: Stewart
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Jasmin
full_name: Bahlo, Jasmin
last_name: Bahlo
- first_name: Sandra
full_name: Kluth, Sandra
last_name: Kluth
- first_name: Ivana
full_name: Božić, Ivana
last_name: Božić
- first_name: Michael
full_name: Lawrence, Michael
last_name: Lawrence
- first_name: Sebastian
full_name: Böttcher, Sebastian
last_name: Böttcher
- first_name: Scott
full_name: Carter, Scott
last_name: Carter
- first_name: Kristian
full_name: Cibulskis, Kristian
last_name: Cibulskis
- first_name: Daniel
full_name: Mertens, Daniel
last_name: Mertens
- first_name: Carrie
full_name: Sougnez, Carrie
last_name: Sougnez
- first_name: Mara
full_name: Rosenberg, Mara
last_name: Rosenberg
- first_name: Julian
full_name: Hess, Julian
last_name: Hess
- first_name: Jennifer
full_name: Edelmann, Jennifer
last_name: Edelmann
- first_name: Sabrina
full_name: Kless, Sabrina
last_name: Kless
- first_name: Michael
full_name: Kneba, Michael
last_name: Kneba
- first_name: Matthias
full_name: Ritgen, Matthias
last_name: Ritgen
- first_name: Anna
full_name: Fink, Anna
last_name: Fink
- first_name: Kirsten
full_name: Fischer, Kirsten
last_name: Fischer
- first_name: Stacey
full_name: Gabriel, Stacey
last_name: Gabriel
- first_name: Eric
full_name: Lander, Eric
last_name: Lander
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
- first_name: Hartmut
full_name: Döhner, Hartmut
last_name: Döhner
- first_name: Michael
full_name: Hallek, Michael
last_name: Hallek
- first_name: Donna
full_name: Neuberg, Donna
last_name: Neuberg
- first_name: Gad
full_name: Getz, Gad
last_name: Getz
- first_name: Stephan
full_name: Stilgenbauer, Stephan
last_name: Stilgenbauer
- first_name: Catherine
full_name: Wu, Catherine
last_name: Wu
citation:
ama: Landau D, Tausch E, Taylor Weiner A, et al. Mutations driving CLL and their
evolution in progression and relapse. Nature. 2015;526(7574):525-530. doi:10.1038/nature15395
apa: Landau, D., Tausch, E., Taylor Weiner, A., Stewart, C., Reiter, J., Bahlo,
J., … Wu, C. (2015). Mutations driving CLL and their evolution in progression
and relapse. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15395
chicago: Landau, Dan, Eugen Tausch, Amaro Taylor Weiner, Chip Stewart, Johannes
Reiter, Jasmin Bahlo, Sandra Kluth, et al. “Mutations Driving CLL and Their Evolution
in Progression and Relapse.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15395.
ieee: D. Landau et al., “Mutations driving CLL and their evolution in progression
and relapse,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp.
525–530, 2015.
ista: Landau D, Tausch E, Taylor Weiner A, Stewart C, Reiter J, Bahlo J, Kluth S,
Božić I, Lawrence M, Böttcher S, Carter S, Cibulskis K, Mertens D, Sougnez C,
Rosenberg M, Hess J, Edelmann J, Kless S, Kneba M, Ritgen M, Fink A, Fischer K,
Gabriel S, Lander E, Nowak M, Döhner H, Hallek M, Neuberg D, Getz G, Stilgenbauer
S, Wu C. 2015. Mutations driving CLL and their evolution in progression and relapse.
Nature. 526(7574), 525–530.
mla: Landau, Dan, et al. “Mutations Driving CLL and Their Evolution in Progression
and Relapse.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015,
pp. 525–30, doi:10.1038/nature15395.
short: D. Landau, E. Tausch, A. Taylor Weiner, C. Stewart, J. Reiter, J. Bahlo,
S. Kluth, I. Božić, M. Lawrence, S. Böttcher, S. Carter, K. Cibulskis, D. Mertens,
C. Sougnez, M. Rosenberg, J. Hess, J. Edelmann, S. Kless, M. Kneba, M. Ritgen,
A. Fink, K. Fischer, S. Gabriel, E. Lander, M. Nowak, H. Döhner, M. Hallek, D.
Neuberg, G. Getz, S. Stilgenbauer, C. Wu, Nature 526 (2015) 525–530.
date_created: 2018-12-11T11:53:21Z
date_published: 2015-10-22T00:00:00Z
date_updated: 2021-01-12T06:52:23Z
day: '22'
department:
- _id: KrCh
doi: 10.1038/nature15395
ec_funded: 1
external_id:
pmid:
- '26466571'
intvolume: ' 526'
issue: '7574'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815041/
month: '10'
oa: 1
oa_version: Submitted Version
page: 525 - 530
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5484'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutations driving CLL and their evolution in progression and relapse
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 526
year: '2015'
...
---
_id: '1667'
abstract:
- lang: eng
text: We consider parametric version of fixed-delay continuoustime Markov chains
(or equivalently deterministic and stochastic Petri nets, DSPN) where fixed-delay
transitions are specified by parameters, rather than concrete values. Our goal
is to synthesize values of these parameters that, for a given cost function, minimise
expected total cost incurred before reaching a given set of target states. We
show that under mild assumptions, optimal values of parameters can be effectively
approximated using translation to a Markov decision process (MDP) whose actions
correspond to discretized values of these parameters. To this end we identify
and overcome several interesting phenomena arising in systems with fixed delays.
acknowledgement: The research leading to these results has received funding from the
People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreement n∘ [291734]. This work is partly
supported by the German Research Council (DFG) as part of the Transregional Collaborative
Research Center AVACS (SFB/TR 14), by the EU 7th Framework Programme under grant
agreement no. 295261 (MEALS) and 318490 (SENSATION), by the Czech Science Foundation,
grant No. 15-17564S, and by the CAS/SAFEA International Partnership Program for
Creative Research Teams.
alternative_title:
- LNCS
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: L'Uboš
full_name: Korenčiak, L'Uboš
last_name: Korenčiak
- first_name: Jan
full_name: Krčál, Jan
last_name: Krčál
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Vojtěch
full_name: Řehák, Vojtěch
last_name: Řehák
citation:
ama: Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. Optimizing performance
of continuous-time stochastic systems using timeout synthesis. 2015;9259:141-159.
doi:10.1007/978-3-319-22264-6_10
apa: 'Brázdil, T., Korenčiak, L., Krčál, J., Novotný, P., & Řehák, V. (2015).
Optimizing performance of continuous-time stochastic systems using timeout synthesis.
Presented at the QEST: Quantitative Evaluation of Systems, Madrid, Spain: Springer.
https://doi.org/10.1007/978-3-319-22264-6_10'
chicago: Brázdil, Tomáš, L’Uboš Korenčiak, Jan Krčál, Petr Novotný, and Vojtěch
Řehák. “Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout
Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22264-6_10.
ieee: T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, and V. Řehák, “Optimizing
performance of continuous-time stochastic systems using timeout synthesis,” vol.
9259. Springer, pp. 141–159, 2015.
ista: Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. 2015. Optimizing performance
of continuous-time stochastic systems using timeout synthesis. 9259, 141–159.
mla: Brázdil, Tomáš, et al. Optimizing Performance of Continuous-Time Stochastic
Systems Using Timeout Synthesis. Vol. 9259, Springer, 2015, pp. 141–59, doi:10.1007/978-3-319-22264-6_10.
short: T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, V. Řehák, 9259 (2015) 141–159.
conference:
end_date: 2015-09-03
location: Madrid, Spain
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2015-09-01
date_created: 2018-12-11T11:53:22Z
date_published: 2015-08-22T00:00:00Z
date_updated: 2021-01-12T06:52:24Z
day: '22'
department:
- _id: KrCh
doi: 10.1007/978-3-319-22264-6_10
ec_funded: 1
intvolume: ' 9259'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.4777
month: '08'
oa: 1
oa_version: Preprint
page: 141 - 159
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5482'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Optimizing performance of continuous-time stochastic systems using timeout
synthesis
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9259
year: '2015'
...
---
_id: '1664'
abstract:
- lang: eng
text: Over a century of research into the origin of turbulence in wall-bounded shear
flows has resulted in a puzzling picture in which turbulence appears in a variety
of different states competing with laminar background flow. At moderate flow speeds,
turbulence is confined to localized patches; it is only at higher speeds that
the entire flow becomes turbulent. The origin of the different states encountered
during this transition, the front dynamics of the turbulent regions and the transformation
to full turbulence have yet to be explained. By combining experiments, theory
and computer simulations, here we uncover a bifurcation scenario that explains
the transformation to fully turbulent pipe flow and describe the front dynamics
of the different states encountered in the process. Key to resolving this problem
is the interpretation of the flow as a bistable system with nonlinear propagation
(advection) of turbulent fronts. These findings bridge the gap between our understanding
of the onset of turbulence and fully turbulent flows.
acknowledgement: We acknowledge the Deutsche Forschungsgemeinschaft (Project No. FOR
1182), and the European Research Council under the European Union’s Seventh Framework
Programme (FP/2007-2013)/ERC Grant Agreement 306589 for financial support. B.S.
acknowledges financial support from the Chinese State Scholarship Fund under grant
number 2010629145. B.S. acknowledges support from the International Max Planck Research
School for the Physics of Biological and Complex Systems and the Göttingen Graduate
School for Neurosciences and Molecular Biosciences. We acknowledge computing resources
from GWDG (Gesellschaft für wissenschaftliche Datenverarbeitung Göttingen) and the
Jülich Supercomputing Centre (grant HGU16) where the simulations were performed.
author:
- first_name: Dwight
full_name: Barkley, Dwight
last_name: Barkley
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Mukund
full_name: Vasudevan, Mukund
id: 3C5A959A-F248-11E8-B48F-1D18A9856A87
last_name: Vasudevan
- first_name: Grégoire M
full_name: Lemoult, Grégoire M
id: 4787FE80-F248-11E8-B48F-1D18A9856A87
last_name: Lemoult
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. The rise of fully
turbulent flow. Nature. 2015;526(7574):550-553. doi:10.1038/nature15701
apa: Barkley, D., Song, B., Vasudevan, M., Lemoult, G. M., Avila, M., & Hof,
B. (2015). The rise of fully turbulent flow. Nature. Nature Publishing
Group. https://doi.org/10.1038/nature15701
chicago: Barkley, Dwight, Baofang Song, Mukund Vasudevan, Grégoire M Lemoult, Marc
Avila, and Björn Hof. “The Rise of Fully Turbulent Flow.” Nature. Nature
Publishing Group, 2015. https://doi.org/10.1038/nature15701.
ieee: D. Barkley, B. Song, M. Vasudevan, G. M. Lemoult, M. Avila, and B. Hof, “The
rise of fully turbulent flow,” Nature, vol. 526, no. 7574. Nature Publishing
Group, pp. 550–553, 2015.
ista: Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. 2015. The rise
of fully turbulent flow. Nature. 526(7574), 550–553.
mla: Barkley, Dwight, et al. “The Rise of Fully Turbulent Flow.” Nature,
vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 550–53, doi:10.1038/nature15701.
short: D. Barkley, B. Song, M. Vasudevan, G.M. Lemoult, M. Avila, B. Hof, Nature
526 (2015) 550–553.
date_created: 2018-12-11T11:53:20Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2021-01-12T06:52:22Z
day: '21'
department:
- _id: BjHo
doi: 10.1038/nature15701
ec_funded: 1
intvolume: ' 526'
issue: '7574'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.09143
month: '10'
oa: 1
oa_version: Preprint
page: 550 - 553
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5485'
quality_controlled: '1'
scopus_import: 1
status: public
title: The rise of fully turbulent flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 526
year: '2015'
...
---
_id: '1672'
abstract:
- lang: eng
text: Composable notions of incoercibility aim to forbid a coercer from using anything
beyond the coerced parties’ inputs and outputs to catch them when they try to
deceive him. Existing definitions are restricted to weak coercion types, and/or
are not universally composable. Furthermore, they often make too strong assumptions
on the knowledge of coerced parties—e.g., they assume they known the identities
and/or the strategies of other coerced parties, or those of corrupted parties—
which makes them unsuitable for applications of incoercibility such as e-voting,
where colluding adversarial parties may attempt to coerce honest voters, e.g.,
by offering them money for a promised vote, and use their own view to check that
the voter keeps his end of the bargain. In this work we put forward the first
universally composable notion of incoercible multi-party computation, which satisfies
the above intuition and does not assume collusions among coerced parties or knowledge
of the corrupted set. We define natural notions of UC incoercibility corresponding
to standard coercion-types, i.e., receipt-freeness and resistance to full-active
coercion. Importantly, our suggested notion has the unique property that it builds
on top of the well studied UC framework by Canetti instead of modifying it. This
guarantees backwards compatibility, and allows us to inherit results from the
rich UC literature. We then present MPC protocols which realize our notions of
UC incoercibility given access to an arguably minimal setup—namely honestly generate
tamper-proof hardware performing a very simple cryptographic operation—e.g., a
smart card. This is, to our knowledge, the first proposed construction of an MPC
protocol (for more than two parties) that is incoercibly secure and universally
composable, and therefore the first construction of a universally composable receipt-free
e-voting protocol.
acknowledgement: Joël Alwen was supported by the ERC starting grant (259668-PSPC).
Rafail Ostrovsky was supported in part by NSF grants 09165174, 1065276, 1118126
and 1136174, US-Israel BSF grant 2008411, OKAWA Foundation Research Award, IBM Faculty
Research Award, Xerox Faculty Research Award, B. John Garrick Foundation Award,
Teradata Research Award, Lockheed-Martin Corporation Research Award, and the Defense
Advanced Research Projects Agency through the U.S. Office of Naval Research under
Contract N00014 -11 -1-0392. The views expressed are those of the author and do
not reflect the official policy or position of the Department of Defense or the
U.S. Government. Vassilis Zikas was supported in part by the Swiss National Science
Foundation (SNF) via the Ambizione grant PZ00P-2142549.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Rafail
full_name: Ostrovsky, Rafail
last_name: Ostrovsky
- first_name: Hongsheng
full_name: Zhou, Hongsheng
last_name: Zhou
- first_name: Vassilis
full_name: Zikas, Vassilis
last_name: Zikas
citation:
ama: 'Alwen JF, Ostrovsky R, Zhou H, Zikas V. Incoercible multi-party computation
and universally composable receipt-free voting. In: Advances in Cryptology
- CRYPTO 2015. Vol 9216. Lecture Notes in Computer Science. Springer; 2015:763-780.
doi:10.1007/978-3-662-48000-7_37'
apa: 'Alwen, J. F., Ostrovsky, R., Zhou, H., & Zikas, V. (2015). Incoercible
multi-party computation and universally composable receipt-free voting. In Advances
in Cryptology - CRYPTO 2015 (Vol. 9216, pp. 763–780). Santa Barbara, CA, United
States: Springer. https://doi.org/10.1007/978-3-662-48000-7_37'
chicago: Alwen, Joel F, Rafail Ostrovsky, Hongsheng Zhou, and Vassilis Zikas. “Incoercible
Multi-Party Computation and Universally Composable Receipt-Free Voting.” In Advances
in Cryptology - CRYPTO 2015, 9216:763–80. Lecture Notes in Computer Science.
Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_37.
ieee: J. F. Alwen, R. Ostrovsky, H. Zhou, and V. Zikas, “Incoercible multi-party
computation and universally composable receipt-free voting,” in Advances in
Cryptology - CRYPTO 2015, Santa Barbara, CA, United States, 2015, vol. 9216,
pp. 763–780.
ista: 'Alwen JF, Ostrovsky R, Zhou H, Zikas V. 2015. Incoercible multi-party computation
and universally composable receipt-free voting. Advances in Cryptology - CRYPTO
2015. CRYPTO: International Cryptology ConferenceLecture Notes in Computer Science,
LNCS, vol. 9216, 763–780.'
mla: Alwen, Joel F., et al. “Incoercible Multi-Party Computation and Universally
Composable Receipt-Free Voting.” Advances in Cryptology - CRYPTO 2015,
vol. 9216, Springer, 2015, pp. 763–80, doi:10.1007/978-3-662-48000-7_37.
short: J.F. Alwen, R. Ostrovsky, H. Zhou, V. Zikas, in:, Advances in Cryptology
- CRYPTO 2015, Springer, 2015, pp. 763–780.
conference:
end_date: 2015-08-20
location: Santa Barbara, CA, United States
name: 'CRYPTO: International Cryptology Conference'
start_date: 2015-08-16
date_created: 2018-12-11T11:53:23Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2022-06-07T09:51:55Z
day: '01'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.1007/978-3-662-48000-7_37
ec_funded: 1
file:
- access_level: open_access
checksum: 5b6649e80d1f781a8910f7cce6427f78
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T08:55:29Z
date_updated: 2020-07-14T12:45:11Z
file_id: '7853'
file_name: 2015_CRYPTO_Alwen.pdf
file_size: 397363
relation: main_file
file_date_updated: 2020-07-14T12:45:11Z
has_accepted_license: '1'
intvolume: ' 9216'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 763 - 780
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Advances in Cryptology - CRYPTO 2015
publication_identifier:
eisbn:
- 978-3-662-48000-7
isbn:
- 978-3-662-47999-5
publication_status: published
publisher: Springer
publist_id: '5476'
quality_controlled: '1'
scopus_import: '1'
series_title: Lecture Notes in Computer Science
status: public
title: Incoercible multi-party computation and universally composable receipt-free
voting
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9216
year: '2015'
...
---
_id: '1669'
abstract:
- lang: eng
text: Computational notions of entropy (a.k.a. pseudoentropy) have found many applications,
including leakage-resilient cryptography, deterministic encryption or memory delegation.
The most important tools to argue about pseudoentropy are chain rules, which quantify
by how much (in terms of quantity and quality) the pseudoentropy of a given random
variable X decreases when conditioned on some other variable Z (think for example
of X as a secret key and Z as information leaked by a side-channel). In this paper
we give a very simple and modular proof of the chain rule for HILL pseudoentropy,
improving best known parameters. Our version allows for increasing the acceptable
length of leakage in applications up to a constant factor compared to the best
previous bounds. As a contribution of independent interest, we provide a comprehensive
study of all known versions of the chain rule, comparing their worst-case strength
and limitations.
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Maciej
full_name: Skórski, Maciej
last_name: Skórski
citation:
ama: Pietrzak KZ, Skórski M. The chain rule for HILL pseudoentropy, revisited. 2015;9230:81-98.
doi:10.1007/978-3-319-22174-8_5
apa: 'Pietrzak, K. Z., & Skórski, M. (2015). The chain rule for HILL pseudoentropy,
revisited. Presented at the LATINCRYPT: Cryptology and Information Security in
Latin America, Guadalajara, Mexico: Springer. https://doi.org/10.1007/978-3-319-22174-8_5'
chicago: Pietrzak, Krzysztof Z, and Maciej Skórski. “The Chain Rule for HILL Pseudoentropy,
Revisited.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22174-8_5.
ieee: K. Z. Pietrzak and M. Skórski, “The chain rule for HILL pseudoentropy, revisited,”
vol. 9230. Springer, pp. 81–98, 2015.
ista: Pietrzak KZ, Skórski M. 2015. The chain rule for HILL pseudoentropy, revisited.
9230, 81–98.
mla: Pietrzak, Krzysztof Z., and Maciej Skórski. The Chain Rule for HILL Pseudoentropy,
Revisited. Vol. 9230, Springer, 2015, pp. 81–98, doi:10.1007/978-3-319-22174-8_5.
short: K.Z. Pietrzak, M. Skórski, 9230 (2015) 81–98.
conference:
end_date: 2015-08-26
location: Guadalajara, Mexico
name: 'LATINCRYPT: Cryptology and Information Security in Latin America'
start_date: 2015-08-23
date_created: 2018-12-11T11:53:22Z
date_published: 2015-08-15T00:00:00Z
date_updated: 2021-01-12T06:52:24Z
day: '15'
ddc:
- '005'
department:
- _id: KrPi
doi: 10.1007/978-3-319-22174-8_5
ec_funded: 1
file:
- access_level: open_access
checksum: 8cd4215b83efba720e8cf27c23ff4781
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:29Z
date_updated: 2020-07-14T12:45:11Z
file_id: '5351'
file_name: IST-2016-669-v1+1_599.pdf
file_size: 443340
relation: main_file
file_date_updated: 2020-07-14T12:45:11Z
has_accepted_license: '1'
intvolume: ' 9230'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 81 - 98
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5480'
pubrep_id: '669'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: The chain rule for HILL pseudoentropy, revisited
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9230
year: '2015'
...
---
_id: '1671'
abstract:
- lang: eng
text: This paper studies the concrete security of PRFs and MACs obtained by keying
hash functions based on the sponge paradigm. One such hash function is KECCAK,
selected as NIST’s new SHA-3 standard. In contrast to other approaches like HMAC,
the exact security of keyed sponges is not well understood. Indeed, recent security
analyses delivered concrete security bounds which are far from existing attacks.
This paper aims to close this gap. We prove (nearly) exact bounds on the concrete
PRF security of keyed sponges using a random permutation. These bounds are tight
for the most relevant ranges of parameters, i.e., for messages of length (roughly)
l ≤ min{2n/4, 2r} blocks, where n is the state size and r is the desired output
length; and for l ≤ q queries (to the construction or the underlying permutation).
Moreover, we also improve standard-model bounds. As an intermediate step of independent
interest, we prove tight bounds on the PRF security of the truncated CBC-MAC construction,
which operates as plain CBC-MAC, but only returns a prefix of the output.
alternative_title:
- LNCS
author:
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Stefano
full_name: Tessaro, Stefano
last_name: Tessaro
citation:
ama: 'Gazi P, Pietrzak KZ, Tessaro S. The exact PRF security of truncation: Tight
bounds for keyed sponges and truncated CBC. In: Vol 9215. Springer; 2015:368-387.
doi:10.1007/978-3-662-47989-6_18'
apa: 'Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). The exact PRF security
of truncation: Tight bounds for keyed sponges and truncated CBC (Vol. 9215, pp.
368–387). Presented at the CRYPTO: International Cryptology Conference, Santa
Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-47989-6_18'
chicago: 'Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “The Exact PRF
Security of Truncation: Tight Bounds for Keyed Sponges and Truncated CBC,” 9215:368–87.
Springer, 2015. https://doi.org/10.1007/978-3-662-47989-6_18.'
ieee: 'P. Gazi, K. Z. Pietrzak, and S. Tessaro, “The exact PRF security of truncation:
Tight bounds for keyed sponges and truncated CBC,” presented at the CRYPTO: International
Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9215, pp.
368–387.'
ista: 'Gazi P, Pietrzak KZ, Tessaro S. 2015. The exact PRF security of truncation:
Tight bounds for keyed sponges and truncated CBC. CRYPTO: International Cryptology
Conference, LNCS, vol. 9215, 368–387.'
mla: 'Gazi, Peter, et al. The Exact PRF Security of Truncation: Tight Bounds
for Keyed Sponges and Truncated CBC. Vol. 9215, Springer, 2015, pp. 368–87,
doi:10.1007/978-3-662-47989-6_18.'
short: P. Gazi, K.Z. Pietrzak, S. Tessaro, in:, Springer, 2015, pp. 368–387.
conference:
end_date: 2015-08-20
location: Santa Barbara, CA, United States
name: 'CRYPTO: International Cryptology Conference'
start_date: 2015-08-16
date_created: 2018-12-11T11:53:23Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:52:25Z
day: '01'
ddc:
- '004'
- '005'
department:
- _id: KrPi
doi: 10.1007/978-3-662-47989-6_18
ec_funded: 1
file:
- access_level: open_access
checksum: 17d854227b3b753fd34f5d29e5b5a32e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:38Z
date_updated: 2020-07-14T12:45:11Z
file_id: '4827'
file_name: IST-2016-673-v1+1_053.pdf
file_size: 592296
relation: main_file
file_date_updated: 2020-07-14T12:45:11Z
has_accepted_license: '1'
intvolume: ' 9215'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 368 - 387
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5478'
pubrep_id: '673'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The exact PRF security of truncation: Tight bounds for keyed sponges and truncated
CBC'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9215
year: '2015'
...
---
_id: '1673'
abstract:
- lang: eng
text: 'When a new mutant arises in a population, there is a probability it outcompetes
the residents and fixes. The structure of the population can affect this fixation
probability. Suppressing population structures reduce the difference between two
competing variants, while amplifying population structures enhance the difference.
Suppressors are ubiquitous and easy to construct, but amplifiers for the large
population limit are more elusive and only a few examples have been discovered.
Whether or not a population structure is an amplifier of selection depends on
the probability distribution for the placement of the invading mutant. First,
we prove that there exist only bounded amplifiers for adversarial placement-that
is, for arbitrary initial conditions. Next, we show that the Star population structure,
which is known to amplify for mutants placed uniformly at random, does not amplify
for mutants that arise through reproduction and are therefore placed proportional
to the temperatures of the vertices. Finally, we construct population structures
that amplify for all mutational events that arise through reproduction, uniformly
at random, or through some combination of the two. '
acknowledgement: 'K.C. gratefully acknowledges support from ERC Start grant no. (279307:
Graph Games), Austrian Science Fund (FWF) grant no. P23499-N23, and FWF NFN grant
no. S11407-N23 (RiSE). '
article_number: '20150114'
author:
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: 'Adlam B, Chatterjee K, Nowak M. Amplifiers of selection. Proceedings of
the Royal Society A: Mathematical, Physical and Engineering Sciences. 2015;471(2181).
doi:10.1098/rspa.2015.0114'
apa: 'Adlam, B., Chatterjee, K., & Nowak, M. (2015). Amplifiers of selection.
Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2015.0114'
chicago: 'Adlam, Ben, Krishnendu Chatterjee, and Martin Nowak. “Amplifiers of Selection.”
Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences. Royal Society of London, 2015. https://doi.org/10.1098/rspa.2015.0114.'
ieee: 'B. Adlam, K. Chatterjee, and M. Nowak, “Amplifiers of selection,” Proceedings
of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.
471, no. 2181. Royal Society of London, 2015.'
ista: 'Adlam B, Chatterjee K, Nowak M. 2015. Amplifiers of selection. Proceedings
of the Royal Society A: Mathematical, Physical and Engineering Sciences. 471(2181),
20150114.'
mla: 'Adlam, Ben, et al. “Amplifiers of Selection.” Proceedings of the Royal
Society A: Mathematical, Physical and Engineering Sciences, vol. 471, no.
2181, 20150114, Royal Society of London, 2015, doi:10.1098/rspa.2015.0114.'
short: 'B. Adlam, K. Chatterjee, M. Nowak, Proceedings of the Royal Society A: Mathematical,
Physical and Engineering Sciences 471 (2015).'
date_created: 2018-12-11T11:53:24Z
date_published: 2015-09-08T00:00:00Z
date_updated: 2021-01-12T06:52:26Z
day: '08'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1098/rspa.2015.0114
ec_funded: 1
file:
- access_level: open_access
checksum: e613d94d283c776322403a28aad11bdd
content_type: application/pdf
creator: kschuh
date_created: 2019-04-18T12:39:56Z
date_updated: 2020-07-14T12:45:11Z
file_id: '6342'
file_name: 2015_rspa_Adlam.pdf
file_size: 391466
relation: main_file
file_date_updated: 2020-07-14T12:45:11Z
has_accepted_license: '1'
intvolume: ' 471'
issue: '2181'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences'
publication_status: published
publisher: Royal Society of London
publist_id: '5477'
quality_controlled: '1'
scopus_import: 1
status: public
title: Amplifiers of selection
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 471
year: '2015'
...
---
_id: '1668'
abstract:
- lang: eng
text: "We revisit the security (as a pseudorandom permutation) of cascading-based
constructions for block-cipher key-length extension. Previous works typically
considered the extreme case where the adversary is given the entire codebook of
the construction, the only complexity measure being the number qe of queries to
the underlying ideal block cipher, representing adversary’s secret-key-independent
computation. Here, we initiate a systematic study of the more natural case of
an adversary restricted to adaptively learning a number qc of plaintext/ciphertext
pairs that is less than the entire codebook. For any such qc, we aim to determine
the highest number of block-cipher queries qe the adversary can issue without
being able to successfully distinguish the construction (under a secret key) from
a random permutation.\r\nMore concretely, we show the following results for key-length
extension schemes using a block cipher with n-bit blocks and κ-bit keys:\r\nPlain
cascades of length ℓ=2r+1 are secure whenever qcqre≪2r(κ+n), qc≪2κ and qe≪22κ.
The bound for r=1 also applies to two-key triple encryption (as used within Triple
DES).\r\nThe r-round XOR-cascade is secure as long as qcqre≪2r(κ+n), matching
an attack by Gaži (CRYPTO 2013).\r\nWe fully characterize the security of Gaži
and Tessaro’s two-call "
alternative_title:
- LNCS
author:
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Jooyoung
full_name: Lee, Jooyoung
last_name: Lee
- first_name: Yannick
full_name: Seurin, Yannick
last_name: Seurin
- first_name: John
full_name: Steinberger, John
last_name: Steinberger
- first_name: Stefano
full_name: Tessaro, Stefano
last_name: Tessaro
citation:
ama: 'Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. Relaxing full-codebook
security: A refined analysis of key-length extension schemes. 2015;9054:319-341.
doi:10.1007/978-3-662-48116-5_16'
apa: 'Gazi, P., Lee, J., Seurin, Y., Steinberger, J., & Tessaro, S. (2015).
Relaxing full-codebook security: A refined analysis of key-length extension schemes.
Presented at the FSE: Fast Software Encryption, Istanbul, Turkey: Springer. https://doi.org/10.1007/978-3-662-48116-5_16'
chicago: 'Gazi, Peter, Jooyoung Lee, Yannick Seurin, John Steinberger, and Stefano
Tessaro. “Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension
Schemes.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48116-5_16.'
ieee: 'P. Gazi, J. Lee, Y. Seurin, J. Steinberger, and S. Tessaro, “Relaxing full-codebook
security: A refined analysis of key-length extension schemes,” vol. 9054. Springer,
pp. 319–341, 2015.'
ista: 'Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. 2015. Relaxing full-codebook
security: A refined analysis of key-length extension schemes. 9054, 319–341.'
mla: 'Gazi, Peter, et al. Relaxing Full-Codebook Security: A Refined Analysis
of Key-Length Extension Schemes. Vol. 9054, Springer, 2015, pp. 319–41, doi:10.1007/978-3-662-48116-5_16.'
short: P. Gazi, J. Lee, Y. Seurin, J. Steinberger, S. Tessaro, 9054 (2015) 319–341.
conference:
end_date: 2015-03-11
location: Istanbul, Turkey
name: 'FSE: Fast Software Encryption'
start_date: 2015-03-08
date_created: 2018-12-11T11:53:22Z
date_published: 2015-08-12T00:00:00Z
date_updated: 2020-08-11T10:09:26Z
day: '12'
department:
- _id: KrPi
doi: 10.1007/978-3-662-48116-5_16
ec_funded: 1
intvolume: ' 9054'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2015/397
month: '08'
oa: 1
oa_version: Submitted Version
page: 319 - 341
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5481'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: 'Relaxing full-codebook security: A refined analysis of key-length extension
schemes'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9054
year: '2015'
...
---
_id: '1674'
abstract:
- lang: eng
text: We consider N × N random matrices of the form H = W + V where W is a real
symmetric Wigner matrix and V a random or deterministic, real, diagonal matrix
whose entries are independent of W. We assume subexponential decay for the matrix
entries of W and we choose V so that the eigenvalues of W and V are typically
of the same order. For a large class of diagonal matrices V, we show that the
rescaled distribution of the extremal eigenvalues is given by the Tracy-Widom
distribution F1 in the limit of large N. Our proofs also apply to the complex
Hermitian setting, i.e. when W is a complex Hermitian Wigner matrix.
article_number: '1550018'
author:
- first_name: Jioon
full_name: Lee, Jioon
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Edge universality for deformed Wigner matrices. Reviews
in Mathematical Physics. 2015;27(8). doi:10.1142/S0129055X1550018X
apa: Lee, J., & Schnelli, K. (2015). Edge universality for deformed Wigner matrices.
Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X1550018X
chicago: Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner
Matrices.” Reviews in Mathematical Physics. World Scientific Publishing,
2015. https://doi.org/10.1142/S0129055X1550018X.
ieee: J. Lee and K. Schnelli, “Edge universality for deformed Wigner matrices,”
Reviews in Mathematical Physics, vol. 27, no. 8. World Scientific Publishing,
2015.
ista: Lee J, Schnelli K. 2015. Edge universality for deformed Wigner matrices. Reviews
in Mathematical Physics. 27(8), 1550018.
mla: Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner Matrices.”
Reviews in Mathematical Physics, vol. 27, no. 8, 1550018, World Scientific
Publishing, 2015, doi:10.1142/S0129055X1550018X.
short: J. Lee, K. Schnelli, Reviews in Mathematical Physics 27 (2015).
date_created: 2018-12-11T11:53:24Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:52:26Z
day: '01'
department:
- _id: LaEr
doi: 10.1142/S0129055X1550018X
intvolume: ' 27'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.8015
month: '09'
oa: 1
oa_version: Preprint
publication: Reviews in Mathematical Physics
publication_status: published
publisher: World Scientific Publishing
publist_id: '5475'
quality_controlled: '1'
scopus_import: 1
status: public
title: Edge universality for deformed Wigner matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2015'
...
---
_id: '1679'
article_number: '091102'
author:
- first_name: Grégoire M
full_name: Lemoult, Grégoire M
id: 4787FE80-F248-11E8-B48F-1D18A9856A87
last_name: Lemoult
- first_name: Philipp
full_name: Maier, Philipp
id: 384F7C04-F248-11E8-B48F-1D18A9856A87
last_name: Maier
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Lemoult GM, Maier P, Hof B. Taylor’s Forest. Physics of Fluids. 2015;27(9).
doi:10.1063/1.4930850
apa: Lemoult, G. M., Maier, P., & Hof, B. (2015). Taylor’s Forest. Physics
of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4930850
chicago: Lemoult, Grégoire M, Philipp Maier, and Björn Hof. “Taylor’s Forest.” Physics
of Fluids. American Institute of Physics, 2015. https://doi.org/10.1063/1.4930850.
ieee: G. M. Lemoult, P. Maier, and B. Hof, “Taylor’s Forest,” Physics of Fluids,
vol. 27, no. 9. American Institute of Physics, 2015.
ista: Lemoult GM, Maier P, Hof B. 2015. Taylor’s Forest. Physics of Fluids. 27(9),
091102.
mla: Lemoult, Grégoire M., et al. “Taylor’s Forest.” Physics of Fluids, vol.
27, no. 9, 091102, American Institute of Physics, 2015, doi:10.1063/1.4930850.
short: G.M. Lemoult, P. Maier, B. Hof, Physics of Fluids 27 (2015).
date_created: 2018-12-11T11:53:26Z
date_published: 2015-09-24T00:00:00Z
date_updated: 2021-01-12T06:52:28Z
day: '24'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1063/1.4930850
file:
- access_level: open_access
checksum: 604bba3c2496aadb3efcff77de01ce6c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:35Z
date_updated: 2020-07-14T12:45:12Z
file_id: '5019'
file_name: IST-2017-748-v1+1_1.4930850.pdf
file_size: 872366
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 27'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Physics of Fluids
publication_status: published
publisher: American Institute of Physics
publist_id: '5469'
pubrep_id: '748'
quality_controlled: '1'
scopus_import: 1
status: public
title: Taylor's Forest
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: 27
year: '2015'
...
---
_id: '1684'
abstract:
- lang: eng
text: Many species groups, including mammals and many insects, determine sex using
heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila
melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting
of six chromosomal arms (five large rods and a small dot), but superficially similar
karyotypes may conceal the true extent of sex chromosome variation. Here, we use
whole-genome analysis in 37 fly species belonging to 22 different families of
Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among
flies. We identify over a dozen different sex chromosome configurations, and the
small dot chromosome is repeatedly used as the sex chromosome, which presumably
reflects the ancestral karyotype of higher Diptera. However, we identify species
with undifferentiated sex chromosomes, others in which a different chromosome
replaced the dot as a sex chromosome or in which up to three chromosomal elements
became incorporated into the sex chromosomes, and others yet with female heterogamety
(ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has
evolved multiple times in flies, consistently through up-regulation of the single
X in males. However, X chromosomes generally show a deficiency of genes with male-biased
expression, possibly reflecting sex-specific selective pressures. These species
thus provide a rich resource to study sex chromosome biology in a comparative
manner and show that similar selective forces have shaped the unique evolution
of sex chromosomes in diverse fly taxa.
acknowledgement: "This research was funded by NIH grants (R01GM076007 and R01GM093182)
to DB. The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript.\r\nWe thank the people listed in S2
Table for samples, Jere Schweikert for identifying Tephritid species, and Zaak Walton
for technical assistance."
article_number: e1002078
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Doris
full_name: Bachtrog, Doris
last_name: Bachtrog
citation:
ama: Vicoso B, Bachtrog D. Numerous transitions of sex chromosomes in Diptera. PLoS
Biology. 2015;13(4). doi:10.1371/journal.pbio.1002078
apa: Vicoso, B., & Bachtrog, D. (2015). Numerous transitions of sex chromosomes
in Diptera. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002078
chicago: Vicoso, Beatriz, and Doris Bachtrog. “Numerous Transitions of Sex Chromosomes
in Diptera.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002078.
ieee: B. Vicoso and D. Bachtrog, “Numerous transitions of sex chromosomes in Diptera,”
PLoS Biology, vol. 13, no. 4. Public Library of Science, 2015.
ista: Vicoso B, Bachtrog D. 2015. Numerous transitions of sex chromosomes in Diptera.
PLoS Biology. 13(4), e1002078.
mla: Vicoso, Beatriz, and Doris Bachtrog. “Numerous Transitions of Sex Chromosomes
in Diptera.” PLoS Biology, vol. 13, no. 4, e1002078, Public Library of
Science, 2015, doi:10.1371/journal.pbio.1002078.
short: B. Vicoso, D. Bachtrog, PLoS Biology 13 (2015).
date_created: 2018-12-11T11:53:27Z
date_published: 2015-04-16T00:00:00Z
date_updated: 2021-01-12T06:52:30Z
day: '16'
ddc:
- '570'
doi: 10.1371/journal.pbio.1002078
extern: '1'
file:
- access_level: open_access
checksum: 92a300d7b97eafb477885303f7632fe1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:05Z
date_updated: 2020-07-14T12:45:12Z
file_id: '4858'
file_name: IST-2016-492-v1+1_journal.pbio.1002078.pdf
file_size: 1104701
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5463'
pubrep_id: '492'
quality_controlled: '1'
status: public
title: Numerous transitions of sex chromosomes in Diptera
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: '2015'
...
---
_id: '1687'
abstract:
- lang: eng
text: Guided cell movement is essential for development and integrity of animals
and crucially involved in cellular immune responses. Leukocytes are professional
migratory cells that can navigate through most types of tissues and sense a wide
range of directional cues. The responses of these cells to attractants have been
mainly explored in tissue culture settings. How leukocytes make directional decisions
in situ, within the challenging environment of a tissue maze, is less understood.
Here we review recent advances in how leukocytes sense chemical cues in complex
tissue settings and make links with paradigms of directed migration in development
and Dictyostelium discoideum amoebae.
author:
- first_name: Milka
full_name: Sarris, Milka
last_name: Sarris
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Sarris M, Sixt MK. Navigating in tissue mazes: Chemoattractant interpretation
in complex environments. Current Opinion in Cell Biology. 2015;36(10):93-102.
doi:10.1016/j.ceb.2015.08.001'
apa: 'Sarris, M., & Sixt, M. K. (2015). Navigating in tissue mazes: Chemoattractant
interpretation in complex environments. Current Opinion in Cell Biology.
Elsevier. https://doi.org/10.1016/j.ceb.2015.08.001'
chicago: 'Sarris, Milka, and Michael K Sixt. “Navigating in Tissue Mazes: Chemoattractant
Interpretation in Complex Environments.” Current Opinion in Cell Biology.
Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.08.001.'
ieee: 'M. Sarris and M. K. Sixt, “Navigating in tissue mazes: Chemoattractant interpretation
in complex environments,” Current Opinion in Cell Biology, vol. 36, no.
10. Elsevier, pp. 93–102, 2015.'
ista: 'Sarris M, Sixt MK. 2015. Navigating in tissue mazes: Chemoattractant interpretation
in complex environments. Current Opinion in Cell Biology. 36(10), 93–102.'
mla: 'Sarris, Milka, and Michael K. Sixt. “Navigating in Tissue Mazes: Chemoattractant
Interpretation in Complex Environments.” Current Opinion in Cell Biology,
vol. 36, no. 10, Elsevier, 2015, pp. 93–102, doi:10.1016/j.ceb.2015.08.001.'
short: M. Sarris, M.K. Sixt, Current Opinion in Cell Biology 36 (2015) 93–102.
date_created: 2018-12-11T11:53:28Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:52:31Z
day: '01'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1016/j.ceb.2015.08.001
ec_funded: 1
file:
- access_level: open_access
checksum: c29973924b790aab02fdd91857759cfb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:21Z
date_updated: 2020-07-14T12:45:12Z
file_id: '4875'
file_name: IST-2016-445-v1+1_1-s2.0-S0955067415001064-main.pdf
file_size: 797964
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 36'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 93 - 102
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '5458'
pubrep_id: '445'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Navigating in tissue mazes: Chemoattractant interpretation in complex environments'
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: 36
year: '2015'
...
---
_id: '1685'
abstract:
- lang: eng
text: "Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph
is a subgraph of G such that cutting Σ along G yields a topological disk. We provide
a fixed parameter tractable approximation scheme for the problem of computing
the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε)
approximation of the shortest cut graph in time f(ε, g)n3.\r\nOur techniques first
rely on the computation of a spanner for the problem using the technique of brick
decompositions, to reduce the problem to the case of bounded tree-width. Then,
to solve the bounded tree-width case, we introduce a variant of the surface-cut
decomposition of Rué, Sau and Thilikos, which may be of independent interest."
alternative_title:
- LNCS
author:
- first_name: Vincent
full_name: Cohen Addad, Vincent
last_name: Cohen Addad
- first_name: Arnaud N
full_name: De Mesmay, Arnaud N
id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87
last_name: De Mesmay
citation:
ama: 'Cohen Addad V, de Mesmay AN. A fixed parameter tractable approximation scheme
for the optimal cut graph of a surface. In: Vol 9294. Springer; 2015:386-398.
doi:10.1007/978-3-662-48350-3_33'
apa: 'Cohen Addad, V., & de Mesmay, A. N. (2015). A fixed parameter tractable
approximation scheme for the optimal cut graph of a surface (Vol. 9294, pp. 386–398).
Presented at the ESA: European Symposium on Algorithms, Patras, Greece: Springer.
https://doi.org/10.1007/978-3-662-48350-3_33'
chicago: Cohen Addad, Vincent, and Arnaud N de Mesmay. “A Fixed Parameter Tractable
Approximation Scheme for the Optimal Cut Graph of a Surface,” 9294:386–98. Springer,
2015. https://doi.org/10.1007/978-3-662-48350-3_33.
ieee: 'V. Cohen Addad and A. N. de Mesmay, “A fixed parameter tractable approximation
scheme for the optimal cut graph of a surface,” presented at the ESA: European
Symposium on Algorithms, Patras, Greece, 2015, vol. 9294, pp. 386–398.'
ista: 'Cohen Addad V, de Mesmay AN. 2015. A fixed parameter tractable approximation
scheme for the optimal cut graph of a surface. ESA: European Symposium on Algorithms,
LNCS, vol. 9294, 386–398.'
mla: Cohen Addad, Vincent, and Arnaud N. de Mesmay. A Fixed Parameter Tractable
Approximation Scheme for the Optimal Cut Graph of a Surface. Vol. 9294, Springer,
2015, pp. 386–98, doi:10.1007/978-3-662-48350-3_33.
short: V. Cohen Addad, A.N. de Mesmay, in:, Springer, 2015, pp. 386–398.
conference:
end_date: 2015-09-16
location: Patras, Greece
name: 'ESA: European Symposium on Algorithms'
start_date: 2015-09-14
date_created: 2018-12-11T11:53:27Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:52:31Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/978-3-662-48350-3_33
ec_funded: 1
intvolume: ' 9294'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1507.01688
month: '09'
oa: 1
oa_version: Preprint
page: 386 - 398
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5462'
quality_controlled: '1'
scopus_import: 1
status: public
title: A fixed parameter tractable approximation scheme for the optimal cut graph
of a surface
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9294
year: '2015'
...
---
_id: '1688'
abstract:
- lang: eng
text: 'We estimate the selection constant in the following geometric selection theorem
by Pach: For every positive integer d, there is a constant (Formula presented.)
such that whenever (Formula presented.) are n-element subsets of (Formula presented.),
we can find a point (Formula presented.) and subsets (Formula presented.) for
every i∈[d+1], each of size at least cdn, such that p belongs to all rainbowd-simplices
determined by (Formula presented.) simplices with one vertex in each Yi. We show
a super-exponentially decreasing upper bound (Formula presented.). The ideas used
in the proof of the upper bound also help us to prove Pach’s theorem with (Formula
presented.), which is a lower bound doubly exponentially decreasing in d (up to
some polynomial in the exponent). For comparison, Pach’s original approach yields
a triply exponentially decreasing lower bound. On the other hand, Fox, Pach, and
Suk recently obtained a hypergraph density result implying a proof of Pach’s theorem
with (Formula presented.). In our construction for the upper bound, we use the
fact that the minimum solid angle of every d-simplex is super-exponentially small.
This fact was previously unknown and might be of independent interest. For the
lower bound, we improve the ‘separation’ part of the argument by showing that
in one of the key steps only d+1 separations are necessary, compared to 2d separations
in the original proof. We also provide a measure version of Pach’s theorem.'
acknowledgement: R. K. was supported by the Russian Foundation for Basic Research
Grant 15-31-20403 (mol_a_ved) and grant 15-01-99563. J. K., Z. P., and M. T. were
partially supported by ERC Advanced Research Grant No. 267165 (DISCONV) and by the
project CE-ITI (GAČR P202/12/G061) of the Czech Science Foundation. J. K. was also
partially supported by Swiss National Science Foundation Grants 200021-137574 and
200020-14453. P. P., Z. P., and M. T. were partially supported by the Charles University
Grant GAUK 421511. P. P. was also partially supported by the Charles University
Grant SVV-2014-260107. Z. P. was also partially supported by the Charles University
Grant SVV-2014-260103.
author:
- first_name: Roman
full_name: Karasev, Roman
last_name: Karasev
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
- first_name: Pavel
full_name: Paták, Pavel
last_name: Paták
- first_name: Zuzana
full_name: Patakova, Zuzana
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
citation:
ama: Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. Bounds for Pach’s selection
theorem and for the minimum solid angle in a simplex. Discrete & Computational
Geometry. 2015;54(3):610-636. doi:10.1007/s00454-015-9720-z
apa: Karasev, R., Kynčl, J., Paták, P., Patakova, Z., & Tancer, M. (2015). Bounds
for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete
& Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9720-z
chicago: Karasev, Roman, Jan Kynčl, Pavel Paták, Zuzana Patakova, and Martin Tancer.
“Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.”
Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9720-z.
ieee: R. Karasev, J. Kynčl, P. Paták, Z. Patakova, and M. Tancer, “Bounds for Pach’s
selection theorem and for the minimum solid angle in a simplex,” Discrete &
Computational Geometry, vol. 54, no. 3. Springer, pp. 610–636, 2015.
ista: Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. 2015. Bounds for Pach’s
selection theorem and for the minimum solid angle in a simplex. Discrete &
Computational Geometry. 54(3), 610–636.
mla: Karasev, Roman, et al. “Bounds for Pach’s Selection Theorem and for the Minimum
Solid Angle in a Simplex.” Discrete & Computational Geometry, vol.
54, no. 3, Springer, 2015, pp. 610–36, doi:10.1007/s00454-015-9720-z.
short: R. Karasev, J. Kynčl, P. Paták, Z. Patakova, M. Tancer, Discrete & Computational
Geometry 54 (2015) 610–636.
date_created: 2018-12-11T11:53:28Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:52:32Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-015-9720-z
intvolume: ' 54'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1403.8147
month: '10'
oa: 1
oa_version: Preprint
page: 610 - 636
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '5457'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bounds for Pach's selection theorem and for the minimum solid angle in a simplex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2015'
...